ntp laboratory network assessment (2016) country’s three major island groups and their land areas...

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NTP LABORATORY NETWORK ASSESSMENT

(2016)

Arthur B. Lagos MD Lynette P. Adorio-Arce MD Marlon L. Bayot RMT

March 2017

Disclaimer:

This document is a draft and is provided for information only. The information contained herein is

subject to change and does not commit USAID, SIAPS, MSH and the authors. The final version of the

report will be published as soon as adopted.

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NTP LABORATORY NETWORK ASSESSMENT

(2016)

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Table of Contents

List of Acronyms

Preface

Executive Summary

Page 1 Introduction

Page 7 Findings

Page 7 I. Laboratory Services

Page 7 1. TB sputum microscopy

Page 13 2. Xpert MTB/RIF Assay

Page 21 3. Culture and DST

Page 28 4. Line Probe Assay

Page 29 5. External Quality Assurance Program

Page 34 II. Laboratory systems

Page 34 1. Human resources

Page 34 2. Training and supervision

Page 36 3. Financing

Page 37 4. Information management

Page 38 5. Supply chain management

Page 39 6. Equipment, facility (physical plant) and infrastructure Page 41 7. Monitoring and evaluation system

Page 41 8. Leadership and management of the lab network

Page 42 9. Biosafety

Page 42 10. Infection control

Page 42 11. Waste management

Page 43 12. Laboratory health promotion and education

Page 45 Recommendations

Page 48 References

Page 51 Annex A. Summary results of smear quality assessment

Page 52 Annex B. Types of inconclusive test results in Xpert testing

Page 53 Annex C. List of facilities included in the assessment

Page 54 Annex D. List of persons interviewed

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List of Acronyms

Biomed Biomedical Department (RITM)

BHMC Barangay Health Management Council

BHS Barangay Health Station

BSC Biological Safety Cabinet

CHO City Health Office

CTRL Cebu TB Reference Laboratory

CXR Chest X-ray

DOH Department of Health

DSSM Direct Sputum Smear Microscopy

DR drug resistant

DST Drug susceptibility testing

EPTB Extra-pulmonary tuberculosis

EQA External Quality Assurance Program / External Quality Assessment

EVRMC Eastern Visayas Regional Medical Center

HC Health center

HIV Human Immunodeficiency Virus

IC Infection control

ILW Informal laboratory worker

ITR Inconclusive test result

LCP Lung Center of the Philippines

LED-FM Light emitting diode – Fluorescence Microscopy

LNW Laboratory Network

LPA Line Probe Assay

LTBI Latent TB Infection

MDRTB Multiple Drug-resistant Tuberculosis

MTB Mycobacterium tuberculosis

NGO Non-governmental organization

NTM Non-tuberculous Mycobacteria

NTP National TB control Program

NTRL National TB Reference Laboratory

NR No result (from an Xpert test)

PCR Polymerase Chain Reaction

PhilPACT Philippine Plan of Action to Control Tuberculosis

PPE Personal Protective Equipment

PTC Presumptive TB Cases

RHU Rural Health Unit

RITM Research Institute for Tropical Medicine

RR An Xpert test result: MTB detected, Rifampicin resistant

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RSS Remote Smearing Station

PMDT Programmatic Management of Drug Resistant Tuberculosis

PTSI Philippine Tuberculosis Society, Inc.

QAC Quality Assurance Center

SIAPS Systems for Improved Access to Pharmaceuticals and Services

SLH San Lazaro Hospital

T An Xpert test result: MTB detected, Rifampicin susceptible

TAT Turnaround time

TI An Xpert test result: MTB detected, Rifampicin resistance indeterminate

TML TB microscopy laboratory

XDRTB Extremely drug resistant tuberculosis

ZN Ziehl-Neelsen

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Preface

Draft version - please do not quote or circulate

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Executive Summary


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Introduction

I. The Philippines

The Philippines is an archipelago composed of 7,107 islands located at the southeast coast of Asia with a

total land area of approximately 343,448.32 km2. The country’s three major island groups and their land

areas are: Luzon, covering 147,947.63 km2; Visayas with 59,873.84 km2; and Mindanao with 135,626.85

km2. The country has a diverse terrain consisting of high mountains, volcanoes and extensive valleys and

plateaus that are surrounded by bodies of water such as rivers and lakes.

The Philippines is a tropical country with an average temperature of 27°C. There are two seasons

experienced each year: wet and dry1. The dry season can be divided into the cool dry season from

December to January; and a hot dry season extending from March to May2. The highest temperatures

recorded in the period of 2014 to 2016 were recorded in Tuguegarao City, Cagayan Province and in

Metro Manila with temperatures exceeding 40 degrees Celsius3,4,5.

The country is divided into 18 administrative regions with the addition of the newly established Negros

Island Region (NIR) in mid-2016. NIR includes the provinces of Negros Occidental and Negros Oriental

and Bacolod City. The population in 2015 was almost 101 million with an average annual population

growth rate of 1.72% from 2010 to 2015 (Census and Housing Population, Philippine Statistics

Authority). Region 4-A (CALABARZON) had the biggest population with 14.41 million, followed by the

National Capital Region (NCR) with 12.88 million, and Region 3 (Central Luzon) with 11.22 million. The

combined population of these three regions accounted for about 38.1 percent of the Philippine

population in 2015.

The Philippines is composed of 81 provinces and 144 cities, 1,490 municipalities and 42,036 barangays6.

The country has 33 highly urbanized cities (HUCs), 4 of which have a population of over 1 million, these

are Quezon City (2.94 million), City of Manila (1.78 million), Davao City (1.63 million), and Caloocan City

(1.58 million)7. There are 1,489 municipalities in the Philippines.

Cavite province (Region 4-A) is the most populous province in 2015 with a population of 3.68 million;

followed by Bulacan in Region 3 (3.29 million); and Laguna in Region 4A (3.04 million). Batanes province

has the smallest population size with 17,246 persons. Two other provinces had a population of less than

100,000 namely, Siquijor (95,984) and Camiguin (88,478).

1 Philippine Statistics Authority (PSA). A view of the Philippines. Geography. 2010.

2 Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA). Climate of the Philippines. 2016. 3 Corrales, N. Inquirer.Net. Tuguegarao City records hottest temperature–Pagasa. 2014 4 Locsin, J. GMA News. PAGASA: Highest temperature of 2015 so far recorded in Cagayan on Sunday. 2015. 5 Santos, E. PAGASA: Election day records hottest temperature of 2016 so far. 2016. 6 Philippine Standard Geographic Codes (PSGC). List of regions. 2016. 7 Philippine Statistics Authority (PSA). Highlights of the Philippine Population 2015 Census of Population. 2016

13 Asian Development Bank. Philippines: Transport Sector Assessment, Strategy and Road Map. 2012.

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There are three municipalities with big populations, namely: Rodriquez (pop: 369,222); Cainta (pop:

332,128); and Taytay (pop: 319,104), these are all located in Rizal province (Region 4A). The municipality

of Kalayaan in Palawan province (Region 4B) has the smallest population with 184 persons. The

population in urban areas is 41.9 million, while the rural population is 50.5 million which translates to an

urban to rural population ratio of 0.83 (2013).

The Philippine population is characterized by the rapid growth of the working age groups, and the slowly

but steadily increasing elderly population. From 1970 to 2010, the proportion of the older age group (65

years and older) had increased faster than the younger age group (0-14 years and 15-64 years age

group). However, the younger age group still has the bigger part of the population8.

There were more males than females in the age groups 0 to 54 years (2010), but there were more

females than males in the older age groups of 55 years and over9. The gender proportions are 50.4%

males and 49.6% females. This pattern of age and gender distribution is also observed for 2016 based on

population estimates. Life expectancy of Filipinos in 2015 is lower in males (65 years) than in females (72

years).10

In 2013, the literacy rate among Filipinos aged 15 to 24 remained high at 98.1% with women having a

slightly higher literacy rate than men. One of every 10 Filipinos aged 6 to 24 years were out-of-school,

which translates to about 24 million Filipinos in the country (2010). ARMM had the highest out-of-school

population at 14.4% which is higher than the national average of 10.6%.11 The country is classified as a

lower middle income country. The poverty incidence is 26.3% and the proportion of Filipino families in

extreme poverty was estimated at 9.2% in the first half of 2015.12

The country has a developed transport infrastructure but services are still inadequate due to lack of

sustainable financing. There were modest improvements in the country’s transport services but large

parts of the road network remain in poor which is largely due to poor and inadequate maintenance and

is linked closely to weak transport sector governance. Significant developments were made in water

transport with the upgraded Roll on – Roll off (ro-ro) ferry services as an alternative to the traditional

inter-island shipping services. However, serious capacity limitation for air transport is anticipated as

domestic and international air traffic grows.

The urban transport system is mainly composed of buses, mass transport system (trains in Metro

Manila), jeepneys, taxis, tricycles and pedicabs.13 From 2007 to 2013, motorcycles and tricycles

8 Castro, L.V. Efforts of the Philippine Statistical System (PSS) in Compiling Statistics on Population Ageing. 2015.

9 Philippine Statistics Authority (PSA). The Age and Sex Structure of the Philippine Population. 2012. 10 World Health Organization (WHO). Philippines Statistics. 2016. 11 Rodriguez, F. In numbers: #PHvote and PH education. 2016. 12 Philippine Statistics Authoriry (PSA). Poverty incidence among Filipinos registered at 26.3%, as of first semester of 2015 – PSA. 2016.

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comprised the highest proportion of type of vehicle used and has contributed significantly to road and

traffic congestion.14 Telecommunications in the Philippines consist of telephones (landlines) and mobile

phones, digital subscriber lines (DSL), cable networks, cellular sites and communication devices. These

have improved communications capabilities for Filipinos. More Filipinos are now using cellular (mobile)

phones as communication devices in place of the traditional landlines. The use of smart phones mobile

computers also increased due to the improved internet access.15

Epidemiology of TB in the Philippines

The Philippines belongs to two of the three global high TB burden country lists. It is one of the world’s

top 20 high TB burden (in absolute numbers) countries of the world, and one of the top 20 countries

with a high MDR-TB burden.16 The trend of case notification is increasing since 2009, and may have been

due to the increased case finding efforts.17

Table 1. Estimated TB incidence by age and sex (thousands)

2015 (source: WHO Global TB Report, 2016)

0-14 yrs >14 yrs Total

Females 14 (6.4-22) 100 (64-135) 114 (71-156)

Males 17 (11-23) 194 (152-236) 211 (163-259)

Total 31 (22-40) 294 (266-322) 324 (279-373)

Table 2 shows data from the 2016 WHO Global TB Report where a total of 286,544 cases were notified

in the Philippines in 2015; of these, 276,672 were new and relapse cases, 97% of whom are pulmonary

TB (PTB) cases. However, only 36% of the notified PTB cases have bacteriologic confirmation of their

disease. In addition, only 20% of the total new and relapse cases were tested with the new rapid

diagnostic tests (RDT).

Table 2. TB case notifications, Philippines 2015 (source: WHO Global TB Report 2016)

Total cases notified 286,544

Total new and relapse 276,672

- % Tested with RDTs at time of Dx 20%

- % known HIV status 13%

- % PTB 97%

- % Bacteriologically confirmed PTB 36%

14 Philippine Statistics Authority. Philippine Yearbook: Transportation. 2013. 15 Philippine Star Online. More Filipinos use cellphones as 'mobile computers': study. 2013. 16 WHO Global TB Report, 2015. World Health Organization. 17

Yamada N. Epidemiology Review, Philippines NTP Joint Program Review; 2016.

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The epidemiology review by Yamada for the 2016 JPR showed that the trend in the number of

presumptive TB cases (PTC) who were tested with smear microscopy has been increasing since 2005.

However the number of smear positive cases has not increased significantly and the trend in smear

positivity rates has been declining. The latter observation is common seen when case finding efforts are

intensified (Yamada, 2016).18 There has been a sharp increase in the number of smear negative cases in

recent years.

The declining diagnostic smear positivity rates lead to an increasing proportion of PTCs who are smear

negative (SN-PTC). However, the proportion of SN-PTCs who proceeded to the next level of diagnosis –

underwent chest X-ray (CXR) - appear to be low. Limited data from Quezon City BHMCs indicates that

only an estimated 18% to 22% of SN-PTCs had CXRs after the microscopy examination; the rest are

assumed to have dropped out of the NTP diagnostic process.19

This scenario is a reflection of patients’ limited access to CXR due to limited availability and accessibility,

and relatively high cost for poor patients. We believe that a significant proportion of patients who

dropped out of the diagnostic process belong to the pool of the so-called “missing TB cases” (Figure 1).

In addition, the issue of diagnostic quality emerges given the sharp increase in the number and

proportion of smear negative PTB cases despite the patients’ limited access to CXR.

Recent NTP policy changes in case finding provide that patients with negative diagnostic smears, but

have CXR findings suggestive of PTB, are eligible to be tested with Xpert. However, data is not available

at this time to describe these patients.

18 Yamada N. Epidemiology Review, Philippines NTP Joint Program Review; 2016. 19 Lagos AB, Adorio-Arce LP. Quezon City BHMC workshop notes. Philippines; 2014.

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The NTP Laboratory Network

The country is currently developing its strategic plan for TB elimination. To support the country TB

Elimination Plan, the NTP is expanding its laboratory services to improve access to reliable TB diagnosis.

The NTP has established a network of laboratories to provide the bacteriologic basis for TB diagnosis, for

monitoring treatment response, and support TB surveillance. The NTP laboratory network (LNW) has

adopted a variety of technologies using mainly sputum as the test specimen. These technologies include

sputum smear microscopy, Xpert MTB/RIF assay (GX), TB culture, drug susceptibility test (DST) and line-

probe assay (LPA). The services are generally free of charge particularly in public primary care facilities

for eligible patients under the TB control program.

However, diagnostic tests such as chest X-ray (CXR) and other imaging procedures, as well as serologic

tests to detect TB infection, and histologic examination to detect disease particularly extra-pulmonary

TB (EPTB), are not part of the NTP’s free diagnostic services. This has negative consequences on the

results of case finding activities because they form part of the entire diagnostic process. For example,

the detection of active PTB among smear negative patients may be reduced; furthermore, the quality of

clinical diagnosed PTB may be compromised without the CXRs. Without support to tests for non-

pulmonary specimens, the diagnosis of EPTB will remain low.

