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Diagnostic Microbiology Development Program
Laboratory Strengthening and the Diagnostic Microbiology Development Program
Robert Martin, MPH, DrPH President, Diagnostic Microbiology Development Program
http://dmdp.org Kathmandu, Nepal, May 2018
Diagnostic Microbiology Development Program
Global Burden of Infectious Disease
DALY = Disability Adjusted Life Year
Diagnostic Microbiology Development Program
Infectious diseases still cause ~40% of
mortality in RLC’s
Morens et al Nature, July 2004; 430, 242-249
Fauci and Morens,, N Engl J Med February 2012; 366:454-461
Diagnostic Microbiology Development Program
Laboratory Testing Supports:
• Patient Care
• Public Health Disease Reporting
• International Obligations
Diagnostic Microbiology Development Program
Value of a Diagnostic Microbiology Laboratory
• Individual case management by detection and identification of microbial agents of bloodstream infections, pneumonia, wound infections, meningitis, diarrhea, urinary tract infections
• Detection of emerging antibiotic resistance and prevention of spread of resistance
• Antimicrobic stewardship (AMS) • Hospital infection prevention and control (IPC) • Early detection of microbial pathogens with public
health importance • Support of outbreak investigations
Diagnostic Microbiology Development Program
Regulatory Agencies and
Professional Organizations
Diagnostic Microbiology Development Program
Complexity of a Laboratory System
Patient/Client Prep Sample Collection
Sample Receipt & preparation
Sample Transport
Quality Control Testing
Record Keeping
Reporting
Personnel Competency
Diagnostic Microbiology Development Program
LQMS model
Organization Personnel Equipment
Purchasing
&
Inventory
Process
Control
Information
Management
Documents
&
Records
Occurrence
Management
Assessment
Process
Improvement
Customer
Service
Facilities
&
Safety
Diagnostic Microbiology Development Program
• Limited or no gov’t. oversight
• Few or no national policies
• No or weak laboratory network
• No registration of labs, no accreditation of laboratories
• No process for procurement of quality laboratory reagents/kits
• Few professional organizations
• Limited testing menu
• Weak academics for lab medicine
Most Resource-Limited Countries:
Diagnostic Microbiology Development Program
DMDP background
• Created in 2008
• Vision: To establish diagnostic microbiology laboratories in low resource settings
• Supported by DTRA since 2013
– Media production and distribution
– Diagnostic microbiology mentoring
– Broadened to other laboratory disciplines in 2015
– Clinical mentoring
Diagnostic Microbiology Development Program
DMDP-Diagnostic Microbiology Development Program
• DMDP Mission:
To build capacity for reliable laboratory testing by strengthening the infrastructure of laboratories and the technical capabilities of laboratory technicians in resource-poor countries.
