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HEALTH MAY 31 2016, 6:34 AM ET

Searching for Superbugs: The LabLooking f or the Next Big Threatby MAGGIE FOX

Erik Snesrud of the Walter Reed Army Institute

of Research checks bacterial gene sequences.

%Maggie Fox / NBC News

SILVER SPRING, Md. — It was a Friday in mid-May, and Erik Snesrud was

checking out the first batch of samples under a new directive.

The order had just come in to look for a new gene called mcr-1 that hadalready achieved global notoriety among microbiologists. It gives germs the

ability to withstand the effects of colistin, a last-resort antibiotic used to save

the lives of people infected with serious superbugs.

The sample was loaded into one of

the super-fast gene sequencers at

the lab inside the bowels of the

Walter Reed Army Institute of

Research. The small team at the

Multidrug Resistant Organism

Repository and Surveillance Network(MRSN) lab specializes in testing

germs for antibiotic resistance,

which has become the scourge of

hospitals all over the world.

The results were back in minutes. One of the samples — some E. coli bacteria

taken from a woman with a urinary tract infection in Pennsylvania — carried the

gene.

Snesrud knew he was going to lose his weekend. He prepared to work for the

next 48 hours. "We wanted to know what we were dealing with," he said.

The news startled doctors across the country. Center for Disease Control and

Prevention director Dr. Thomas Frieden upstaged his own speech about Zika

virus last week to warn about what the arrival of mcr-1 means for people

everywhere. "The medicine cabinet is empty for some patients. It is the end of

the road for antibiotics unless we act urgently," he said.

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Patrick McGann of the Walter Reed Army

Institute of Research shows off one of the super-

fest gene sequencers that helped his team track

down a superbug with an "ultimate" resistance

gene called mcr-1. %Maggie Fox / NBC News

Snesrud, however, wasn't shocked. Once bacteria acquire new characteristics,

they generally do get around quickly. The mcr-1 gene had been identified in

food animals and people around the world going back for decades. But never

before in the United States.

"Everything was going so fast. It was 'Oh, my God,'" said Patrick McGann, chief

of molecular research for the MRSN.

"We got it Friday. We were done Monday afternoon."

Snesrud's colleague, Rosslyn Maybank, stayed late that Friday, setting up the

giant PacBio sequencing machine that can read out the entire genome of

microbes and tell researchers not only what genes can be found in an

organism, but where they are.

"We were looking for where the gene was located," said the quiet and

seemingly unflappable Snesrud.

"Was it on the plasmid? Was it in the chromosome?" It was, as expected, on the

plasmid — the worst of the two places.

Plasmids are little structures of DNA that exist outside the chromosomes where

most of the DNA is found. They're handy little carriers that can pass off a

stretch of DNA as easily as a courier hands an envelope to a client.

Bacteria can acquire resistance to

antibiotics in several ways. They can

evolve it naturally, through

mutations. Or they can share them

with one another through what's

known as horizontal gene transfer.

They exchange the plasmid through

bacterial sex, often through

structures called pili. "They create a

little channel and they pass the DNA

through it," McGann said. First,

however, they make a copy for

themselves, so they can also pass that DNA down to their own daughter cells.

Related: Here's Why Doctors Are Worried About the Superbug

Plasmids come in different types, also, said McGann. He likens them to cars. "Is

it a really fast one, like a Ferrari, or is it like a Skoda?" And plasmids don't

respect species distinctions, so bacteria can pass them to different species of

bacteria — as if a cat gave some of its genes to a dog, for instance.

It also means doctors don't have to be on the lookout for something as simple

as a methicillin resistant staphylococcus aureas (MRSA) infection. They need to

watch for an already resistant bacteria that's grabbed some genes from, for

exam le a t e of su erbu called carba enem-resistant enterobacteriaceae

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Some of the 40,000 samples of bacteria stored

at the Multidrug Resistant Organism Repository

and Surveillance Network (MRSN) lab at the

Walter Reed Army Institute of Research in Silver

Spring, Md. %Maggie Fox / NBC News

"IT'S VERY IMPORTANT

TO SPOT THESE GUYS

COMING IN EARLY."

or CRE. CRE are the germs that Frieden calls "nightmare bacteria."

In this particular sample, the plasmid was one that can get from one germ to

another very quickly. "It was definitely up there with the Lexus or the BMW,"

said the chatty, Irish-born McGann.

"We are very concerned to see it in there with this particular plasmid." Making

matters worse, the plasmid was carried by E. coli, itself a highly contagious

germ. And this particular E. coli already had superbug characteristics, even

before it picked up the new mcr-1 gene.

It has seven of its own resistance

genes, permanently encoded in the

DNA of its chromosomes. Then it has

seven more on the plasmid.