NTP laboratory facilities are generally provided by the institutions hosting the laboratory. Peripheral TB

microscopy (TMLs), and some Xpert laboratories, are lodged in primary care units (e.g. RHUs/HCs) that

are owned and managed by LGUs, non-profit NGOs, private-for-profit and other non-health government

facilities. Essential laboratory equipment and supplies are provided mainly by the government, external

partners and donors (e.g. The Global Fund).

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The other intermediate level facilities are the Quality Assurance Centers (QAC). These centers are

managed by the local governments and implement the quality assurance (QA) program for TB

microscopy. Some of the QACs also perform other lab services including TB microscopy and/or Xpert.

Remote Smearing Stations (RSS) are located in barangay health stations (BHS) that are owned and

managed by the LGUs and/or Barangays. The Remote Smearing Stations continue to provide services in

remote areas functioning as sputum collection and smear preparation facilities.

Framework for the fully functional NTP diagnostic services

In order for the laboratory network to support the attainment of the country’s TB strategic objectives in

terms of providing effective, reliable and sustainable services, the NTP is working within a framework

that aims to strengthen the TB diagnostic services and ensure that these are fully functional20.

Figure 1: Framework for the fully functional TB diagnostic services in the National TB Control Program of the Philippines2

(Source: Philippines NTP Laboratory Leadership and Management Development Program Workshop, Strengthening

Pharmaceutical Systems Project, Management Sciences for Health, 2010)

National policy, standards and legal regulatory framework

Inputs 1. Infrastructure 2. Equipment 3. Consumables 4. Transport 5. Staff 6. Money

Systems & Processes 1. Leadership 2. Management 3. Planning 4. Laboratory organization

(networks & referral systems)

5. Quality management 6. Supply chain management 7. Equipment management 8. Logistics management 9. Information management 10. Human resource

management 11. Supervision 12. Monitoring and evaluation 13. Infection control 14. Waste management 15. Health promotion

Measurable Outputs 1. Proficient staff 2. High quality and reliable

test results 3. Accredited laboratories 4. Service efficiency 5. Increased clinician

confidence on lab results 6. Patient satisfaction

Outcomes: Clinical & Public Health Impact 1. Rapid diagnosis and treatment 2. Increased TB case detection 3. Early & increased detection of

drug resistance 4. Reduction of initial defaulters 5. Early detection of treatment

adherence problems and treatment failures

6. Decreased morbidity & mortality

20 NTP Laboratory Network Strategic Plan 2013 – 2016. DOH; Philippines, 2013.

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The framework includes the following elements: (a) national policies and standards that form the legal

regulatory framework; (b) human, financial and material inputs to enable the effective and sustainable

delivery of services; and (c) the systems and processes that support the staff in providing the services

(Figure 1). Working together, these elements will generate measurable outputs such as proficient staff,

high quality test results, accredited laboratories, service efficiency, increased clinician confidence on lab

results and patient satisfaction. These are expected to lead to program outcomes that have clinical and

public health impact

About the assessment

Case finding in the NTP needs to improve in order to achieve the country’s vision of TB elimination.

Finding all TB cases in the community, providing them with effective treatment and getting them cured

are basic interventions to stop ongoing transmission of TB, and to reduce TB morbidity and mortality. A

fully functional TB diagnostic network is essential for finding the TB cases in the community.

The laboratories are an important part of the diagnostic services. The laboratories must always be

functional in order to provide the needed services to find the TB cases. The assessment was done to

gather information regarding the performance of the NTP lab network. This information will be useful

for NTP, NTRL and sub-national program managers to guide them in developing the strategies and plans

for strengthening the lab networks in their respective areas of jurisdiction.

The description of NTP-LNW performance was based on the analysis and interpretation of routinely

reported indicator-based data, as well as other data using custom indicators for this study. Review of

relevant reports and other documents (published and unpublished), interviews, field observations, and

group discussions were done to come up with the study findings. The study adopted a systems approach

to identify and organize the findings and develop recommendations.

A total of 33 laboratories located in 8 regions were assessed for this study (Box 1). The study

laboratories include (a) culture labs at the central (n=1) and intermediate levels (n=11), all of which also

function as Xpert labs, and 3/11 labs performing DST; (b) 8 full-time quality assurance centers (QAC), 3

of which provide DSSM services; (c) 4 RHU/HC based laboratories performing DSSM, but are also

functioning as QACs, with 3/4 also performing Xpert tests; (d) 8 TMLs based in RHU/HC that provide

DSSM and other lab services for their patients and for patients referred by other RHU/HCs; and (e) 1

Xpert laboratory located in a PMDT treatment center (TC).

Data collection was started in March 2016 and lasted till August 2016. Data management and analysis

was from September to December 2016; report writing was started in December 2016.

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Box 1: Laboratories for this study in 8 regions, total: 33 Central level 1 national reference laboratory (NTRL) Intermediate level 11 culture labs:

1/11: regional reference lab: culture, DST

3/11: culture and DST 8/11: culture only

8 QACs 11/11: with Xpert;

3/8 provide DSSM services;

5/8 are for QA only Peripheral level 4 HC labs with TML and other services

4/4: function also as QACs

3/4 TML/QACs: with Xpert services 8 TMLs in RHU/health center

8/8 perform other lab tests (e.g. CBC, urinalysis, blood chemistry)

8/8 serve other RHU/HCs 1 TC with Xpert

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Findings:

I. Laboratory Services

1. TB sputum microscopy

TB smear microscopy is currently the initial bacteriologic test under the NTP and the test is still used to

monitor bacteriologic response to treatment. The NTP will gradually replace sputum microscopy with

Xpert as the initial test for all PTCs to diagnose active PTB.

TB smear microscopy is still considered an important laboratory test in the country’s TB control program

for case finding and for monitoring treatment response. This is despite the use of GeneXpert, with its

higher sensitivity, specificity, short turnaround time, and ability to detect resistance to Rifampicin.

Microscopy laboratories, however, are still more available and accessible particularly in the remote, or

difficult to reach areas, such as in island or mountain barangays and municipalities, and in many urban

poor settlements.

The 2013 mapping survey done by NTRL reported that there were 2,561 TMLs in the country, 85% of

which are in the public services, and the remaining 15% are in the private sector. However, this number

has not been updated since the time of the survey. Additionally, the survey did not include the remote

smearing stations (RSS) that have been established in the country since 2007. LED-Fluorescent

Microscopy (LED-FM) was introduced in 2014 in selected laboratories in regions 3 (Central Luzon), 4A

(Southern Tagalog) and NCR (Metro Manila). As of June 2016, 59 TMLs were equipped with LED-

Fluorescent microscopes, most of which are in NCR.

In the Philippines, most peripheral public health laboratories provide other services aside from TB

sputum microscopy such as, CBC, HIV testing, newborn screening, hepatitis screening, urinalysis, and in

some, including the recently adopted GeneXpert tests. All of the peripheral laboratories assessed are

providing a range of laboratory services to a number of referring facilities, both public and/or private,

ranging from 5 to 11 referring health centers. A number of TMLs are also functioning as QA centers for

the TB microscopy EQA program. In our study labs, 4 of the 12 TMLs (33%) are QACs.

In addition, Med Techs in 4 of 8 study TMLs (50%) are also functioning as part-time EQA Controllers in

their respective province or city. Many of the “part-time controllers” were not trained adequately due to

the limited availability of training opportunities. These multi-tasking arrangements have increased staff

workload considerably and have resulted to the reduction in workers’ efficiency and effectiveness, and

loss of motivation.

TB laboratory case finding data in the study showed that 69,379 presumptive TB cases (PTCs) underwent

diagnostic DSSM from 2013 to 2015 wherein 10,073 smear-positive cases were identified (Table 1). The

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3-year average smear positive rate in this group is 15%, which is higher than the national average of

13%, but within the range of 10% to 20% that is expected in areas with a high TB burden21. However, the

number of PTCs tested increased, but the number of smear positive cases detected, did not change

significantly.

Table 3. TB Microscopy Laboratory performance in study sites, 2013-2015

No. of

Year PTCs examined

Smear (+) Smear (-)

No. No. % No. %

2013 21,560 3,334 15% 18,226 85%

2014 24,575 3,321 14% 21,254 86%

2015 23,244 3,418 15% 19,826 85%

Total 69,379 10,073 15% 59,306 85%

A related finding is that among the PTCs who were smear negative (SN-PTCs), information is not

available on how many of them were able to proceed to the next round of diagnostics, usually a chest X-

ray (CXR), as this is not included in the regular reporting system.

Our observations in Quezon City BHMCs showed that only an estimated 18% to 22% of the smear

negative PTCs were able to have a CXR in 2014, diagnosed with reasonable accuracy, and given the

appropriate treatment22. In succeeding years with LGU interventions, the proportion of SN-PTCs with

CXRs increased to 64% among whom around 74% were X-ray PTB+ (SN-PTCs/CXR-PTB+). This resulted to

an 84% increase in the number of TB cases found and treated that contributed to an increase in CDR All

Forms.23 This is an area in the case finding process that needs to be strengthened to find some of the so-

called “missing cases”.

The policy of 2-specimen collection for diagnosis was introduced by NTP in 2012 to improve patients’

convenience and with the expectation that patients’ compliance to the diagnostic protocol will improve.

Health facilities were given the option to collect both specimens on the same day (spot-spot) with an

interval of one hour, or within 2 days: spot + early morning (EM) specimen. Data on 2-specimen

collection was available only in 9 study TMLs. Only 4 of the 9 TMLs were able to collect 2 specimens

from all PTCs tested (Table 2); overall, an average 88% of PTCs submitted 2 specimens.

Discussions with field health workers and lab staff revealed variable specimen collection practices in the

field. The following are examples of these patterns:

1. 2 spot-specimens collected with 1-hour interval under supervision at the health facility on

day of consultation;

21 Department of Health. NTP Case Finding and Case Holding Report. 2015.

22 Lagos AB, Adorio-Arce LP. BHMC Planning Workshop Notes. SIAPS, Philippines; 2014. 23 See KG, Lagos AB, Adorio-Arce. Improved case finding in Old Balara. Quezon City; 2016.

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2. 1 spot specimen on day of consultation, 1 EM specimen submitted on the following day;

3. 2 EM specimens collected at home (day after consultation);

4. 1 EM specimen collected at home (day after consultation), and 1 spot collected upon

submission of the first EM specimen

Table 3. Number of PTCs with 2 specimens for diagnostic TB microscopy in selected laboratories,

2013-2014

No. PTCs

No. w/

2-sp. %

San Lazaro Hosp. 9,125 7,043 77%

Kamuning SHC 982 982 100%

Sindalan RHU 366 349 95%

Batangas Med Ctr. 1,036 1,021 99%

Batangas Health Ofc. 3,155 3,154 100%

Naic RHU 1,660 1,656 100%

Tacloban City Health Ofc. 1,461 1,396 96%

EVRMC 3,636 2,965 82%

Carmen RHU 2,753 2,753 100%

It was observed that the collection of 2-specimens was more efficient in labs that strictly implemented

the one-day collection process (Pattern 1) compared to those that used the other patterns. Many health

workers implement patterns 2, 3 and 4 to enable the collection of early morning specimens - which they

perceive are of better quality and will yield more positive results24. However, the evidence is insufficient

to support this theory. Field observations also suggest that specimens collected at home tend to have

lower quality compared to specimens collected under supervision at the health facility25.

Data from selected QA centers in 2014 and 2015 show that only 79% of slides assessed under the EQA

program had acceptable specimen quality (Annex A. Summary of Smear Quality Assessment in study

LGUs, 2014-2015). Health workers reported several issues in the specimen collection process that

contribute to poor specimen quality, these include:

1. Inadequate instruction and supervision of sputum collection which is often attributed to:

Timing and location of sputum collection process that cause inconvenience to patients

(e.g. spot versus early morning; at the facility versus at home; schedule of sputum

collection at the facility);

Weak capacity of HWs, especially non-professional lab staff, to provide correct

instruction and/or adequately supervise the collection process; this matter is related to

the quality of training and supervision that they received;

24 Lagos AB. DOH-JICA QTBCP Field Notes. Philippines; 2003. 25 Ibid

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Inadequate time for health staff to instruct and supervise patients; this is claimed to be

due to their high workload.

2. Unacceptable physical conditions of the sputum collection area (e.g. inadequate privacy,

uncomfortable, inadequate ventilation and light). Sputum collection areas that are poorly

ventilated increases the risk of infection among other people / patients without TB.

3. Poor conditions during storage after collection, and/or transport, of specimens to the TML.

Some examples are: placement of specimen in areas exposed to heat and/or sunlight; leakage of

specimens due to improper packaging for transport (usually in plastic bags packed with ice), and

in some cases, the use of non-screw type specimen containers; seepage of water from melted

ice into the specimen container; and exposure to heat during transport. In one study RHU, as

much as 30% of specimens brought to their labs had some form of spillage.

Health workers also expressed dismay since expenses for the packaging and transport of specimens are

shouldered either by them or by patients – both of whom have limited financial resources. In a few

instances, funds generated by the health center through clients’ donations are used for this purpose.

The use of sub-standard packaging contributes to the poor quality of the specimen for TB microscopy

once it reaches the laboratory. For example, due to the unavailability of standard specimen transport

boxes, health workers resort to using plastic bags packed with ice to transport specimens that usually

leads to seepage of water into the specimen container when the ice melts.

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EQA data for smear quality showed that majority of the slides assessed did not reach acceptable levels

(at least 90%) in four of the six assessment points, including specimen quality, smear thickness, size and

evenness (Figure 2).

Some of the operational factors that contributed to this situation include poor quality of training; lack of

supervision; work space inadequacies; high workload; poor quality and/or expired stains; inadequate

equipment; sub-standard specimen containers; and weak implementation of EQA activities.

