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Sex in the Sink: Gene-Swapping Bacteria Are Making New Superbugs

Plasmid transfer between bacterial species can be investigated with single-molecule DNA sequencing technology. Plasmids, small mobile pieces of DNA, carry genes encoding resistance to antibiotics, including carbapenems, a powerful class of antibiotics used to treat serious infections. Darryl Leja / NHGRI/NIH

Bacteria appear to be having the microbial equivalent of inter-species sex in hospital sinks, swapping chunks of DNA that render them impervious to antibiotics, researchers reported Wednesday.

The findings may help explain the rise in drug-resistant “superbugs” in hospitals, and they suggest that they may sometimes be breeding on site, as opposed to being carried in by patients.

The team at the National Institutes of Health found carbapenem-resistant Enterobacteriaceae (CRE) that appeared to have exchanged pieces of genetic material called plasmids that gave them resistance to antibiotics. CRE resist most, if not all antibiotics, and they are becoming more common: they are found in about 4 percent of hospitals now and 18 percent of long-term care facilities.

"Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria."

They found the superbugs on patients and in the sinks at the NIH clinical center outside Washington D.C., a large hospital that had a bad outbreak of drug-resistant Klebsiella in 2011 in which 17 patients got badly infected and six died.

They tested all the patients in two wards in 2012 and 2013 –- 1,000 in all -- and found 10 patients colonized with CRE. There was clear evidence the germs were getting new plasmids from somewhere. More searching turned them up in sink drains, although there’s no direct evidence that’s where the patients got them from.

Image: Antibiotic resistance is becoming a huge medical challenge.
Antibiotic resistance is becoming a huge medical challenge. Antibiotic resistance is caused by resistance genes carried on plasmids, small circles of DNA separate from the chromosomal DNA. Resistance spreads by horizontal gene transfer, in which plasmid genes from a donor bacterial cell spread to a recipient bacterial cell during cell-to-cell contact. When the DNA that is transferred includes antibiotic-resistance genes, the bacterium receiving this DNA becomes antibiotic-resistant too. C. Schaffer / Science/AAAS

It's also not clear where the bacteria are getting the new plasmids, says Julia Segre of the National Human Genome Research Institute, part of NIH.

Bacteria reproduce by splitting in half, but they can also exchange genetic material. This DNA exchange helps them evolve and can help them evolve resistance to antibiotics.

“Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria, a trend that poses a serious threat to the U.S. medical system,” Segre and colleagues wrote in their report, published in the journal Science Translational Medicine.

“At the same time, development of antimicrobial drugs has nearly ground to a halt, with only two new antibiotics approved since 2009. In the face of a dwindling selection of drugs to fight health care–associated infections, prevention is critical.”

In other words, hospitals need to clean the sinks. They also need to keep an eye on bacteria infecting or colonizing patients. Patients can carry these bacteria without being sickened by them, but they can pass them to other patients who may become ill.

Cleaning the sinks isn't always straightforward -- NIH actually took the plumbing apart at the clinical center and still struggled to eradicate the infestation of superbugs at its clinical center. But even just pouring bleach into the drains can help, Segre says.

The researchers recommend that hospitals test all patients when they're admitted. A quick swab can be wiped on a lab plate; if a colony of suspicious-looking bacteria grows overnight, it's well worth the cost of the genetic sequencing test to see if the bacteria are drug-resistant. "We need to know if a patient comes into the hospital colonized with CRE," Segre says.

Hospitals are especially dangerous because the sickest patients are there and their bodies might not be able to fight off these infections. More than two million people are infected by drug-resistant germs each year, and 23,000 die of their infections, the Centers for Disease Control and Prevention says.

Rates of Klebsiella pneumonia infection jumped 550 percent between 2001 and 2011.

Bacteria develop resistance to drugs quickly. Even before penicillin was introduced in 1943, staphylococcus germs were identified that were resistant to its effects. Just nine years after tetracycline was introduced in 1950, a resistant strain of Shigella evolved. Methicillin-resistant Staphylococcus aureas (MRSA) evolved just two years after methicillin hit the market in 1960.

The last new antibiotic to be introduced was ceftaroline, in 2010. It took just a year for the first staph germ to emerge that resisted its effects.

The CDC has asked Congress for $30 million to open specialized laboratories in five parts of the country to help local hospitals more quickly diagnose and combat drug-resistant infections.