• www.dmdp.org
• In-country staff: 16
• Visiting experts
Diagnostic Microbiology Development Program
DMDP supported laboratories
2
1, 7, 8
4
3
6
5 Kampot
Province Implement
Microbiology
Bed
Number
1 National Pediatric
Hospital
2011 150
2 Kampong Cham 2009 260
3 Battambang 2011 240
4 Takeo 2011 270
5 Kampot 2013 150
6 Siem Reap 2014 300
7 CMML 2013 NA
8 NPHL US CDC 2010
DMDP 2016
NA
Diagnostic Microbiology Development Program
How DMDP Strengthens Diagnostic Laboratories
• 2017: Onsite mentoring- 6 laboratories • 5 diagnostic laboratories
– Kampong Cham, Takeo, Siem Reap, Battambang, NPHL
• 1 media making laboratory – Central Media Making Laboratory
• Remote assistance
• Support manager’s meetings – all government microbiology labs (NMMLN)
– 13 government microbiology laboratories
– Invite collaboration with with partners
– Leadership from Bureau of Medical Laboratory
Services
Diagnostic Microbiology Development Program
Pathogen Identification & Antibiotic Susceptibility Testing (AST)
• Strategy: Mentoring in sustainable microbiology practices needed for health care at Provincial Hospitals
• Pathogen Identification:
– Bench-top Diagnostic Microbiology (Biosafety Level II)
– Flow charts developed by Dr. Ellen Jo Baron
– Train in the ‘art’ of recognition of Gram stain and colony morphology
• AST Method-International standard: – CLSI M100S and M02-A12
– Disc diffusion testing
– Agar diffusion with E-test to determine Minimal Inhibitory Concentration (MIC)
– Beta-Lactamase testing with Nitrocefin-based test (cefinase)
Diagnostic Microbiology Development Program
Sputum Specimen
Primary pathogens: Streptococcus pneumoniae, Klebsiella species, Haemophilus
influenzae, Staphylococcus aureus, Pseudomonas aeruginosa
NOT pathogens: Yeast, viridans streptococci, coagulase negative staphylococci
Patient should rinse mouth
with water, cough from
deep in lung, do not spit
#1
• Make Gram stain to screen if
acceptable for culture
• Call significant Gram stain
results to Doctor ASAP
#2
#3
Good: Rare squamous
epithelial cells
Optochin disk
Incubate up
to 48 hours
in CO2
#4
Plate to Choc,
BAP, Mac
#5
Reject: Many
squamous
epithelial cells
Klebsiella pneumoniae
Identify & perform susceptibilities
on significant pathogens
Staph aureus
Strep. pneumo
Bile solubility +
Optochin +
Haemophilus influenzae
Diagnostic Microbiology Development Program
Implementation of international standard AST
Implementation of Antibiotic Susceptibility Testing (AST) for resistance tracking using Clinical and Laboratory Standards
Institute (CLSI) M100 and M02 in Cambodian Microbiology Laboratories S. Oeng1, J. Letchford1
1Diagnostic Microbiology Development Program (DMDP), Phnom Penh, CAMBODIA
Modified Abstract
Introduction
Background: DMDP collaborates with the Cambodian Ministry of Health (CMoH) to
build microbiology diagnostic capacity as part of the National Strategic Plan for
Laboratory Services. We introduced CLSI M100 and M02 disc diffusion to 6 Cambodian
laboratories to achieve quality AST result reporting to clinicians and to begin collection
of surveillance data by CMoH.
Methods: DMDP used a multi-strategy approach in 2014-15 which included 9 manager
meetings, the CLSI annual AST update webinar and CLSI M100 and M02 documents to
prepare AST guidelines adapted to fit Cambodia. Mentors, DMDP staff with expertise in
diagnostic microbiology, provided regular on bench training at 6 sites.
Results: 5 of 6 DMDP supported laboratories have implemented AST according to
CLSI M100 and M02. In 2015, 5 of 6 laboratories performed weekly AST Internal
Quality Control (IQC). Problems diminished from weekly to none over 12 months.
Conclusions: The multi-strategy approach strengthened Cambodian laboratory
capacity for AST. Regular on site mentoring was essential.
Results
Conclusions
Methods
Diagnostic Microbiology
Development Program
Phone: 415-722-7629
Table 1: Cambodian hospital
microbiology laboratories
• 5 of 6 DMDP supported laboratories implemented AST according to CLSI M100 & M02
• AST IQC failures diminished from 13% (77/598) in Jan. 2015 to 1% (9/657) in Dec. (Fig 7).
• By Nov and Dec. 2015, 3 of 5 labs recorded no AST IQC failures.
• Laboratory assessments in Dec 2015 showed that ‘AST’ was a top component (Fig 8).
• Of the 3% (273/7805) of AST IQC failures in 2015, corrective action in 45% (122/273) was not
applied (Fig 9)
• In 2015, laboratories achieved scores of 85%-95% in the pathogen ID and AST EQA.
• AST Workshop Pre / Post test scores showed 13% improvement from mean 72% (range
43-90) to mean 85% (range 67-97) t-test p value= 0.0004
• A multi-strategy approach strengthened Cambodian government microbiology capacity.