In our study sites, stock-outs of Ziehl-Neelsen (ZN) stains were experienced in the past year and this led

to the use of expired stains. The same was reported in places where LED-FM was deployed. Stock-outs

of the auramine stain was frequent which forced lab staff to revert back to the use of ZN stains; the lab

staff shifted back to Fluorescence Microscopy when auramine stain became available26.

26 Lagos, A.B. Notes from EQA Policy Workshop. SIAPS, Philippines; 2016.

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The occurrences of slide reading errors, particularly major errors, were infrequent and at a low level in

the study labs. Blinded slide rechecking results showed that the proportion of slides with reading errors

is only 3% in 2014 and 2015; major errors constitute less than 1% of the total error slides. However,

issues regarding EQA program implementation, discussed in another section of this report, tend to cast

some doubts to these results.

Data for diagnostic microscopy turnaround time (TAT) is limited since this is not routinely recorded and

monitored in the study labs. Available data showed TATs that varied from 1 to 3 days; diagnostic tests

usually take 3 days, while follow-up examinations take 2 days on average. However, data for RHUs that

are referring to other TMLs was not available. We noted that in other areas (e.g. Quezon City), results

for DSSM from referral TMLs are usually obtained after about 5 working days27.

Microscopy test results were released to patients, rather than to the clinic staff, in more than 50% of our

study sites; the rest forwarded the results to the clinic nurse or midwife in charge. For referring units,

patients were usually asked to get the lab results using their own money for transport. There are areas

where lab results were collected by health workers from the referring units using their facilities’ funds.

The practice of releasing diagnostic lab results to patients is not always good because there had been

instances in the past, although poorly documented, wherein these patients are lost in the diagnostic

process28.

27 Lagos, A.B., Adorio-Arce LP. Quezon City BHMC Workshop Notes. SIAPS Project. Philippines; 2014-2015. 28 Lagos, A.B. Field Notes. TB LINC Project. Philippines; 2008.

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2. Xpert MTB/RIF Assay

The use of XPERT-MTB/RIF assay (Xpert) was introduced in the NTP lab network in the last quarter of

2011 with 16 laboratories providing the test. The Xpert network continued to grow, and by 2016, a total

of 188 functional Xpert laboratories are functional out of the 207 that have been established. Xpert

testing was done mainly for patients suspected of having DRTB, specifically MDRTB. In 2014 the use of

Xpert was extended to other types of patients including EPTB, and smear-negative PTCs with CXR

findings suggestive of active TB.

Recent policy discussions indicate that NTP will use Xpert as the initial diagnostic test for all PTCs, with

the view of replacing smear microscopy as the initial diagnostic test. Xpert has shown a higher level of

test sensitivity and specificity, and is capable of detecting Rifampicin-resistance (Rr), the presence of

which is currently used as a proxy indicator for the presence of multi-drug-resistant TB (MDR-TB).

In this assessment, we gathered data from 16 study Xpert labs for the period 2013 to 2015. Data was

available in only 6, 10 and 16 functional laboratories for 2013, 2014 and 2015, respectively. Again, this

reflects the problem of reporting in the Xpert services.

The issues regarding sputum collection, packaging and transport described previously for TB microscopy

were also seen in peripheral Xpert labs. These issues include the inadequate instruction and supervision

of health workers on sputum collection; poor physical condition of sputum collection areas; and

improper packaging of specimens.

The quality of specimen storage after collection, and the conditions during transport to the Xpert lab are

also in need of improvement. Some examples of these practices include: placement of collected

specimen in areas exposed to heat and/or sunlight (near windows, or underneath air condition units);

leakage of specimens due to improper packaging for transport (usually in plastic bags packed with ice);

seepage of water from the melted ice into the specimen container due to poorly capped specimen

containers; and exposure to heat during transport in motorcycles.

In one i-DOTS center in Quezon City, poor communication and coordination between referring facilities

and Xpert laboratories, as well as the unclear procedures for lab referrals, are causing confusion and

frustration among patients and health workers. It prolongs the testing process, increases the patients’

costs and inconvenience due to the repeated going back-and-forth to different health facilities, and

contributes to delays in diagnosis and treatment. At the health center level, the cost of transporting

specimens to the Xpert laboratories is shouldered mostly by patients.

A total of 33,724 drug-resistant presumptive TB cases (DR-PTCs) were tested in the 3-year period (Table

3). Of these patients, 4,418 (13%) were classified as New; 12,395 (37%) as Relapses; 16,491 (49%) as

Other Retreatment; and 420 (1%) were reported as Unknown. The patients tested were still reported as

DR-PTCs; no data was available for EPTB and non-DR (DS) PTCs such as the smear negative PTCs with

CXR findings suggestive of PTB.

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The trend in the proportions of the various types of patients showed that those classified as New and

Relapses, were increasing while the Other Retreatment and Unknown were decreasing from 2013 to

2015 (Table 3). This is likely to be due to an improvement in the health workers’ ability to classify

patients.

Year No. PTC tested

Table 4. Number and proportion of tests by type of patients in study Xpert laboratories, 2013-2015

PTC type

New Relapse Other Ret. Unknown

No. % No. % No. % No. %

2013 4,711 97 2% 670 14% 3,770 80% 174 4%

2014 12,778 1,365 11% 4,010 31% 7,157 56% 246 2%

2015 16,274 2,956 18% 7,715 47% 5,564 34% 0 0%

Total 33,763 4,418 13% 12,395 37% 16,491 49% 420 1%

Table 4 shows test results of New DR-PTCs: MTB was positive in 1,051 (24%), and among these cases,

13% were Rifampicin-resistant (Rr) and considered MDRTB cases; 85% were Rifampicin susceptible (T)

and 2% showed indeterminate results for Rifampicin resistance (TI).

Table 5. Xpert test results of New DR-PTCs in study Xpert laboratories, 2013-2015

Year No.

tested

MTB (+)

MTB (-) Rr T TI

No. % No. % No. % No. % No. %

2013 97 37 38% 11 30% 26 70% 0 0% 56 58%

2014 1,365 285 21% 41 14% 239 84% 5 2% 1,070 78%

2015 2,956 729 25% 80 11% 632 87% 17 2% 2,224 75%

Total 4,418 1,051 24% 132 13% 897 85% 22 2% 3,350 76%

Among Relapse (Table 5) and Other Retreatment PTCs (Table 6), results were MTB positive in 29% and

42%, respectively. Rifampicin resistance was found in 37% of MTB+ Relapse cases, and 34% of MTB+

Other Retreatment cases.

In all three types of patients tested, MTB detection as well as Rifampicin resistance rates, were higher in

Relapses and Other Retreatment patients compared to New DRTB presumptive cases. We noted that

the majority of MTB+ cases were Rifampicin susceptible at 85% for new cases, 61% for Relapse cases,

and 64% for Other Retreatment cases.

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In addition, the majority of the three types of patients tested showed MTB negative results (MTB not

detected). However, it is useful to remember that it is possible for some TB patients to show negative

Xpert results even in the presence of active disease. This may be due to instances where the bacillary

load in the specimen is too small to be detected by the machine (e.g. some HIV+ TB patients, smear

negative TB)29. Issues that diminish specimen quality may also lead to negative results.

Table 6. Xpert results of Relapse DR-PTCs in study Xpert laboratories, 2013-2015

No. Year tested

MTB (+)

MTB (-)

Rr T TI

No. % No. % No. % No. % No. %

2013 670 399 60% 168 42% 230 58% 1 0% 265 40%

2014 4,010 1,385 35% 538 39% 819 59% 28 2% 2,631 66%

2015 7,715 1,763 23% 614 35% 1,119 63% 30 2% 5,914 77%

Total 12,395 3,547 29% 1,320 37% 2,168 61% 59 2% 8,810 71%

Table 7. Xpert results of Other Retreatment PTCs in selected Xpert laboratories, 2013-2015

Year No. PTCs

tested

MTB (+)

Rr T TI MTB (-)

No. % No. % No. % No. % No. %

2013 3,770 1,723 46% 587 34% 1,110 64% 26 2% 1,920 51%

2014 7,157 3,008 42% 999 33% 1,946 65% 63 2% 4,079 57%

2015 5,564 2,165 39% 763 35% 1,374 63% 28 1% 3,596 65%

Total 16,491 6,896 42% 2,349 34% 4,430 64% 117 2% 9,595 58%

Inconclusive Xpert test results (ITR)

Xpert tests also generate inconclusive test results (ITR) due to a wide range of operational issues. The

five leading Xpert labs in our study with the highest proportion of ITRs over the 3-year period are: NTRL,

LCP, Batangas Medical Center, San Lazaro Hospital and PTSI (Table 7). We also noted 25 types of ITRs in

the Xpert tests (see Annex H. Types of ITRs).

29 Cepheid. Xpert MTB/RIF insert manual. 2010.

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Table 8. List of top 5 Xpert labs by frequency

of ITRs, 2013-2015

PTCs tested ITRs

No. No. %

1 NTRL 3,027 277 9%

2 LCP 6,359 500 8%

3 Batangas Medical Center 1,458 112 8%

4 SLH 2,904 186 6%

5 PTSI 10,253 384 4%

Data from 11/16 Xpert study labs showed the number and proportions of ITRs per year 656 (14%), 608

(5%) and 695 (4%) out of the total tests made in 2013, 2014 and 2015, respectively (Table 8). The

national averages for ITRs based on NTRL reports for the same years are: 6%, 6% and 5%, respectively.

The table shows that the three most frequent ITRs in the study labs from 2013 to 2015 are Errors,

followed by Invalid, and No Result; the table also shows the respective values compared to standards set

by the manufacturer. In 2015, the ITR type No Result (NR) went down at 0.44% and met the standard;

Invalid Result (IR), however, remained at 1% which is still over the standard.

Table 9. Frequency of three leading ITRs in study Xpert labs from 2013 to 2015

2013 2014 2015

No. % No. % No. %

No. tests 4,711

No. tests 12,778

No. tests 16,274

Standards30

Errors* 614 13% Errors* 433 3% Errors* 401 2.5% Less than 3%

NR 31 0.66% IR 88 1% IR 223 1% Less than 1%

IR 11 0.23% NR 87 1% NR 71 0.44% Less than 1%

Total 656 14% Total 608 5% Total 695 4%

Table 10 shows the 10 most frequent ITRs out of the 25 types of ITRs that occurred from 2013 to 2015;

these accounted for more than 90% of the total ITRs recorded. For practical reasons, we focused on the

5 most frequent ITRs in 2014 and 2015 which accounted for more than 80% of the total. These include:

INVALID; Error 5007; Error 5011; No Result (NR); and Error 2127. These accounted for 88% and 82% of

the total error results in 2014 and 2015, respectively. In 2013, Invalid (IR) was not among the top 5 GX-

ITRs.

30 Ibid

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Table 10. Ten most frequent Xpert inconclusive test results (GX-ITR), 2013 to 2015

2013

GX-ITR No. %

2014

GX-ITR No. %

2015

GX-ITR No. %

1

2

3

4

5

5007 175 49%

2008 71 20%

5011 35 10%

NR 31 9%

5006 13 4%

1

2

3

4

5

5011 135 23%

5007 121 21%

INVALID 88 15%

2127 87 15%

NR 80 14%

1

2

3

4

5

INVALID 223 33%

5007 149 22%

5011 77 11%

NR 71 11%

2127 35 5%

6

7

8

9

10

INVALID 11 3%

2014 10 3%

2127 6 2%

1001 4 1%

1002 3 1%

6

7

8

9

10

5006 23 4%

2008 20 3%

1001 12 2%

1002 9 2%

2037 9 2%

6

7

8

9

10

5006 33 5%

1001 32 5%

1002 26 4%

2014 17 3%

2005 11 2%

Total 359 100% Total 584 100% Total 674 100%

Table 11 describes the possible reasons for the occurrence of the ITRs. The occurrence of ITRs can be

attributed to issues related to:

1. People (staff, patients) 2. Training

3. Supervision

4. Supplies (e.g. Xpert cartridges, buffer solutions)

5. Equipment (Xpert machine, software,)

6. Processes (machine installation, sputum collection and transport, sample preparation, supply

storage)

7. Infrastructure (e.g. power supply stability)

8. Environment (temperature).

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31

Table 11. Description of Xpert inconclusive test results (ITRs)

ITRs Possible reasons for ITR occurrence

(Source: Cepheid Xpert Users’ Manual )

Authors’ remarks: possible underlying reasons

Error 5007

Error 5011

Error 2127

Sputum viscosity and/or wrong sample volume, or cartridge reaction tube improperly filled, contains bubbles, or probe integrity issues detected.

Loss of tube pressure because the cartridge tube is not airtight, or cartridge valve is not working right.

Power supply issue (main power or UPS fluctuations); Ethernet cable between PC and GX instrument; Communication cable between gateway and GX Module.

Poor sample preparation practices – related to lab worker performance due to gaps in training effectiveness, inadequate supervision, lack of proper measuring equipment (e.g. graduated measuring cup)

Poor sample preparation practices related to poor quality of cartridge can be due to improper storage; gaps in lab worker performance; gaps in training effectiveness; inadequate supervision.

Unstable power supply and recurrent power outages; improper machine installation.

Error 2008

Error 5006

Sample is too viscous; The filter is clogged by debris in sample; Pressure sensor failed.

An incorrect amount of reagent was inserted

into the cartridge; The reagent is bad; Fluid

transfer failed.

Poor sample preparation practices – related to lab worker performance due to gaps in training effectiveness; inadequate supervision.

Poor sample preparation practices; poor quality of

reagent can be due to improper storage; defective

machine.

Error 1001

Environment temperature is too warm; Fan

Failure

High environment temperature; improper machine

placement; defective machine

Error 1002

The difference between the temperatures of

the two thermistors has exceeded the

acceptable difference of 5 °C.

High machine temperature

Error 2014

The heater A/heater B/module’s/optical

block thermistor failed.

High machine temperature

Invalid PCR was inhibited due to inhibitors (pus, food particles)

Poor specimen quality - can be due to inadequate instruction to patients on sputum collection; poor training of HWs in sputum collection.

