More bad news about the global spread of antibiotic-resistant bacteria

Last month, researchers from China reported in The Lancet Infectious Diseases that they had identified a gene (MCR-1) that confers antibiotic resistance to a last-resort antibiotic (colistin) and then found that gene in E. coli isolates from pigs, meat, and hospital patients. This prompted Danish researchers to re-examine the genomes of bacteria they had mapped previously, and they found the MCR-1 gene in sample from a patient who suffered a blood infection in 2015. They also found it in five food samples imported between 2012 and 2014.

Mike the Mad Biologist found the plasmid and protein sequences of MCR-1 in Genbank, and checked to see whether it had appeared anywhere else. He reports that the identical protein has been found in E. coli from Malaysia isolated in 2013, and also in a Salmonella strain identified in Portugal in 2011.

This gene has now been found in both Europe and Asia, and analyses of bacteria collected on other continents is necessary to know whether it has spread elsewhere. But it’s clear now that this gene is spreading, and if it isn’t in the US already it could be here soon.

A separate but related story comes from the CDC, where researchers report on “nightmare bacteria” CRE (carbapenem-resistant Enterobacteriaceae) isolates collected from US patients between June 2010 and August 2015. They found that 52 CRE isolates collected from patients in 19 states carry enzymes that inactivate carbapenems, a class of broad-spectrum antibiotics used as a last resort for many serious infections. The enzymes are called OXA-48-like carbapenemases, and CDC found them in only one isolate from 2010, but 11 per year in 2013, 2014, and 2015. The Washington Post’s Lena Sun explains why this particular finding is so worrisome:

Unlike more common types of CRE, it carries a plasmid, or mobile piece of DNA, with an enzyme that breaks down antibiotics. And what makes these bacteria even more dangerous is their ability to transfer that plasmid--and that antibiotic resistance--to normal bacteria that are present in our bodies.

… Bacteria develop antibiotic resistance in two ways.

Many can evolve their own genome in ways that deactivate antibiotics, although that ability can't be shared with pathogens outside their own family.

Yet other bacteria rely on a shortcut: They get infected with a plasmid carrying the resistance gene. That makes them more dangerous because plasmids can make copies of themselves and transfer within a family of bugs and as well as jump to other families of bacteria, which can then "catch" the resistance directly without having to develop it through evolution.

This is also what makes the MCR-1 gene so alarming: It can be transferred easily from one type of bacteria to another. Colistin and carbapenems are drugs we often turn to for infections that can’t be treated effectively with other antibiotics – but now these last lines of defense are also under attack.

My George Washington University colleagues at the Antibiotic Resistance Action Center (ARAC) have been studying the spread of antibiotic resistance and how to stop it. In response to the latest bad news, ARAC Director Lance Price recommends:

We must act swiftly to contain the spread of colistin-resistant bacteria, or we will face increasing numbers of untreatable infections. Leaders from every nation should immediately implement a ban on the use of colistin in animal agriculture. While China appears to be the biggest user of the drug, it is approved for use in the the European Union and many other countries. It also is approved for use in food animals in the U.S., but drug companies holding those approvals are not actively marketing the drugs. Drug companies with these approvals should immediately withdraw these label claims to ensure that colistin is never used in U.S. animal agriculture, otherwise our livestock production facilities could become breeding grounds for untreatable superbugs.

In addition, we need to remember why colistin is the last drug available for treating these dangerous infections. We turned to it because the preferred drug class – carbapenems – became powerless against some superbugs due to overuse. Carbapenems are still effective against many bacteria, but for how long? While carbapenems are not approved for use in animal agriculture in many parts of the world, their use is not explicitly banned. World leaders should call for an immediate ban on carbapenems to protect them for future generations.

Colistin and carbapenems are the last lines of defense between humans and some of the most dangerous bacteria. Protecting these drugs is of the utmost importance and urgency. Superbugs are gaining strength because we continue to squander these precious medicines through over use in human medicine and as cheap production tools in animal agriculture.

It seems fitting for this news to come out as world leaders gather at the COP21 Paris climate summit. Antimicrobial resistance and greenhouse gases have both increased rapidly because we’ve pursued cheap, fast production whose costs are spread across the globe instead of being paid by those who reap the benefits. Both problems worsen unseen and can only be addressed effectively with large-scale action. In both cases, I hope the repeated alarming discoveries finally prompt the kind of action we need to keep global health and wellbeing from getting substantially worse.