• Regular on site mentoring was essential.
• Practice, encouragement and cultural awareness were key components to success.
• Access to CLSI M100S and M02 and American Type Culture Collection organisms was
essential-DMDP & World Health Organization purchased CLSI M100S & M02. Now, CLSI
M100S FREE is available.
• This activity provided stimulation and opportunity for Cambodia CMoH to collect National
AMR surveillance data and enroll in Global AMR Surveillance System (GLASS).
• Surveillance for priority pathogens, Typhoidal Salmonella, Burkholderia pseudomallei and
Streptococcus suis highlights the importance of continued laboratory support in Cambodia.
• Mentoring in “on bench” diagnostic microbiology
• Bi-monthly microbiology manager meetings
• Interactive AST and pathogen identification workshops
• Review and feedback of Microbiology Activity Reports and clinician reports
• DMDP developed & implemented:
• AST guidelines adapted for Cambodia
• AST workshop practical exercise book
• Electronic tool for monitoring & troubleshooting AST IQC performance
• Monthly Microbiology Activity Reports
Figure 6: Follow up workshop training
December 2015
Support; consulting
James McLaughlin- Ph.D.; D(ABMM), Prof. Emerita Univ. of New Mexico SOM, President
DMDP, Ellen Jo Baron- Ph.D., D(ABMM), Prof. Emerita, Stanford Univ., Janet A. Hindler-
MCLS, MT (ASCP), Em Rattanak- DMDP Laboratory mentor, Morn Sineang- DMDP
Laboratory mentor, Angelo Caon- DMDP Expert mentor.
MONDAY-142
Table 2: DMDP AST guidelines 2015
Fig 4: AST workshop 2015
Table 4: Monthly microbiology activity report Province Implement Microbiology Bed Number
1 National Pediatric Hospital Oct 2008 150
2 Kampong cham Jan 2009 260
3 Battambang Jan 2011 240
4 Takeo May 2011 270
5 Kampot Dec 2013 150
6 Siem Reap June 2014 300
1
2
3
4
5
6
DMDP have been strengthening microbiology diagnostic capacity in Cambodia since 2008
(Fig 1, Table 1), using sustainable diagnostics according to Professor Ellen Jo Baron’s
diagnostic flow charts (Fig 2 & Fig 3). In 2013, DMDP developed and implemented AST
guidelines adapted for Cambodia (Table 2). In 2014, DMDP chose to implement a training
of CLSI M02 and CLSI M100 (Fig 4), review of the AST guidelines and mentoring at 6
government hospitals. Laboratories were encouraged to perform weekly AST IQC. Sites
electronically submitted AST IQC (Table 3) and a monthly Microbiology Activity Report
(Table 4) for review. Mentors worked side by side with government staff (Fig 5). DMDP
included AST in the agenda of training workshops and meetings (Fig 6).