One piece of good news: the E. coli

wasn't invincible — yet. It could be

killed with a class of antibioticscalled carbapenems. The patient, a

49-year-old woman who hasn't been

identified, was treated with

intravenous antibiotics and as now

home and well, said Dr. Mary Hinkle,

an expert in antibiotic resistance

who works on the MRSN team.

CDC and state health officials are

helping track down everyone the

patient had been in contact with, in

hopes of finding where and how

she got it.

The big fear is that a CRE will

acquire the mcr-1 gene. A patient

infected with such a bug would

have very little hope of treatment.

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From left, Rosslyn Maybank, Ana Ong and Erik Snesrud of the Multidrug Resistant Organism

Repository and Surveillance Network (MRSN) at the Walter Reed Army Institute of Research

worked overtime to identify the first sample for a U.S. patient carrying the mcr-1 antibiotic

resistance gene. % Maggie Fox / NBC News

Another piece of good news: The MRSN team has not yet found another

example of the mcr-1 gene in any of the samples they have tested. "We have

tested about another 40 of them so far. There's no sign of it since," McGann

said.

Related: Superbugs Kill 23,000 People a Year

They are painstakingly going through 40,000 samples of bacteria they have

stored in freezers in their labs inside the main blue and yellow building of the

Walter Reed annex in Silver Spring, a suburb of Washington, D.C.

Super-fast sequencers developed in the 15 years since the first human genome

was mapped help a lot. What used to take weeks or months can now be done

in a matter of hours.

A strong work ethic doesn't hurt, either. Snesrud went two days on little or no

sleep; Maybank worked extra hours standing on her feet even though she's

eight months pregnant.

"We pride ourselves on our turnaround time," McGann said.

There aren't many rewards — no overtime, no big bonuses for these

government employees. But there are some perks. Snesrud's getting one of

the ultimate honors for a microbiologist — a new species named after him. The

team has proposed calling it Pseudomonas snesrudii. It was taken from

someone's skin in Baltimore.

The lab tests samples from around

the world, not only from U.S. military

'

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Patrick McGann of the Walter Reed Army

Institute of Research displays a culture of

multiple drug resistant E coli taken from a

Pennsylvania patient. %Maggie Fox / NBCNews

"THEY SAY, 'HEY, WE

HAVE AN E.COLI HERE.

IT'S WEIRD. CAN YOU

GUYS CHECK IT OUT?'"

,

Institut Pasteur and elsewhere,

McGann said.

Related: Startling New Superbug

Found in US for the First Time

"They say, 'Hey, we have an E.coli

here. It's weird. Can you guys checkit out?'" said McGann.

The hope is to catch and stop

outbreaks of dangerous new

pathogens fast.

"It's very important to spot these

guys coming in early," says McGann.

One outbreak the team thinks they

could have stopped sooner was the spread of a drug-resistant strain of

Acinetobacter baumanii that caused an eight-year-long outbreak among

servicemembers starting in Iraq in 2002.

A baumanii was known for causing horrible wound infections among soldiers in

the Vietnam War. The normally harmless bacteria, found in soil and on skin, got

into the wounds of men and women serving in Iraq and Afghanistan, causing

baffling bloodstream infections.

"If this lab had existed 15 years ago, we would have been able to provide

feedback ... so we could make much smarter choices," Hinkle said.

The team would have been able

to sequence the samples quickly

and tell military doctors which

antibiotic to use, and which

patients to isolate so the bug

didn't spread.

Instead, doctors were forced to try one antibiotic after another and had no idea

that certain patients were more dangerous than others. Each one failed.

In the end, it was colistin that worked. That's one reason the team's so

concerned to see mcr-1 and its properties that make colistin useless, too.

The CDC, World Health Organization and other groups warn that it's only a

matter of time before people start becoming infected with ultimate superbugs

that cannot be killed by any of the antibiotics in the arsenal.

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Patrick McGann of the Multidrug Resistant Organism Repository and Surveillance Network

(MRSN) lab at Walter Reed Army Institute of Research points to the screen of a Pacific

Biosciences PacBio sequencer used to help sequence the genome of a sample of E. coli bacteria

that turned out to carry the dreaded mcr-1 resistance gene. %Maggie Fox / NBC News

President Barack Obama has directed government agencies to get busy

working on a solution, and the MRSN team at Walter Reed in part of that effort.

Other labs in the large blue complex are working to develop antibiotics that will

bypass all the known resistance mechanisms, and kill even the worst

superbugs.

So are academic centers and a few drug companies, although not as many as

experts would like to see. And drug development takes years.

In the meantime, the MRSN team is acting as one of the first lines of defense,

trying to catch dangerous superbug infections before they can cause

outbreaks.