No Result

Windows or Software freeze; Power failure; STOP TEST function has been activated (accidentally or deliberately)

Computer-related bugs; power interruption; premature termination of test (e.g. during close of office at 5:00 pm).

31 Cepheid. GeneXpert Dx System Operator Manual. 2012.

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Issues related to people are often linked to process-related problems such as: specimen collection,

specimen quality, poor sample preparation, machine installation, and on some occasions, the premature

termination of testing procedure. These can be attributed to gaps in training quality and effectiveness,

and the lack of effective supervision of health workers.

Specimen quality problems can be connected to the inadequate supervision of patients during specimen

collection, to storage of specimens, and to the packaging and transport of specimens. These apply to all

of the diagnostic technologies that use sputum as the test specimen.

Issues related to the condition of the supplies (e.g. cartridges and buffer solutions) used for the tests

reflect poor supply management procedures and practices. As examples, we saw storage areas with

room temperatures exceeding 35 Celsius (note that the heat index can even be higher especially during

the summer months). In many places, the storage areas are air-conditioned but these are turned off

after office hours and during weekends and holidays. Temperature monitoring is not routinely done.

On the other hand, machine related problems can be due to procedures and practices related to storage

conditions and handling prior to installation; and the operators’ use, care and maintenance of the

machine and related equipment. This also reflects the measures taken by the laboratory managers to

protect the machine from environmental and infrastructure related issues such as very hot weather and

unstable power supply.

The occurrence of ITRs requires repeat testing which is not always easy to do because patients may not

return to submit another specimen. Repeat testing due to errors and inconclusive test results increases

the financial, material and opportunity costs related to testing. While the proportions of ITRs seem

small, the absolute number of affected patients is substantial.

We have no information on how many of the patients were retested in these labs, as these are not

routinely reported. However, we have to keep in mind that patients who are supposed to be retested

but were not, have the potential of being lost in the diagnostic process and may not receive appropriate

treatment. If they are active TB cases, whether drug susceptible or drug-resistant, they are at risk of

developing complications and dying from TB. Moreover, they continue to be sources of infection for

other people.

Turnaround time (TAT) for the labs covers the time from receipt of specimen to the time test results are

released to a person designated to collect the result (driver, courier, clinic staff, or in some cases,

patients themselves). Data for TAT is limited because these are not routinely recorded, monitored and

reported. We were able to gather TAT data from 11 Xpert study labs which showed the following TATs

for release of results are: 1 day (36%), 2 days (18%), and 3 days (46%). Peripheral level facilities had

shorter TATs (i.e. 1 day) presumably due to the lower workload compared to intermediate and central

level laboratories.

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Xpert test results were released to the relevant clinic staff in 83% (10/12) of labs; on the other hand,

results are transmitted by commercial courier or by a PMDT assigned transport driver to PMDT facilities

(i.e. treatment center and/or satellite treatment centers). However, since courier pick-up schedules are

not on a daily basis, results are initially transmitted by SMS, email or phone calls, at the lab staff’s

expense, to facilitate the transmittal process. One lab is using ITIS to send lab results using an off-facility

internet café for this purpose.

Other peripheral health facilities such as RHU/HCs collect the results through their own clinic staff when

they go out for other tasks such when picking up medical supplies. On the other hand, 17% (2/12) of

labs released Xpert results to patients who are then expected to submit these to their attending clinical

staff (doctors or nurses). As mentioned previously in the microscopy section of this report, releasing

results directly to patients entails some risks.

3. Culture and DST

TB culture and drug susceptibility test (DST) is used mainly for Xpert MTB+/Rifampicin resistant patients

who are under PMDT treatment, to identify the individual patient’s drug-resistance pattern which will

help the clinicians make drug regimen adjustments. Culture/DST is also used to monitor bacteriologic

response during treatment, and for drug resistance surveillance.

Most of the NTP’s TB culture laboratories are located in DOH regional laboratories, tertiary hospitals or

medical centers, and several private medical facilities. These culture laboratories receive financial and

operational support from The Global Fund, while technical supervision and support is provided mainly

by NTRL. The NTP planned to have 28 functional culture labs by 2016. However, progress has been slow

in operationalizing the laboratories with only 22 functional culture laboratories in 2014, 23 in 2015 and

25 in mid-2016 (Table 11). The slow progress has been attributed to various factors such as delays in

infrastructure improvements that were due to bureaucratic processes; issues related to procurement of

equipment, services and supplies; technical issues related to facility standards32.

Seven DST centers were expected to be functional by 2015, but only three are functional by end of 2016

namely, NTRL, CTRL and DTRL. The status of the culture/DST laboratory expansion as of 2016 is shown in

Table 12.

In NTRL, liquid culture using the Mycobacterial Growth Inhibitor Tube (MGIT) is utilized for baseline

PMDT tests, while solid culture is used for the follow-up tests among MDR-TB patients. DSTs, either for

first-line drugs (FLD) or second-line drugs (SLD), are performed in selected regional TB reference

laboratories and at the National TB Reference Laboratory (NTRL).

32 Bayot, M.L. Interview notes with NTRL-PSQM. 2016.

33 World Health Organization. 2007.

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NTRL sees the broader use of liquid culture in the NTP. WHO’s recommendation on the adoption of

liquid culture is that this “should be taken in a step-wise manner and integrated into a country specific

comprehensive plan for laboratory capacity strengthening and addressing the following key issues

related to appropriate biosafety level; staff training; maintenance of infrastructure and equipment;

customer plan with details of manufacturers’ commitments and guarantees; quick transport of

specimens from peripheral health facilities; and rapid transmission of results”33.

Given the findings of this study on matters regarding laboratory network support systems, such as

leadership and management; training; supervision; biosafety; waste management; specimen transport;

referral system; facility and equipment maintenance, it is likely that the broader use of liquid culture

may not be forthcoming in the short term.

Table 11. List of functional TB culture laboratories in NTP lab network, 2016 (NTRL, March 2016)

LUZON

Public (n=9) Private (n = 4)

1. National TB Reference Laboratory (NCR) 1. De La Salle Health Sciences Institute (Reg. IV-A)

2. DOH-Region II TB Laboratory (Reg.II) 2. Sorsogon Medical Mission Group of Hospital and

Health Services Cooperative (Reg.V)

3. DOH- Region III TB Laboratory (Reg.III) 3. Philippine Tuberculosis Society Inc. (NCR)

4. Batangas Medical Center (Reg. IV-A) 4. Dagupan Doctors Villaflor Memorial Hospital

(Reg. I)

5. Bicol TB Regional Laboratory (Reg. V)

6. Baguio General Hospital and Medical Center (CAR)

7. Lung Center of the Philippines (NCR)

8. San Lazaro Hospital (NCR)

9. UP PGH Medical Research Laboratory (NCR)

VISAYAS

Public (n=3) Private (n =1)

1. Western Visayas Medical Center (Reg. VI) 1. Dr. Pablo O. Torre Memorial Hospital (Reg. VI)

2. Cebu TB Reference Laboratory (Reg. VII)

MINDANAO

Public (n=5) Private (n =3)

1. Zamboanga City Medical Center (Reg. IX) 1. Jamelarin Hospital (Reg. IX)

2. Northern Mindanao TB Reference Laboratory

(Reg. X) 2. CDO Polymedic Medical Plaza (Reg. X)

3. Davao TB Reference Laboratory (Reg. XI) 3. Dr. Arturo Pingoy Medical Center *(Reg. XII)

4. Davao Regional Hospital (Reg. XI)

5. CARAGA Culture laboratory (CARAGA)

34 National TB Reference Laboratory. TB culture laboratories report 2014-2015.

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Table 12. Culture and DST Laboratories under NTP laboratory network, 2016

Region Status

NTRL NCR Functional; performing FLD & SLD DST

LCP NCR Non-functional; awaiting completion of proficiency requirements.

PTSI-QI NCR Functional; performing FLD DST

ITRMC I Non-functional; awaiting completion of ventilation and AC systems

CTRL VII Functional; performing FLD & SLD DST

NMTRL X Non-functional; Lab. Staff still for DST Training

DTRL XI Functional; performing FLD DST; will start SLD by April

A major weakness of the culture lab network is recording and reporting. We observed that recording

and reporting forms are not standardized, records are not updated, reporting is frequently delayed, and

the quality of data needs improvement. These issues indicate that caution is needed when doing data

analysis and interpretation.

In 2014, only 8 of the 23 (35%) functional culture laboratories submitted reports and only 19 of 23 (83%)

laboratories in 201534. There is no official set of standard indicators in place for monitoring the culture

laboratories’ performance. Data from culture laboratory reports are rarely analyzed or used at the

national and sub-national level. Additionally, the staffs responsible for culture lab data and information

management and use are not well equipped to perform the tasks. Supervision of the recording and

reporting process is inadequate.

The formulas used by laboratory staff to compute and report the culture lab performance indicators

varied across the different culture labs. To standardize the computation for the performance indicators

for this assessment, we used the study labs’ raw data and our staff performed the computation. On the

other hand, we used NTRL’s own reported data to assess their culture lab performance. Due to the

paucity of available data, only the following indicators were used for this assessment: (1) culture

positivity rate; (2) contamination rate; and (3) culture recovery rate.

Culture positivity rates (Table 13): The standard for this indicator is from 10% to 15%; it is population

dependent, and baseline values are needed to establish a trend to develop a standard level that is

appropriate for a particular region. Data for this indicator are incomplete as shown in the blacked out

portions of table 13 and reflects the problems in reporting. The available data show wide variation in

Culture (+) rates among the study laboratories and may reflect the variations in the characteristics of

their region, population and types of patients.

Contamination rates (Table 14): The acceptable range for contamination rate is from 3% to 5% of culture

tubes using solid media, and 8% to 10% using liquid media (MGIT). The values seen in our study labs are

fluctuating from high to low suggesting inconsistent quality of performance. The contamination rates for

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liquid culture in NTRL for 2014 and 2015 also showed wide shifts in quarterly trend: high during quarters

1 and 2, and falls within acceptable levels during quarters 3 and 4. Note that contamination is always a

problem in the use of liquid culture.

Table 13. Culture positivity rates in study laboratories 2014-2015

2014 2015

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

NTRL* 79% 73% 74% 67%

LCP 62% 59%

Batangas MC 44% 19% 50% 46%

DOH-Region 3 42% 39% 56% 29% 36% 53% 49% 31%

CTRL 57% 81% 65% 74% 76% 72% 64% 77%

NMTRL 91% 85% 63% 38% 34% 35% 59% 63%

*Liquid culture.

Contamination rates may be influenced by the type of population under study, by specimen collection,

and by the laboratory’s level of proficiency in specimen processing35. High contamination rates can be

attributed to administrative and technical factors related to culture processing, such as: incomplete

processing; and use of contaminated media, reagents or equipment. On the other hand, contamination

rates below the minimum level indicate the use of harsh decontamination reagents, and/or excessive

processing times36.

Table 14. Contamination rates for solida and liquidb culture in selected TB culture labs,

2014-2015

2014 2015

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

NTRL* 20% 21% 7% 6%

LCP 2% 2% 2% 3%

BGHMC 0% 14% 4% 6%

DOH-Region 3 11% 16% 7% 8%

13% 26% 6% 3%

2% 2% 6% 2%

3% 3% 2% 0%

3% 1% 2% 2%

0% 2% 4% 1%

3% 8% 5% 5%

Batangas Med. Ctr.

CTRL 1% 11% 3% 2%

NMTRL 5% 1% 5% 3%

DTRL 3% 3% 4% 6%

5% 7% 4% 3% a Contamination rate for solid culture: 3-5%; b Contamination rate for liquid culture: 8-10% *NTRL uses liquid culture.

35 Association of Public Health Laboratories (APHL). Performance Indicators for the Laboratory. 36 McCarthy K. Division of Tuberculosis Elimination. CDC. Laboratory Performance Indicators. 2007.

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Culture recovery rate: The acceptable range for culture recovery rate for solid culture is at least 85% to

90% of smear positive cultures; and 95% to 98% for liquid culture. A number of factors can influence

culture recovery rates and may include the following: type of population tested (TB suspects versus

confirmed TB cases); type of facility performing the tests such as intermediate (e.g. hospital) versus

reference labs; seasonal variations; contamination of specimens during collection; cross-contamination

inside the laboratory; procedural problems; sub-optimal reagents; and poorly performing equipment37.

The culture recovery rates shown (Table 15) are generally low; for NTRL, the culture recovery rate using

liquid culture are high except in quarters 3 and 4 of 2015.

Table 15. Culture recovery rates in study labs, 2014-2015

2014 2015

Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4

NTRL* 98% 99% 96% 97% 97% 93% 84% 78%

LCP 74% 95%

BGHMC 100% 100% 100% 100% 73%

DOH-RO3 culture lab 90% 80% 65% 38% 77% 69% 68% 58%

Batangas MC 9% 12% 14% 13% 100% 100% 63% 62%

CTRL 61% 88% 69% 80% 82% 79% 65% 80%

NMTRL 90% 85% 71% 82% 77% 78% 88% 86%

DTRL 100% 92% 92% 91% 73% 86% 94% 93% *Liquid culture

Drug susceptibility testing

In 2016, drug susceptibility tests (DST) for TB is available in three NTP culture laboratories; these are: the

National TB Reference Laboratory (Muntinlupa City, NCR), Cebu TB Reference Laboratory (Cebu City,

Region 7) and Davao TB Regional Laboratory (Davao City, Region 11).

Most of the patients with DST are previously treated cases including the Other retreatment cases

(average, 46%); with a smaller proportion of relapses, 24% on average, and 27% consisting of

retreatment patients with no specific categorization (Table 16).

Drug susceptibility results of DR cases were reported by NTRL, LCP and CTRL for 2014; while in 2015, DST

reports came from NTRL, CTRL and DTRL only. LCP temporarily stopped performing DST for NTP patients

in 2015 due to procedural issues that remain unresolved.

37 Revised National TB Control Program (RNTCP). New Delhi. Training Manual for Mycobacterium tuberculosis Culture and Drug Susceptibility Testing.