Fig 3: Salmonella Paratyphi A
Disc diffusion & biochemical testing Fig 2: Dr Ellen Jo Baron Chart
Disc Diffusion testing
Figure1: Cambodia Ref - http://www.asiavipa.com/cambodia-map
Figure 5: DMDP mentor training
Table 3: AST IQC-October 2015, week 2, all labs
87%
81%
80%
80%
75%
74%
70%
67%
65%
60%
ANTIBIOTIC
SENSITIVITY TESTING
(AST)
BIOSAFETY
MICROSCOPY/GRAM STAIN
PATHOGEN
IDENTIFICATION
OTHER
SPECIMEN PROCESSING
MAKING MEDIA
QUALITY ASSURANCE
CULTURE INTERPRETATION
REPORTING/URGENT RESULTS
13%
4%
2%
4%
2% 2% 2%
4%
5%
2% 1% 1%
0%
2%
4%
6%
8%
10%
12%
14%
Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec
Fig 7: Percentage failed AST IQC, 2015 in 5
Cambodian Microbiology laboratory Fig 8: 9 components of lab assessment
Average result from 5 microbiology in Cambodia 2015
No problem
(97%, 7532)
Problem
(3%, 273)
No C
orr
ective
actio
n (
45
%,
12
2)
Co
rre
ctiv
e a
ctio
n (
55
%,
15
1)
Fig 9: AST IQC result (7805 tests) from 5
Microbiology labs in 2015
Implementation of CLSI M100S and M02 • On site mentoring • Development of Pathogen AST guidelines, updated annually • Development SOPs and job aids • Managers meetings, workshops (networking 13 microbiology laboratories)
Diagnostic Microbiology Development Program
National Public Health Laboratory (NPHL)
• Strengthen NPHL microbiology • Assessment February 2016
• Placement of expat mentors at NPHL
• Activities: • Establish National Reference Laboratory-
beginning with national AMR surveillance
• Assist NPHL to develop a national microbiology EQA program 2017-2018
NPHL AST guideline training
Diagnostic Microbiology Development Program
Microbiology meetings Agenda topics
March 2016 2 days
Culture interpretation Antibiotic Susceptibility Testing (AST) Guideline
Sept/Oct 2016 3 days
Bioterrorism agents Pathogen identification CLSI update and orientation to use revised AST Guideline Specimen processing and culture interpretation
January 2017 2 days Takeo UHS NIPH
Case presentations-lab presentation Peter H Gilligan, PhD • Clinical case presentations • Pathogen identification interactive quiz • Antimicrobial Resistance
Diagnostic Microbiology Development Program
• Human blood is readily available (outdated human
bank blood or volunteers)
• It is free
• Wool sheep too hard
to maintain & bleed
Why are Resource poor Micro Lab results often wrong?
One reason - use of human blood in blood agar
Staph aureus Strep. pyogenes
Diagnostic Microbiology Development Program
DMDP supporting and strengthening production and distribution of quality media
Brain Heart Infusion Adult 50ml Pediatric 25ml
MacConkey agar Mueller Hinton II Sheep Blood MH II
Biochemical tube media: Urea, Citrate, SIM, LIA, KIA
Sheep Blood Agar Plates
Central Media Making Laboratory
•Internal Quality Control •External Quality Control Sihanouk Hospital Centre of Hope
Ashdowns agar
Diagnostic Microbiology Development Program
Kossamak NPH Kampot Battambang TakeoKampong
ChamSiem Reap
Privateclient
Tubes 0 0 0 0 160 160 480 0
Bottles 200 1300 250 1001 2063 990 1630 3240
Plates 520 0 1120 6160 5680 7177 8470 290
0
2000
4000
6000
8000
10000
12000
Un
its
of
me
dia
Media distribution 2016*, 40891 media units Media plate 29417, Blood culture bottle 10674, tube 800
Diagnostic Microbiology Development Program
Benefit of blood culture: Detect pathogens in Cambodia
Burkholderia pseudomallei Streptococcus suis
You can gain valuable information from observation and simple initial tests
Diagnostic Microbiology Development Program
Burkholderia pseudomallei
Blood culture isolate Sheep blood agar, Day 3
Blood culture isolate MacConkey agar, Day 3
Diagnostic Microbiology Development Program
Burkholderia pseudomallei
B. pseudomallei on sheep blood agar, Day 1
PB: Polymixin B resistant AMC: Amoxicillin Clavulanic acid susceptible CN: Gentamicin resistant
Sheep blood agar
Diagnostic Microbiology Development Program
Major gaps and challenges
• Lack of quality pre-service training for Health Care Workers lab tech, clinician, nurse, pharmacist….
• Lack of clinician understanding of appropriate use of the microbiology service
• Lack of patient information and quality specimens to provide good data
• Lack of quality microbiology lab supply procurement
• Lack of capacity in data management and data analysis
• Limited dissemination of data to range of stakeholders