MAGGIE FOX

TOPICS HEALTH NEWS, MILITARY, SCIENCE NEWS, TECH NEWS

FIRST PUBLISHED MAY 31 2016, 5:06 AM ET

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7/9



& NEXT STORY Can I Ever Get Pregnant? And Other Questions About Zika Virus

HEALTH ZIKA VIRUS OUTBREAK MAY 31 2016, 12:13 PM ET

Can I Ever Get Pregnant? And OtherQuestions About Zika Virusby MAGGIE FOX

Pregnant Woman. %Media for Medical / UIGvia Getty Images

The World Health Organization updated its recommendations Tuesday on

pregnancy, sex and the risk of Zika virus. WHO now agrees with the U.S.

Centers for Disease Control and Prevention, which suggests waiting eight

weeks after any possible exposure to Zika to have unprotected sex.

Zika's steady spread across Latin America and Pacific island nations — and itsinevitable arrival in parts of the continental U.S. — has many people worried.

Here are some answers to some pressing questions about Zika, sex and

pregnancy:

Can the virus be transmitted by any kind of sex?

So far, the evidence points to male semen as the source of transmission. The

virus is mostly carried around by the Aedes mosquitoes, but there are several

clear examples now of sexual transmission. Almost all of the cases have been

of men infecting women, although there's one documented case of a man

infecting his male sexual partner.

How do doctors know? It becomes clear if one sexual partner has traveled to a

Zika-affected region and the other has not. "We don't know if a woman with

Zika can pass the virus to her sex partners," the CDC advises.

What if I get infected now

and want to get pregnant in

a couple of years? Is my

pregnancy at risk?

There is no evidence backing that

up. The body clears the Zika virus

eventually. There are some viruses

that stay in the body permanently —

herpes and the AIDS virus HIV, for

example.

But Zika virus is one that the immune system eventually gets rid of. Several

viruses are known to cause birth defects if the mother is infected during

pregnancy. Rubella, also known as German measles, is an example. But there

was never any evidence that women infected with rubella before they got

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.

How long do I have to wait before I get pregnant?

WHO advises that people wait six months to try for a pregnancy if the male

partner had symptoms of Zika, and waiting eight weeks if either partner has

been in an area where Zika virus infection is possible. If a woman is pregnant

and her male partner could possibly have been infected, they should use a

condom or abstain from sex for the whole pregnancy.

"Zika virus can stay in semen longer than in blood, but we don't know exactly

how long Zika stays in semen," the CDC advises. There's a report of one man

who had Zika virus in his semen more than two months after he showed

symptoms of infection. Since half of the pregnancies in the U.S. are unplanned,

CDC also advises using a condom or abstaining from sex for two months if

there's a chance a man has been infected with Zika.

What if I'm pregnant now and get bitten by a mosquito?

Not all mosquitoes carry Zika, even in the places where the virus is actively

spreading. It's the Aedes aegypti and Aedes albopictus mosquitoes that carry

the virus, and one of them has to have bitten someone who's infected — and

even then, it takes a couple of days for the virus to build up enough in the

mosquito's body for the insect to transmit the virus to someone else.

So unless you are in an area where Zika is spreading, it's not time to panic.

Women in Zika zones need to take the strongest precautions, however and

that includes using repellents such as DEET, covering up, and staying inside as

much as possible. Women who become infected do need to see a doctor right

away and get regularly tested and then have their pregnancy carefully

monitored. There is no known way to protect a developing fetus from Zika

infection, but doctors do know that not every woman who gets infected during

pregnancy goes on to have a baby with birth defects.

The CDC expects some local outbreaks of Zika in the states where the Aedes

mosquitoes are common, but nothing like the epidemics in Latin American and

Caribbean countries.

If my baby is born normal, are we in the clear?

No one can say yet. The most obvious and horrifying birth defect known to be

caused by Zika infection is microcephaly. The child's head is smaller than

normal because the brain itself is badly damaged. Doctors are now starting to

report subtler birth defects in babies born to women who'd been infected.

They include eye abnormalities, hearing defects and other brain damage.

Some birth defects do not become apparent for years. The CDC is keeping a

registry of all U.S. women who are pregnant and infected with Zika. So far,

they're watching 279 in the 50 states and the territories.

MAGGIE FOX

http://www.cdc.gov/zika/pregnancy/http://www.nbcnews.com/storyline/zika-virus-outbreak/use-condom-avoid-zika-cdc-tells-travelers-n512251


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TOPICS HEALTH NEWS, KIDS' HEALTH, LATIN AMERICA, LATINO, TRAVEL, U.S. NEWS

FIRST PUBLISHED MAY 31 2016, 12:13 PM ET

& NEXT STORY WHO Issues Stricter Safe-Sex Guidelines to Prevent Zika

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