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No. No. % No. % No. % No. %

2013 269 20 7% - 0% 20 100% 249 93%

2014 1,215 147 12% 11 7% 136 93% 1,055 87%

2015 1,448 238 16% 6 3% 232 97% 1,219 84%

Total 2,932 405 14% 17 4% 388 96% 2,523 86%

Table 16. Types of patients with DST in study laboratories, 2013-2015 (n=4)

Year

No. Pts w/ DST

New

Relapse Other

Retreatment

Unknown Retreatment

only*

No. No. % No. % No. % No. % No. %

2013

2014

2015

2,832

2,657

3,378

3 0%

19 1%

102 3%

266 9%

361 14%

1491 44%

2115 75%

694 26%

1269 38%

0 0%

52 2%

86 3%

448 16%

1531 58%

430 13%

Total 8867 124 1% 2118 24% 4078 46% 138 2% 2409 27%

*Retreatment only - patients classified as retreatment case without specific category

The vast majority of (77%) of those tested for FLD/DST showed drug resistance with most showing multi-

drug resistant (MDR-TB) patterns, while an average 13% showed other resistance patterns (e.g. mono-

resistance and poly-resistance). A small proportion, average of 17%, had drug-susceptible patterns

(Table 17).

Table 17. Results of First line DST in study DST laboratories (n=4), 2013-2015

No. of Pts Drug-Resistant MDR Other

Drug-

Year resistance Susceptible

No. No. % No. % No. % No. %

2013 2,563 1651 64% 1,239 75% 412 25% 936 37%

2014 1,442 1229 85% 1,090 89% 139 11% 28 2%

2015 1,930 1674 87% 1,639 98% 35 2% 30 2%

Total 5,935 4,554 77% 3,968 87% 586 13% 994 17%

Table 18 shows the results of SLD/DST in the study laboratories. On average, 14% of patients showed

drug resistance patterns, among which 4% were with XDR-TB. An average 86% showed drug susceptible

patterns.

Year

Table 18. Second line DST performance in selected laboratories, 2013-2015 (n=3)

No. Pts Drug-Resistant XDR Other resistance Drug-Susceptible

Observations on the collection, storage and transport of sputum specimens for culture/DST reflect the

same issues encountered in TB microscopy and Xpert services. These include the improper packaging of

specimens for transport, lack of standard packaging materials and supplies, and variable procedures for

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specimen packaging. In addition, the supplies of packaging materials are also inadequate particularly the

primary, secondary and tertiary containers (with “cold dogs”) despite funding support from The Global

Fund.

Specimens for TB culture were packed mostly by health workers at treatment facilities who are not well

versed on proper specimen packaging procedures; appropriate packing is also affected by the lack of

packing materials. In these instances, health workers improvise, and because they pay for the packaging

costs, the improvisation is often inappropriate to limit their expenses.

Some lab workers mentioned that contamination rate is higher when they receive samples that have

packaging issues that result to specimen spillage or leakages. Specimens for culture were transported

mainly by commercial couriers and are paid for by The Global Fund. There is no monitoring or evaluation

of specimen integrity as it goes through the transport system.

The TAT for TB culture from the study labs was from 8 weeks to 16 weeks using solid media. Some of the

study culture labs (i.e. PTSI, NMTRL, SLH) visited exceeded the TAT standard due to the following:

a. Pooling of specimens before processing

b. Delay in recording results due to shortage of encoders

c. Identification of culture growth is done in another lab leading to delayed result

The TAT was not monitored in all study labs because this is not required by the program. Besides, no

standard TAT is implemented on the culture lab network, both for solid and liquid culture (using MGIT).

The standard TAT for solid culture is 3-8 weeks on average38; however, the TAT for culture among study

labs using solid media is 9 weeks (NTRL, LCP, DOH-RO3 culture laboratory, Batangas MC). Culture results

are expected to be reported from 3 to 8 weeks but this covers only the time required for incubating

inoculated culture tubes. This does not include administrative procedures for recording and reporting,

as well as the release and transmittal of results. It takes an additional week after 8 weeks of incubation

(total of 9 weeks) before releasing the final culture result (NTRL, LCP, DOH-RO3 culture laboratory,

Batangas MC). A turnaround time of 9 weeks seems to be more realistic.

NTRL’s TAT for liquid culture (MGIT) is 6 weeks; this is longer than the average TAT of 2 weeks39.

However, detection may be delayed by factors such as harsh specimen processing, tightened caps

during the first week of incubation, incorrect temperature and low bacterial load such as in smear-

negative specimen40.

38

Siddiqi, S.H., and Rüsch-Gerdes, S. MGIT procedure manual. Geneva, FIND. 2006. 39 Association of Public Health Laboratories (APHL). Mycobacterial Culture. 40 Association of Public Health Laboratories (APHL). Mycobacterial Culture.

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Most of the patient types who had DSTs were the Other Retreatment (46%), relapses (24%), and the

unclassified retreatment cases (27%). Observed TAT for solid DST and liquid DST (MGIT) at NTRL is seven

weeks; this is longer than the standard TAT of 4 weeks for solid DST and around 2 weeks for liquid DST41.

Prolonged TAT may be due to batching of specimens, use of conventional identification and DST

methods, suboptimal use of technology and use of national or other reference laboratories42. Delay in

the transmittal of results is due to problems in the courier’s pick-up schedule (as seen in RO3, NMTRL,

NTRL), previously unsettled courier payment by DOH (in PTSI), and delayed encoding of results in ITIS

software (in Batangas MC).

4. Line Probe Assay

Line-Probe Assay (LPA) to detect MDR and XDR-TB is currently used mainly for patients under treatment

with new SLDs including Bedaquiline and Delamanid; and for patients under the pilot implementation of

the new 9-month MDR-TB regimen. Currently, there is only one functional Line Probe Assay (LPA)

laboratory in the country which is at the NTRL. Delays in making additional LPA labs functional were due

to delays in procurement of equipment (thermocycler), and lack of competent staff to perform the

procedure.

Table 18 below describes the results of LPA tests for 1st line anti-TB drugs (FLDs) in 2013. Of 276 MTB

detected specimens, 78 (28%) were MDR-TB, 13 (5%) were with rifampicin (R) mono-resistance and 33

(12%) with INH mono-resistance. More than half of specimens, 152 (55%), were drug susceptible.

Table 18. LPA First line DST results, NTRL 2013

No. %

MTB detected 276

R resistant and H resistant (MDR) 78 28%

R resistant and H susceptible 13 5%

R susceptible and H resistant 33 12%

R susceptible and H susceptible 152 55%

On the other hand, the LPA tests for SLD/DST (3rd quarter of 2015 up to 3rd quarter of 2016) for 537

specimens showed the following results: 369 (69%) were MTB detected; 116 (22%) MTB not detected;

and 49 (9%) had Invalid results. Among the 369 specimens with MTB-detected results, 332 (90%) were

susceptible to both Fluoroquinolones (FQ) and second-line injectable (SLI) drugs. Only 1 specimen had

extensively drug-resistant strains (XDR-TB), or resistance to both FQ and SLI.

41 Association of Public Health Laboratories (APHL). Drug Susceptibility Testing for M. tuberculosis complex 42 McCarthy, K. Division of Tuberculosis Elimination. CDC. Laboratory Performance Indicators. 2007.

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No. %

Number of samples processed 534

Number of samples released within TAT 507

Number of samples released beyond TAT 27

95%

5%

MTB not detected 116 22%

Invalid 49 9%

No. %

No. of specimens processed* 537

MTB detected 369 69%

Table 19. LPA Second line DST results, NTRL Q3 2015- Q3 2016

FQ resistant and SLI resistant (XDR) 1 0.3%

FQ susceptible and SLI resistant 24 6.5%

FQ resistant and SLI susceptible 12 3.2%

FQ susceptible and SLI susceptible 332 90%

*3 specimens are unaccounted

NTRL’s turnaround time for LPA is five days. The NTRL’s TAT is longer than GLI’s standard TAT of 1-2

days. TAT may still be longer if batching of tests is done43. Of the 534 specimens tested from Q3-2015 to

Q4-2016, 507 (95%) were within the 5-day TAT (Table 20).

Table 20. LPA Turn-Around Time in NTRL (Q3 2015 - Q3 2016)

5. Laboratory External Quality Assurance Programs

The NTP has implemented an EQA program for TB smear microscopy but not for the other diagnostic

technologies. The program was implemented since the 1990s, and underwent revision in 2004. The

revision involved the following changes: (1) use of the lot quality assurance system (LQAS) for collection

of sample slides for rechecking replacing the 100% smear (+) / 10% smear negative rule; (2) the lab

network was organized for the implementation of EQA activities; (3) new procedures for EQA were

developed and published and disseminated as a new manual44; and (4) passage of a national policy to

support the implementation of the microscopy QA program45.

The guidelines and procedures of the new EQA program were based on international

recommendations46. The new guidelines aimed to strengthen the implementation of EQA activities

which include quarterly (1) on-site assessment and supervision; (2) blinded slide rechecking; and (3)

panel testing. Panel testing is currently not implemented in the country because of its inherent

43 Global Laboratory Initiative. Training package on LPA. 2012.

44 Department of Health. Quality Assurance for Sputum Smear Microscopy, Philippine National TB Program. 2004. 45 Department of Health (DOH). Administrative Order no. 2007-0019. Guidelines for the Implementation of the Quality Assurance System on Direct Sputum Smear Microscopy. Philippines; 2007. 46

Association of Public Health Laboratories. External Quality Assessment for AFB Smear Microscopy; 2002.

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limitations and challenges. However, there are no country guidelines or procedures for the external

quality assessment of fluorescence microscopy (FM) slides at this time.

We collected data for 2014 and 2015 (recorded data for 2013 was not complete) from 12 QA centers

(QAC) to assess the implementation of the EQA program. We looked into the management of EQA

implementation and its results. EQA program results were measured through the trend in the level of

quarterly participation (coverage) of all TMLs in the local NTP lab network, and the trend in the level of

quarterly microscopy performance (reading proficiency). This is in contrast to the current NTRL practice

of reporting the annual national average level of performance that do not reflect realities on the ground.

To obtain a more realistic picture of the state of EQA implementation in the study areas, the following

indicators were used for this assessment:

1. High EQA participation (coverage): “At least 95% of all TMLs in the LGU’s NTP laboratory

network are participating quarterly in the EQA program”.

2. High EQA performance (reading proficiency): “At least 95% of all TMLs in the LGU’s NTP

laboratory network have less than 5% major errors per quarter”.

Of the 12 QACs, 8 (67%) are located at the intermediate level (provincial/city health offices) while 4

(33%) are peripheral main health centers that were designated to implement EQA in addition to their

regular function of providing health services and managing public health programs. Three of the eight

provincial QACs are also providing sputum microscopy services. Three of the four (75%) peripheral QA

centers are providing public health and clinical services including laboratory tests such as TB microscopy,

Xpert tests, HIV testing, CBC, urinalysis, blood chemistry, among others.

Table 21 shows the number of microscopy laboratories in the respective LGUs’ in 2014 and 2015; note

that 8 of the 12 LGUs (67%) showed an increase in the number of laboratories in their areas as a result

of the NTP’s drive to expand the availability and accessibility of microscopy laboratories. This led to an

increased workload for the QA teams.

The QA teams enumerated a number of operational problems that affected the implemented of EQA

activities. Among the 12 QA teams in the study, 84% reported transport problems as barriers to perform

on-site assessment, slide collection, feedback and supervision; 33% have insufficient funds for travel to

conduct supervisory visits; and 25% have no dedicated budget for EQA activities.

In addition, 84% have shortages of staff including controllers and MD/Nurse coordinators; in 17% of the

QA teams, the nurse and doctor of the QA team are not trained; almost all have inadequate skills and

knowledge to perform on-site assessment, identify performance problems, and provide technical

support to TMLs and help them solve their performance problems. Facility and equipment issues were

also mentioned with 42% of QA teams needing infrastructure improvements in their QA centers; and

17% lacked microscopes for slide rechecking use.

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Table 21. Number of TMLs in local lab network in study LGUs, 2014-2015

2014 2015 % increase

1 Quezon City

2 Baguio City

3 Angeles City

4 Pampanga

5 Batangas

6 Cavite

7 Cebu City

8 Tacloban City

9 Leyte

10 Misamis Oriental

11 Davao City

12 Davao del Norte

40 54 35%

9 9 0%

9 10 11%

48 54 13%

39 48 23%

43 43 0%

5 5 0%

5 5 0%

45 46 2%

27 29 7%

46 48 4%

29 30 3%

Table 22 below shows the trend in the level of EQA participation in the study LGUs. In both years, there

are more low performers than the high performers in terms of EQA coverage. Only 33% of the LGUs in

the study achieved a high level of quarterly EQA participation (coverage) in 2014; this improved to 42%

in 2015. The operational problems described previously account for this situation. Most notable among

these is the lack of operational support to enable the QA teams to travel for slide collection.

Table 22. Trend of quarterly EQA participation (coverage) in study LGUs, 2014-2015

LGU

No. TMLs

2014

No. TMLs

2015

Q1 Q2 Q3 Q4

Level Q1 Q2 Q3 Q4

Level % % % % % % % %

Angeles City 9 89 89 89 89 Low 10 100 100 100 100 High

Baguio City 9 89 89 67 44 Low 9 67 67 67 22 Low

Batangas Province 39 90 92 95 95 Low 48 85 88 90 79 Low

Cavite Province 43 98 98 88 77 Low 43 100 100 100 100 High

Cebu City 5 100 100 100 100 High 5 100 100 100 100 High

Davao City 46 98 98 100 100 High 48 100 96 94 96 Low

Davao del Norte 29 97 97 97 97 High 30 97 97 97 97 High

Leyte Province 45 91 95 91 91 Low 46 93 91 98 98 Low

Misamis Oriental Prov. 27 89 74 89 93 Low 29 89 93 96 97 Low

Pampanga Province 48 73 69 81 90 Low 54 94 90 92 94 Low

Quezon City 40 100 100 100 100 High 54 100 100 100 98 High

Tacloban City 5 0 20 20 20 Low 5 60 60 60 60 Low

Total 2014 High: 4 (33%); Low: 8 (67%) 2015 High: 5 (42%); Low: 7 (58%)

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The data, however, provides evidence that it is feasible for LGUs to implement quarterly EQA activities

as stated in the NTP policy and manual for sputum microscopy quality assurance. The data further show

that LGUs can achieve a high level of coverage if there is adequate support. However, this level of

performance can also quickly change over time (i.e. quarter to quarter, year to year) if support is not

sustained.

In the LGUs that performed well, the improvements in coverage were achieved mainly through better

coordination and planning of slide collection activities, and by adopting modified approaches in slide

collection as seen in 64% of the QA teams. Examples of modified slide collection methods seen in this

study are: (1) slide collection during monthly staff meetings or quarterly DQC activities; (2) RHU staff

brings the slides to the QA center for selection and collection (either monthly or quarterly); and (3)

slides are selected at the RHUs by RHU staff and brought to the QA center for the rechecking process.

The last method, however, may be problematic because it can introduce bias in the slide selection

process.

Table 23 shows the trend of quarterly level of EQA performance (proficiency) in the study LGUs. The

number of high performers in 2014 is higher than in 2015. The low level of performance for TMLs in the

study LGUs can be attributed to the human resource problems especially the lack of controllers to

perform slide rechecking; and the lack of the QA teams’ capacity to conduct field visits, and the

capability to provide feedback and supportive supervision.

Table 23. Trend of EQA performance (proficiency) in study LGUs, 2014-2015

LGU

No. TML

2014

No. TML

2015

Q1 Q2 Q3 Q4

Level Q1 Q2 Q3 Q4

Level % % % % % % % %

Angeles City 9 89 89 89 78 Low 10 100 100 100 100 High

Baguio City 9 89 89 67 44 Low 9 67 67 67 22 Low

Batangas Province 39 87 92 95 90 Low 48 85 83 88 77 Low

Cavite Province 43 98 95 88 74 Low 43 100 88 91 100 Low

Cebu City 5 100 100 100 100 High 5 100 100 100 100 High

Davao City 46 98 98 100 98 High 48 100 94 94 96 Low

Davao del Norte 29 90 93 97 93 Low 30 97 97 93 93 Low

Leyte Province 45 91 91 89 89 Low 46 93 89 91 98 Low

Misamis Oriental Prov 27 85 70 81 81 Low 29 81 89 89 83 Low

Pampanga Province 48 65 67 79 90 Low 54 92 86 92 93 Low

Quezon City 40 100 95 95 100 High 54 93 98 100 94 Low

Tacloban City 5 0 20 20 20 Low 5 60 60 60 60 Low

Total 2014 High: 3 (12%); Low: 9 (75%) 2015 High: 2 (17%); Low: 10 (83%)

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The data further show that performance can quickly vary over time (i.e. from quarter to quarter, year to

year). This is why the continuous assessment, monitoring and provision of technical support to address

problems in performance are necessary to achieve and sustain high levels of performance.

To address the increasing EQA workload and shortage of controllers, 75% of the QA teams used “part-

time controllers” (i.e. microscopists from the peripheral TMLs) to help perform blinded rechecking of

slides. However, the use of “part-time controllers”, who are also the subject of the slide rechecking

process, has some issues that may affect the EQA results. This includes the potential bias in the

rechecking of their colleagues’ slides; as well as the uncertain level of proficiency in slide assessment of

part-time controllers. In addition, the slide rechecking done by “part-time controllers” usually have long

turnaround times, as long as three months in some cases, and contributes to delays in reporting.

Moreover, the added task is adversely affecting the part-time controllers’ regular work in their official

workplaces.

Among the QA teams, the general perspective of EQA is still the identification of individual slide errors

or the validation of individual patient diagnosis, rather than on the identification of laboratories that

may have serious problems. There is also inadequate focus on identifying the root causes of these

problems and on addressing them to improve their performance.

The capacity of the QA teams to manage and implement EQA activities is variable. Majority of the QA

teams (67%) have no comprehensive plans for EQA implementation. In those with plans, the quality of

their plans is often low, and does not focus on addressing the priority problems or challenges. Budgetary

support for these plans is usually inadequate.

The level of technical support and supervision to QA teams from the regional and/or national level after

EQA training is also inadequate. Monitoring, supervision and evaluation of EQA implementation from

the higher level is relatively weak. In addition, there is still no mechanism to assess the competencies of

the QA teams as they perform EQA functions. Some QA staff felt that they have been neglected in terms

of technical support from the higher level.

EQA data management and use

The EQA program generates huge quantities of data based on routine program indicators. These data

are used primarily to create and submit reports in raw form. At regional and provincial/city level, it is not

easy to come by documents that provide information based on the comprehensive analysis of EQA data,

from staff meetings, or from periodic DQC activities. One program manager mentioned that they

generally do not analyze data because this is not “required for reporting”. It was suggested by some

interviewees that the national level is expecting only consolidated data from the lower levels.

Qualitative information from the field is not well documented. This is not a priority for the QA Teams

because this is not required for reporting. It was observed that most of the QA teams’ appreciation of,

and their capacity to gather and analyze, qualitative data is inadequate. The QA teams expressed the

need for more skills in data analysis and interpretation.

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II. Laboratory support systems

1. Human resource system

Human resources are the most important resource of any organization. The shortage of appropriate

staff in the laboratory network is a continuing problem. Task shifting has been tried in some areas at

various levels of the network to address the human resource shortage particularly in the use of informal

laboratory workers for smearing and microscopy work in TB microscopy in difficult to reach areas; there

are instances where non-med tech professional are utilized to perform Xpert testing. The effectiveness

of this intervention has not been assessed, however.

Issues related to organizational positions, compensation, benefits, lack of clear career development, as

well as poor workplace conditions remain. These persist as important factors that deter laboratory

professionals from working in the NTP laboratory network whether as laboratory staff, supervisors or

laboratory network managers.

Most staffs in the specialized NTP laboratories (i.e. Xpert, culture/DST) are project-hired contractual

employees whose salaries and benefits are lower than the permanent staff in the same laboratories. The

contractual (temporary) employment and lower compensation tend to drive project-hired laboratory

workers to leave and seek employment elsewhere.

The use of health center/TML microscopists as part-time EQA controllers is a multi-tasking arrangement

which helped QA centers cope with their workload. However, this does not increase the controllers’

effectiveness, efficiency and motivation; this has even contributed to the weakening of the laboratory

service because their regular work is adversely affected by their EQA activities.

2. Training and supervision

Training and supervision are essential for the optimal performance of the NTP laboratories. Training is a

unique service that has to be provided regularly as new technologies are adopted and new personnel

are recruited. Effective training and post-training supervision are costly activities, but these investments

are necessary in order to ensure that trained workers have the competencies required to perform lab

procedures correctly and safely.

Formal training courses are available for all diagnostic technologies employed in the NTP. The conduct of

microscopy training has been devolved to regional and some LGU level trainers while trainings for Xpert,

culture/DST and LPA remained as NTRL responsibilities centrally.

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The scale-up of Xpert use in the country, and the turnover of Xpert operators, as well as the presence of

new EQA staff in many places, has raised the demand for training to a point where NTRL could no longer

respond to the demand adequately. This has limited the pace in the conduct of Xpert trainings, and may

have contributed to the slowdown in the expansion of Xpert laboratories. The limited availability of EQA

trainings has reduced the capability of some LGUs to implement the EQA program due to the lack of

trained EQA teams.

The quality and effectiveness of the current laboratory trainings has not been thoroughly evaluated.

Competency assessment in the laboratories is not routinely performed after the formal training. The

training curricula for microscopy and EQA have not been updated since these were developed in the

early part of the last decade. Other teaching methods (e.g. mentoring, online learning) have not been

fully utilized in appropriate circumstances. In addition, training materials and job aids need to be

updated and improved.

Though relatively new, the Xpert training course has not been evaluated as well. In addition, Most of the

Xpert trainings conducted in recent years are for operators; clinic staff (doctors and nurses) who refer

patients and use the results for patient diagnosis and management were not trained. When Xpert

results are not straightforward (e.g. R-resistance indeterminate, or MTB not detected in the presence of

symptoms signs and other tests that suggest TB), clinicians may find it difficult to make decisions related

to treatment.

Supervision is limited for all types of laboratory workers including sub-national lab network managers. A

supervisory program for the laboratory network is not yet fully developed and organized. For the culture

laboratories, most supervisory visits facilities were done by NTRL staff during the initial mentoring phase

at the start of their operations. The supervision component of microscopy EQA is not adequately

performed.

In 2016, activities were implemented to start the decentralization process for the implementation and

management of trainings for EQA and Xpert to the regional level. This intervention is expected to have

long term and more permanent improvements in NTP’s capability to provide laboratory trainings.

Building organizational capacity at the sub-national level is ongoing under the laboratory training

decentralization strategy (LTDS). It is a long term process that is being led by NTRL and which requires

substantial financial, political and technical support. When fully implemented, the decentralization

process will enable the regional, including most provincial and city health offices, to organize and

implement selected laboratory trainings to meet the NTP’s training needs.

Another measure that was implemented by the program managers to address the unmet training

demand for Xpert operators is to conduct “informal trainings” (also called on-the-job training). These are

shortened (one or two days) versions of the formal course and are conducted by newly trained lab

implementers (not trainers). On the job trainings were also resorted to for workers in some TMLs, QA

centers and culture laboratories.

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The informal trainings are generally unstructured, and not standardized in terms of its content, and are

lacking in training aids. These trainings are basically a “demo-return demo” activity which does not

ensure that trainees will acquire the minimum competency requirements to perform laboratory

procedures correctly and safely. This makes “informally trained” workers potentially at risk as they work

inside the laboratory.

Sub-national (i.e. regional, provincial) support to training management, implementation and conduct of

supervision is limited because the capacity and mandates at these levels have not been developed to

enable them to perform these functions effectively. Furthermore, sub-national training facilities and

equipment that meet the standards are few; this is another barrier to effective training.

Currently, training courses for trainers and training managers are only for Basic TB Microscopy, and

none for EQA and Xpert trainers; laboratory training courses are designed with only the laboratory

operators and EQA supervisors in mind. There are no courses in place to help lab network managers

enhance their leadership and management capabilities.

The relatively high level of inconclusive test results (e.g. errors) from Xpert tests, inconsistent

performance of the culture laboratories, and low proficiency seen in the study TMLs, as well as some

unsafe laboratory practices that were observed, reflect the sub-optimal level of training effectiveness,

and the consequences of the lack of supervision. In this scenario, the benefits and impact of the

diagnostic technologies may not be fully achieved by the NTP, its stakeholders and beneficiaries despite

the high level of investments to modernize and strengthen the laboratory services.

3. Financing

The establishment and operations of the laboratory network’s specialized technologies are financed

with funds from donors, by the national government through the regional offices of DOH and the private

sector. On the other hand, the devolved microscopy services, EQA activities, and peripheral Xpert labs

are financed by LGUs and private sector. Capacity building activities to strengthen the services are

financed in large part with donor money. Most of the equipment and consumables for the scale-up of

new diagnostic technologies are financed with donor support.

Strengthening the laboratory systems is necessary to ensure that the diagnostic services are effective

and are sustained in the long term. However, this will require higher levels of government funding.

Identifying and mobilizing new domestic sources of financing will be important.

4. Information management

Information is an important resource that can empower leaders and managers in the laboratory

network. A number of gaps in laboratory information management exist including data quality, delayed

reporting, limited feedback and sharing of information, and the inadequate use of information to

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improve the laboratory services. The causes are varied and reflect weaknesses in the laboratory

information system elements such as staff, procedures, equipment, communications capacity and skills.

Underscoring these gaps is the lack of adequate financing that can be traced to a low level of political

support to strengthen the information system. In addition, opportunities for training are lacking; and

supportive supervision from the higher levels is inadequate.

The quality of laboratory records and reports needs improvement. Data quality issues, particularly its

correctness, have made data collection for this study difficult. There are many instances wherein

laboratory records are not updated; and errors are quite common particularly in culture laboratory

performance reports. The set of indicators to monitor the performance of culture laboratories is not yet

standardized. In addition, there is some confusion regarding the formulas for computing the values of

these indicators. The frequent changes in culture recording and reporting forms in the past years

instituted by NTRL also caused confusion among implementers.

Personnel dedicated to perform encoding, recording and reporting tasks are lacking. In the usual

scenario, the updating of records and writing of reports are performed by the medical technologists who

are already burdened by their heavy laboratory workload. Procedures for data management are not

clearly defined; lab workers and managers are in need of guidance that will help them perform data

management tasks properly including feedback to the data generators, and sharing of information with

stakeholders.

Access to essential equipment such as computers, printers and/or copiers especially in the peripheral

level is still limited. The transmittal of reports is still a problem especially in rural areas. In these places,

internet use to strengthen communications capacity is limited because of connectivity problems. An

information management tool, the ITIS (laboratory module), is not yet available in most peripheral

laboratories. Text messaging has become an important tool for transmitting information and has

contributed to the strengthening of the lab services’ communications capability. However, the cost of

using this technology is often shouldered by the laboratory workers themselves.

Laboratory information management skills, particularly among laboratory network managers, needs

improvement. Knowledge and skills on data management, analysis, interpretation, use and information

sharing generated by routine laboratory data are inadequate. The continued practice of reporting

consolidated raw data do not provide the opportunity, and compelling reason, to analyze and interpret

data to be used as basis for the improvement of laboratory operations.

Operational difficulties in the laboratory services also contributed to reporting delays. A good example is

the delay in EQA reporting wherein the delays in sample slide collection, and prolonged duration of the

slide rechecking cascades into a delay in the reporting and feedback processes.

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The level of support for the information system is lacking in terms of finance; mandates; staff;

equipment; infrastructure; training; supervision; work spaces; information flow particularly in terms of

feedback and information sharing; and M&E of the information system.

5. Supply chain management

The effective management of supplies is necessary to ensure that services are provided continuously in

an effective manner. We observed that, in general, laboratory supply chain management is weak and

needs more attention at all levels. Gaps in supply management practices seen in this study have led to

service interruptions due to stock-outs of supplies, and contributed to problems in test results. The

functioning of some newly established laboratories was delayed because of supply related problems.

There are stock outs of the following laboratory supplies in some of our study laboratories:

1. For sputum microscopy: sputum containers, applicator sticks, ZN and auramine staining kits

(Batangas CHO), immersion oil (Naic RHU), slide boxes, alcohol, disinfecting solutions

2. For EQA: ZN staining kits, immersion oil (Cavite PHO), slide boxes (Leyte PHO)

3. For GeneXpert: cartridges (EVRMC), non-powdered gloves, disinfecting solutions (LCP)

4. For culture: conical tubes (DOH-RO3 culture laboratory), culture media, sodium hydroxide,

respirator, gloves, disinfecting solutions (SLH, LCP), hand soap (LCP), lab gowns (DOH-RO3

culture laboratory) and lab registers (NMTRL)

Reasons for stock outs include: (1) inadequate quantities of requested supplies (DOH-RO3 culture

laboratory, Batangas MC); (2) delayed delivery of requested supplies; and (3) unforeseen referrals of

specimens for culture (SLH, PTSI).

TMLs using LED-FM had to revert to ZN staining when stocks of auramine ran out. Stock outs of sodium

hydroxide (NaOH) stopped the processing of specimens for TB culture for up to 10 working days (SLH,

Batangas MC). The stock outs of laboratory materials led to inefficiencies in service delivery and

inaccuracies of test results. This also led to out-of-pocket expenses among patients and lab staff as they

had to buy supplies while waiting for supply replenishments to arrive. Laboratory biosafety practices are

also compromised because of the inadequate quantities (and in some cases, incorrect concentration) of

disinfecting solutions and the lack of personal protective equipment (e.g. N95 mask). Some Xpert

operators used powdered gloves despite this being not recommended; this is because the non-

powdered gloves were not supplied (LCP).

There were instances wherein the expiry dates of auramine written on the box are different from those

printed on the bottles (Batangas CHO). Culture media tubes delivered by NTRL to the culture/DST labs

had no manufacturing date and expiration date (DTRL). The sub-standard quality of sputum containers

remains an issue in two TMLs (Carmen RHU, Kamuning SHC) as specimen leakages occurred in these

settings. One regional TB laboratory (NMTRL) reported overstocks of ZN stains and sputum containers.

Buffer stocks are generally not available in TMLs.

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Ogawa culture media for use by the NTP culture/DST laboratories are prepared by NTRL. Three other

culture labs (LCP, PTSI, CTRL) are also preparing media (Ogawa, Lӧwenstein-Jensen) for their own use.

There is no quality assurance program in place to ensure that these are prepared according to

standardized procedures and are meeting quality standards.

In addition, there were instances wherein commercially bought eggs were used instead of the required

organic eggs, because of supply problems, for the preparation of egg-based media (NTRL, LCP, PTSI,

CTRL). A major concern is that commercially available eggs may contain antibiotics and this might cause

false negative culture results especially among patients with low bacterial load.

Ogawa media tubes are transported via courier from NTRL to sub-national laboratories. Problems

encountered in the distribution process are: (1) breakage of media tubes during transport and; (2) media

tubes getting uncapped during transport (Batangas MC), both of which rendered them unfit for use. The

number of broken media tubes received in study labs ranged from 5 tubes (Batangas MC) to 20 tubes

(NMTRL).

Improper storage of lab supplies (e.g. Xpert cartridges) was observed (Lourdes Sur HC, Cebu CHO). These

can compromise test results such as when Xpert cartridges and/or buffer solutions are subjected to hot

temperatures well above the manufacturer’s recommendations.

In 2015, one culture laboratory (SLH) received laboratory supplies and equipment (such as beakers,

cryovials, Erlenmeyer flasks, beaded tubes) which were not requested for their operations. The reason

for the delivery of these supplies to this lab was not clear.

6. Equipment, facility (physical plant) and infrastructure

Facilities, equipment and infrastructure are necessary elements for the development of the capacity of

the laboratory network in order to provide its services. In general, the study laboratories are fully

equipped, with dedicated laboratory spaces and adequate supply of water and electricity. Laboratory

arrangement and administration is generally good among study culture labs; workflow is logical and

efficient for TB culture processing. The certification and maintenance of newly established culture labs

are performed by the Biomed Services of RITM.

However, some of the study labs have ventilation design flaws that pose hazard to both the laboratory

worker and the persons within the vicinity of the laboratory.

Communications capability is variable although the minimum requirements are met with either

landlines or personal mobile phones. Internet connectivity is present but does not always have the

desired strength.

In TMLs, the minor maintenance of microscopes is performed by microscopists. All TMLs visited had

functional microscopes but only one (Sindalan RHU) had yearly microscope calibration. In the study

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Xpert labs module calibration is performed annually. In culture laboratories, BSC certification is

performed annually. Three culture labs (NTRL, SLH, Batangas MC) were regularly monitoring their lab

equipment. All study culture labs have service records for equipment on file.

The laboratory equipment and facility maintenance program is not well organized at this time. Problems

related to equipment and facility maintenance and other support systems have led to downtimes in the

laboratories. For example, two culture laboratories (LCP, DRH) were rendered non-functional because of

malfunctioning air handling units and staff problems. Table 24 below shows the length of downtimes in

our study laboratories. A total of 408 days downtime occurred in 2015. Equipment maintenance issues

caused the longest downtime (LCP = 220 days, DRH = 60 days).

Table 24. Facility downtime in sample TB laboratories, 2015

No. Type Laboratories Working

Days Causes

TML Naic RHU 7 Staff attendance to meetings and trainings; leave of absence

Carmen RHU 14 Staff attendance to whole day weekly meeting

Xpert XU-CHCC 2 Rotating brown-outs (2.5 hours); no generator

Culture/DST LCP 220 Malfunctioning air-handling unit

SLH 10 Stock-out of NaOH for TB culture processing

Region 3 TB Lab 10 Delay in renewal of employment contract

15 Staff attendance to meetings and trainings

Batangas MC 10 Due to stock-out of NaOH for TB culture processing

DRH 60 Malfunctioning air-handling unit

60 No med tech

Total 408

In XU-CHCC, one Xpert module is not functional. The staff reported that their Xpert unit experienced

frequent breakdowns but the number of downtime days was not tracked. In Cebu CHO, the biosafety

cabinet used for processing specimens and the biological refrigerator for storage of cartridges are non-

functional.

In NTRL, the delay in certifying BSCs is due to HEPA filters not meeting the required standard

specifications. There are no SOPs for culture equipment maintenance. Delays in facility renovations have

contributed to the slow progress in the expansion of culture laboratory services. The imminent pull out

of Biomed Services of RITM in 2017 will further delay the certification and maintenance of culture

laboratories.

7. Monitoring and evaluation

Monitoring activities are implemented by the laboratory network managers / coordinators at all levels.

However, these are not well planned and not adequately supported with funds, time and logistics.

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Monitoring is not well appreciated and not used as a management tool. Monitoring skills need to be

enhanced, especially at the national, regional and provincial level. Findings from monitoring activities

are not analyzed and shared with the stakeholders.

Evaluation of laboratory network performance is hardly implemented. This is largely due to the lack of

skills and resources among the laboratory network managers at all levels to perform evaluation.

8. Leadership and management of the lab network

The strategic direction of the laboratory network was set by the NTP in consultation with NTRL, technical

partners and regional coordinators. Policies and guidelines on the use of microscopy, Xpert, culture and

LPA have been developed and are aligned with NTP diagnostic algorithms. Coordination of laboratory

activities and services are led by regional and provincial coordinators. Strategic planning for the

laboratory network was led by NTRL. Annually, NTRL develops plans in consideration of the needs of the

laboratory network.

In 2016, NTRL resumed the regional consultative workshop to ensure alignment of regional priorities

and activities with regard to the laboratory network. During the regional workshop, technical areas for

capacity building were identified by the regions to support lab expansion, improvement of service

delivery and scale up of adoption of new diagnostic technologies.

However, the participation of the medical technologist in planning activities at the regional and

provincial levels is limited. Laboratory network plans lack the necessary focus to address the local needs.

Most of the planned activities are on training and monitoring visits.

Leadership and management capacities of the regional and provincial teams need enhancement;

organizational capacities at the regional and provincial levels must be strengthened in order to perform

their leadership and management mandates.

9. Biosafety

Biosafety is an important laboratory element that helps ensure the safety of the lab staff and other

individuals who come in contract with the laboratory and its vicinity through the application of safety

practices inside the laboratory. The NTRL/RITM has developed the National Biosafety Guidelines for the

NTP laboratory network. However, these guidelines have not been widely disseminated and

implemented.

Laboratories in the study do not have biosafety plans. Biosafety is not given enough emphasis during

trainings. Monitoring and supervision of safe laboratory practices is inadequate. None of the study

laboratories has a manual on safe laboratory practices. The study lab staffs do not strictly adhere to safe

laboratory practices. For example, staffs perform procedures in poorly ventilated laboratory with non-

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functioning BSC (Cebu City Xpert lab) and the SLH medical technologist performs procedures using a

non-certified BSC. In two laboratories, ventilation apparently does not conform to published biosafety

standards. These scenarios increase the risk of laboratory workers’ exposure to the TB bacilli which may

lead to an infection and subsequent disease.

10. Infection control

Infection control is a set of activities aimed to prevent TB infection within the facility including TB

laboratory. This is complemented by laboratory biosafety. Almost all (92%) study labs are implementing

restricted access to laboratories as part of administrative control. The national infection control

guidelines were approved in 2010 but these are not well disseminated or implemented.

Laboratory specific risk assessment was not performed and there are no local IC plans in the study

facilities. Most study laboratories do not have spill kits. Respirator fit testing is not regularly done at the

subnational level. Screening of laboratory workers for TB infection and/or disease is not regularly done

at all levels.

The lack of biosafety SOPs, use of malfunctioning equipment (e.g. BSC); problems in facility design (poor

ventilation); as well as issues on supply management of PPEs, contribute to risk of exposure to TB bacilli

in addition to the poor biosafety practices of laboratory workers.

11. Waste management

The laboratory services generate a huge amount of waste materials in the course of conducting

diagnostic procedures. As new technologies are adopted and more laboratories are established, waste

generation increases. When the laboratory waste is not managed properly, it can impact on the

environment negatively and pose threats to public health.

The NTP laboratory waste management system is not well developed. National guidelines on hospital

waste management exist but are not well disseminated. The implementation of laboratory waste

management is not adequately supported with plans, budget, policies and procedures. Standard

operating procedures are not available or unclear at all levels.

Laboratory waste management practices show significant gaps and need improvement. In one

laboratory, waste is placed in an unlined carton box. It takes a long time before the laboratory waste is

disposed because of the delayed collection by a third party medical waste collector. Laboratory staffs do

not have information on the final disposal of sputum cups, culture tubes and Xpert cartridges.

Monitoring of laboratory waste management is not routinely done.

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Good health governance dictates that leaders should be accountable for the state of the environment.

Appropriate and responsible laboratory waste management must be practiced at all levels of the

laboratory network to protect people and the environment.

12. Laboratory health promotion and education

Laboratory health promotion is important to ensure that health workers and patients are informed so

they can better understand the use of TB diagnostic procedures.

In general, information on TB diagnostics is provided only to the laboratory workers and clinic staff.

Information provided to patients is often limited to specimen submission. Information on new TB

diagnostic technologies is inadequate for the clinic staff. Training for clinic staff on GeneXpert is not

done.

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Recommendations

The results of the assessment showed that the full functionality of the NTP diagnostic network is

determined by the presence and interaction of the various elements of the laboratory system working

synergistically in order to provide quality assured services, and to achieve the desired NTP outputs and

outcomes. The following are the recommendations based on the study findings:

1. Human resource system

Review and update the staffing pattern, roles, functions and qualifications to meet the

needs of the lab network at all levels.

Address issues on workplace conditions, disparities in compensation and benefits between

contractual and regular employees.

Develop a rewards system to acknowledge good performance and significant contributions

to the program.

Assess task shifting initiatives; expand task shifting coverage where appropriate and

effective.

Limit multitasking initiatives to a minimum to preserve efficiency and effectiveness of the

staff (e.g. part time EQA controllers from RHUs).

2. Training and supervision

Build capacity of the regional and provincial/city staff to implement training decentralization

for microscopy, Xpert and EQA; this should include acquisition of competencies on various

teaching methods.

Standardize the existing training courses and on-the-job trainings.

Monitor and evaluate training quality and effectiveness.

Develop a course that will enhance the leadership and management capacity of lab network

managers.

Develop and implement a post-training supervisory program.

3. Financing

Explore alternative sources of financing for the laboratory network

Implement mechanisms to mobilize LGU resources for laboratory maintenance and

operations including training, monitoring and supervision.

4. Information management

Enhance the laboratory information system considering mandates, staff, funds, procedures,

equipment, supplies, communications capacity and skills.

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Develop the capacity of the regional, provincial/city levels to manage the laboratory

information system including planning, monitoring, supervision and evaluation.

5. Supply chain management

Increase the capacity to manage laboratory supply chain management cycle at all levels to

prevent stock-outs / overstocking, use of expired supplies and ensure quality of supplies

according to specifications.

Strengthen quality assurance of laboratory supplies.

6. Equipment, facility (physical plant) and infrastructure

Develop a maintenance program for equipment, facility and infrastructure.

Develop the capacity of peripheral lab workers (e.g. microscopists) through the provision of

SOPs, job aids and supportive supervision.

7. Monitoring and evaluation

Enhance skills for monitoring and evaluation at all levels

Develop M&E plan and secure funds and other resources for its implementation

Provide venue for discussions and ensure sharing of monitoring and evaluation results.

8. Leadership and management of the lab network

Enhance the planning process to produce evidence based and focused plans

Support organizational strengthening at the regional and provincial/city levels to increase

the capacity of these levels according to mandates.

Develop a framework for effective vertical and horizontal coordination, cooperation and

collaboration in the laboratory network.

9. Biosafety

Develop a biosafety program for the lab network.

Ensure biosafety plans are developed and implemented at all levels.

Develop laboratory safe practices manual for all technologies at all levels.

Strengthen biosafety component in laboratory trainings

Strengthen monitoring and supervision of safe laboratory practices

10. Infection control

Develop an Infection control program for the lab network.

Develop and implement infection control plans in all facilities at all levels.

Monitor the implementation of IC plans

11. Waste management

Develop a laboratory waste management program at all levels

Develop waste management plans, SOPs at all levels

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Monitor and supervise the implementation of plans and adherence to SOPs at all levels

12. Health promotion

Capacitate the lab staff in providing information to patients regarding the importance of TB

diagnostics

Develop job aids for TB diagnostics to be used for information dissemination

Develop and ensure the provision of appropriate training to clinic staff on TB diagnostics

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Annex A Summary of smear quality assessment in study LGUs, 2014-2015

LGU

Slides

Actually Taken

Table A1. Summary of smear quality assessment results in study areas

Smear Quality Assessment Points

Specimen

Quality Staining Cleanness Thickness Size Evenness

No. No. % No. % No. % No. % No. % No. %

Quezon City 5,630 4,754 84% 5,289 94% 5,149 91% 5,258 93% 5,185 92% 5,094 90%

Baguio City 616 351 57% 521 85% 565 92% 409 66% 508 82% 452 73%

Angeles City 1,054 760 72% 920 87% 913 87% 736 70% 744 71% 840 80%

Pampanga 5,130 4,601 90% 4,459 87% 4,839 94% 4,236 83% 4,300 84% 4,027 78%

Batangas 3,930 2,760 70% 3,758 96% 3,580 91% 2,664 68% 2,303 59% 1,862 47%

Cavite 5,289 4,401 83% 4,693 89% 4,771 90% 4,145 78% 4,087 77% 3,805 72%

Cebu City 654 516 79% 639 98% 632 97% 442 68% 498 76% 461 70%

Leyte 5,060 3,329 66% 4,248 84% 4,201 83% 3,360 66% 3,260 64% 2,456 49%

Tacloban City 144 127 88% 136 94% 142 99% 124 86% 123 85% 130 90%

Davao City 2,905 2,677 92% 2,779 96% 2,807 97% 2,407 83% 2,553 88% 2,468 85%

Davao del Norte 3,211 3,027 94% 3,196 100% 3,154 98% 2,770 86% 3,025 94% 2,873 89%

Misamis Oriental 3,064 1,612 53% 2,481 81% 2,531 83% 2,090 68% 1,317 43% 1,117 36%

Overall 36,687 28,915 79% 33,119 90% 33,284 91% 28,641 78% 27,903 76% 25,585 70%

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Annex B Types of Inconclusive Test Results (ITR) in Xpert testing among study laboratories

Table A3. Types of inconclusive Xpert test results among study laboratories, 2013-2015

ITR type and error codes

2013 2014 2015 3-Year Total

No. % No. % No. % No. %

5007 175 48% 121 20% 149 21% 445 27%

Invalid 11 3% 88 14% 223 32% 322 19%

5011 35 10% 135 22% 77 11% 247 15%

NR 31 9% 80 13% 71 10% 182 11%

2127 4 1% 87 14% 35 5% 126 8%

2008 71 20% 20 3% 3 0% 94 6%

5006 13 4% 23 4% 33 5% 69 4%

1001 6 2% 12 2% 32 5% 50 3%

1002 3 1% 9 1% 26 4% 38 2%

2014 10 3% 8 1% 17 2% 35 2%

2005 1 0% 5 1% 11 2% 17 1%

2037 1 0% 9 1% 0 0% 10 1%

1018 0 0% 6 1% 1 0% 7 0% 2022 0 0% 0 0% 5 1% 5 0%

1004 0 0% 0 0% 3 0% 3 0%

4017 0 0% 0 0% 3 0% 3 0%

5001 1 0% 0 0% 2 0% 3 0%

2012 0 0% 2 0% 0 0% 2 0%

4009 0 0% 0 0% 2 0% 2 0%

4012 0 0% 2 0% 0 0% 2 0%

2006 1 0% 0 0% 0 0% 1 0%

2025 0 0% 1 0% 0 0% 1 0%

2034 0 0% 0 0% 1 0% 1 0%

4010 0 0% 0 0% 1 0% 1 0%

4015 1 0% 0 0% 0 0% 1 0%

Total 364 100% 608 100% 695 100% 1667 100%

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Annex C List of facilities included in the assessment

Region TB Laboratories

NCR 1. National TB Reference Laboratory (NTRL)

2. Lung Center of the Philippines – National Center for Pulmonary Research (LCP-NCPR)

3. Philippine Tuberculosis Society, Inc. – Quezon Institute (PTSI-QI)

4. San Lazaro TB Culture Laboratory

5. Quezon City Quality Assurance (QA) Center/

6. Kamuning Super Health Center

CAR 7. Baguio City Health Office QA Center

8. Baguio General Hospital and Medical Center (BGHMC)

3 9. Region 3 TB Culture Laboratory

10. Pampanga Provincial Health Office (PHO) QA Center

11. Lourdes Sur RHU Main (Angeles City QA Center)

12. Sindalan Rural Health Unit (RHU)

4A 13. Cavite Provincial Health Office (PHO) QA Center

14. Batangas Provincial Health Office (PHO) QA Center

15. Batangas Medical Center

16. Batangas City Health Office (CHO)

17. Naic Rural Health Unit (RHU)

7 18. Cebu TB Reference Laboratory (CTRL)

19. Cebu City Health Office (CHO) QA Center

20. Parian Health Center

21. Mabolo Health Center

8 22. Region 8 TB Culture and Xpert Laboratory

23. Leyte Provincial Health Office (PHO) QA Center

24. Tacloban City Health Office (CHO) QA Center

25. Eastern Visayas Regional Medical Center (EVRMC)

10 26. Northern Mindanao TB Reference Laboratory

27. Misamis Oriental Provincial Health Office (PHO) QA Center

28. Carmen Rural Health Unit (RHU)

29. Xavier University Community Health Care Center (XU-CHCC) Xpert laboratory

11 30. Davao TB Reference Laboratory

31. Davao City QA Center

32. Davao del Norte Provincial Health Office (PHO) QA Center

33. Davao Regional Hospital (DRH)

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Annex D List of persons interviewed

National Capital Region (NCR)

National TB Reference Laboratory (NTRL) o Ms. Cristina Villarico – Head, Laboratory Services Unit o Ms. Catherine Ann Sacopon – Medical Technologist o Ms. Maria Althea Sabrina Perez – Science Research Specialist o Mr. Dionisio Cabanela – Laboratory Technician o Mr. Mar Alrey Jumarang – Laboratory Aide

Lung C enter of the Philippines – National Center for Pulmonary Research (LCP-NCPR)

o

o

o

Mr. Randolf Leppago – Medical Technologist Ms. Maria Theresa Remaneses – Medical Technologist Mr. Cyryll Castillo – Medical Technologist

Philippine Tuberculosis Society, Inc. – Quezon Institute (PTSI-QI) o Ms. Emily Datoy – Chief Medical Technologist o Ms. Lirio Borlongan – Medical Laboratory Technician o Mr. Ian Paul Resabal – Medical Technologist

o Mr. Jerson Hortillosa – Medical Technologist o Ms. Rowena Madres – Medical Laboratory Technician

San Lazaro TB Culture Laboratory

o Dr. Arlan Lopez – Laboratory Supervisor o Ms. Ma. Cecilia Belo – Head, Microbiology Department o Ms. Mayline Kong – Medical Technologist o Ms. Ashley Cynna Ong – Medical Technologist o Ms. Mary Joy Nalangan – Medical Technologist

Quezon City Quality Assurance (QA) Center

o Mr. Bernard Yumang – City NTP Medical Technologist Coordinator

Kamuning Super Health Center

o Ms. Ma. Jesusa Chua – Medical Technologist o Ms. Niña Jamille Guerrero – Microscopist o Ms. Elena Escoriaga – Laboratory Aide

Cordillera Administrative Region (CAR)

DOH CAR Regional Health Office

o Mr. Clint Ildefonso – Regional NTP Coordinator

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Baguio City Health Office QA Center o Ms. Ruby Magsino – City NTP Controller

Baguio General Hospital and Medical Center (BGHMC)

o Mr. Andrew Sib-aten – Medical Technologist o Ms. Chris Diane Somera – Medical Technologist

Region 3 – Central Luzon

Region 3 TB Culture Laboratory

o Ms. Catherine Toledo – Regional NTP Medical Technologist Coordinator o Ms. Michelle Bautista – Medical Technologist

Pampanga Provincial Health Office (PHO) QA Center

o Dr. Maria Imelda Labrador-Ignacio – Provincial NTP Medical Coordinator o Mr. Nickson Manlutac – Provincial NTP Nurse Coordinator o Ms. Catherine Zapanta – Provincial NTP Med Tech Controller

Lourdes Sur RHU Main (Angeles City QA Center)

o Ms. Femie Pangilinan – Controller o Ms. Lourdes Pinpin – NTP Nurse Coordinator

Sindalan Rural Health Unit (RHU)

o Dr. Emerito Mercado – Medical Officer o Mr. Richard Puno – Medical Technologist o Ms. Lolita Mabalay – Public Health Nurse

Region 4A - CALABARZON

DOH Regional Office 4A (CALABARZON) o Ms. Myla Velgado – Regional NTP Medical Technologist Coordinator

Cavite Provincial Health Office (PHO) QA Center

o Ms. Rosemarie Gomez – Provincial Lab Coordinator o Ms. Minda Lingan – Provincial NTP Nurse Coordinator

Batangas Provincial Health Office (PHO) QA Center

o Ms. Maria Lourdes Soriano – Medical Technologist o Ms. Viviane Hernandez – Provincial NTP Nurse Coordinator

Batangas Medical Center

o Ms. Dessa Joy Bacay – Medical Technologist o Ms. Mary Ann Cuartero – Medical Technologist o Ms. Maria Angelica Castillo – Medical Technologist

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Batangas City Health Office (CHO) o Ms. Catherine Moral – Chief Medical Technologist o Mr. Edwin Chavez – Medical Technologist o Ms. Marie Jane Lumanglas – Medical Technologist o Ms. Vicky Atienza – City NTP Nurse Coordinator

Naic Rural Health Unit (RHU)

o Ms. Jennifer Casamar – Medical Technologist

Region 7 – Central Visayas

Cebu TB Reference Laboratory (CTRL)

o Ms. Cresilda Cases – Regional NTP Medical Technologist Coordinator

Cebu City Health Office (CHO) QA Center o Mr. Norman Capaning – NTP Medical Technologist Coordinator o Ms. Laurean Jo Cabase – Medical Technologist

Parian Health Center

o Mr. Joselito Manubag – Medical Technologist o Ms. Loreta Canencia – Laboratory Aide

Mabolo Health Center o Mr. Owen Joshua Briones – Medical Technologist

Region 8 – Western Visayas

DOH Regional Office 8

o Mr. Flor Jimenez – Regional NTP Medical Technologist Coordinator

Region 8 TB Culture and Xpert Laboratory o Mr. Brendon Sanilla – Medical Technologist o Ms. Raquel Espina – Laboratory Aide

Leyte Provincial Health Office (PHO) QA Center

o Ms. Joline Ariza – Provincial NTP Medical Technologist Coordinator o Ms. Evelyn Pacheco – Controller o Ms. Karena Cleofe de Veyra – Controller o Ms. Medly Lou Dimzon – Provincial NTP Nurse Coordinator

Tacloban City Health Office (CHO) QA Center

o Dr. Danilo Ecarma – NTP Medical Coordinator o Ms. Imelda Labarda – NTP Medical Technologist o Ms. Nilda Cantay – NTP Controller

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Eastern Visayas Regional Medical Center (EVRMC) o Ms. Ma. Merlina Vistal – Head, Microbiology Section o Ms. Reyna Ann Peques – Medical Technologist

Region 10 – Northern Mindanao

Northern Mindanao TB Reference Laboratory

o Ms. Jenny Alabado – Regional NTP Medical Technologist Coordinator o Ms. Perla Sanchez – Laboratory Supervisor o Ms. Rene Fleur Clutario – Medical Technologist o Ms. Irene Abejuela – Medical Technologist o Ms. Marian Paguidopon – Laboratory Aide

Misamis Oriental Provincial Health Office (PHO) QA Center

o Ms. Maria Carmela Ditona – Controller o Ms. Stephanie Bolos – Project Associate

Carmen Rural Health Unit (RHU)

o Ms. Leah Yvette Pelaez – Medical Technologist o Ms. Juvy Madarang – Medical Technologist

Xavier University Community Health Care Center (XU-CHCC) Xpert laboratory

o Ms. Cheerwind Agcito – Medical Technologist

Region 11 – Davao Region

Davao TB Reference Laboratory

o Ms. Sonia Dapitanon – Regional NTP Medical Technologist Coordinator o Mr. Jordan Kintanar – Medical Technologist

Davao City Chest Center (QA Center)

o Dr. Ashley Lopez – City NTP Medical Coordinator o Ms. Maria Theresa A. Bien – City NTP Medical Technologist Coordinator o Ms. Cynthia Garcia – City NTP Nurse Coordinator o Ms. Viluz Dimatulac – City NTP Controller (Main Laboratory) o Ms. Melody Maghari – City NTP Controller (Main Laboratory) o Ms. Marites Saco – City NTP Controller (Main Laboratory)

Davao del Norte Provincial Health Office (PHO) QA Center

o Ms. Ruby Rosal – Provincial NTP Medical Technologist Coordinator o Ms. Glomerlina Laag – Provincial NTP Nurse Coordinator o Ms. Gemma Nadine Eustaquio – Provincial NTP Controller o Mr. Raymundo Rosales I – Provincial NTP Controller o Ms. Rea Mae Navigar – Provincial NTP Controller o Mr. Reynaldo Rala – Provincial NTP Controller

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o Mr. Lougie Depra-Provincial NTP Controller o Ms. Leona Olila- Provincial NTP Controller

• Davao Regional Hospital (DRH)

o Mr. Jenry Mibato-Medical Technologist


ntp laboratory network assessment (2016) country’s three major island groups and their land areas...

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