NCCID Disease Debriefs provide Canadian public health practitioners and clinicians with up-to-date reviews of essential information on prominent infectious diseases for Canadian public health practice. While not a formal literature review, information is gathered from key sources including the Public Health Agency of Canada (PHAC), the USA Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO) and peer reviewed literature.
This NCCID debrief is different than other NCCID debriefs as it provides public health practitioners and clinicians with up-to date review of essential information on a newly recognized threat to treatment of infectious disease and not on an infectious disease or an outbreak itself.
The recently recognized global distribution of plasmid-mediated resistance to the last resort drug colistin, along with its widespread dissemination within the human microbiome, poses a substantial public health risk as it limits the treatment options for patients with infections caused by multidrug-resistant (MDR) gram-negative bacteria and promotes easier spread of colistin resistance among bacteria and humans; this could lead to outbreaks of untreatable infections.
The goal of this debrief is to provide a review of essential information about the risk for the patients and healthcare systems and about options for actions to reduce the risks and mitigating epidemic dissemination of mcr-1 MDR bacteria.
This debrief was prepared by Aleksandra K. Wierzbowski. Questions, comments and suggestions regarding this debrief are most welcome and can be sent to firstname.lastname@example.org
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What are important characteristics of MCR-1?
WHAT IS MCR-1?
MCR-1 is an acronym for Mobilized Colistin Resistance. It protects bacteria from a polypeptide antimicrobial called colistin (polymyxin E).
WHAT IS THE MODE OF ACTION OF MCR-1?
MCR-1 uses a target site modification mechanism to protect bacteria from the action of colistin (polymyxin E). It is a gene which encodes an enzyme called phosphatidylethanolamine transferase which transfers the phosphatidylethanolamine residue to the lipid A of the Gram negative bacterial cell membrane. The lipid A of the bacterial outer membrane is the target binding site for colistin, which upon binding to it, it disrupts it by displacing magnesium and calcium, thus causing cell death. The presence of this residue lowers the affinity of the lipid A to colistin and related polymyxins therefore rendering the antimicrobial inactive and making the bacteria resistant. To date six different variants of mcr-1 have been found.
WHERE IS THE MCR-1 LOCATED?
The mcr-1 gene has been found to be located on a plasmid (a mobile DNA element that is able to move from one bacterium to another). Being located on a plasmid, the mcr-1 gene has the potential to quickly spread to other bacteria and raises the possibility that bacteria already resistant to major antibiotics could become resistant to colistin as well.
The movement of resistance genes between different bacterial species through plasmid-mediated horizontal gene transfer increases the variety of bacterial populations possessing multidrug-resistant (MDR) potential, and the intense selection pressure exerted by antibiotics selects out antibiotic resistant bacteria capable of causing infection in humans and animals.
In a recent investigation, mcr-1 genes has also been shown on different plasmids suggesting mobilization of the gene between different plasmids.
WHY IS MCR-1 MEDIATED COLISTIN RESISTANCE CONCERNING?
Colistin shows in-vitro activity against a diverse spectrum of clinically important gram-negative bacteria, including many members of the family Enterobacteriaceae and Pseudomonas aeruginosa. With limited development of new antimicrobials and limited pipeline of agents active against gram negative bacteria, colistin is an antimicrobial of last resort for the treatment of infections due to multidrug-resistant gram-negative bacteria. Colistin is often one of the only remaining antimicrobials with in-vitro activity against multidrug-resistant Enterobacteriaceae, including those that produce carbapenemase enzymes such as the Klebsiella pneumoniae carbapenemase and New Delhi metallo-β-lactamase. Therefore, the emergence of plasmid mediated colistin resistance in Escherichia coli from animal, food, and human sources in China is of concern because this drug is one of the last effective drugs for the treatment of multidrug-resistant Gram-negative infections.
WHAT BACTERIA HAS IT BEEN FOUND IN?
The mcr-1 gene has been found in the Enterobacteriaceae, a group of Gram negative bacteria. Most reports to date have identified the mcr-1 gene in E. coli, but it has also been reported from Salmonella species, Shigella sonnei, and K. pneumoniae as well as in E. aerogenes, and E. cloacae. The gene has been found in bacteria from food animals, raw meat and human samples.
SIGNS AND SYMPTOMS
The signs and symptoms of being infected with a bacteria that carries the mcr-1 gene are likely related to the infection and to the bacteria that causes it. Having the gene does not present different signs and symptoms to an individual to our knowledge. The severity of the infection is not affected by the presence of the mcr-1 gene. It is also possible that an individual may be an asymptomatic carrier of mcr-1 containing bacteria.
SEVERITY AND COMPLICATIONS
Severity and complications of having an infection caused by mcr-1 carrying bacteria are the same as for any other infection which might be dependent on the health status of the individual, age and the presence of comorbidities as well as on the pathogenicity of the bacteria. The presence of mcr-1 gene in a bacteria causing the infection can be of concern as it can lead to significant treatment complications if the bacteria is shown to be resistant to several other unrelated antibiotics.
In November 2015, a report from China first described plasmid-mediated colistin-resistance caused by the mcr-1 gene. Following that report, retrospective investigations of historical isolates have identified the rare occurrence of mcr-1 in Enterobacteriaceae from the 1980s. Bacteria with this resistance mechanism have now been identified from humans, food, environmental samples, and food animals in at least 20 countries around the world. Most reports to date have identified the mcr-1 gene in E. coli, but it has also been reported from Salmonella species, S. sonnei, and K. pneumoniae.
The SENTRY project showed that of the 21,006 E. coli and K. pneumoniae isolates collected in 2014-2015, only nineteen were positive for mcr-1 a total prevalence of only 0.1%. These data represent a large global collection of clinical isolates and demonstrate that the overall prevalence of mcr-1 is very low.
As of 2017[update], it has been detected in more than 30 countries on 5 continents in less than a year.
First report in China
In November 2015, mcr -1, a gene that can make bacteria resistant to colistin, an old antibiotic that is the last-resort drug for some multidrug-resistant infections was reported in China.
During a routine surveillance project on antimicrobial resistance in commensal E. coli from food animals in China, a major increase of colistin resistance was observed. Plasmid-mediated colistin resistance encoded by mcr-1 was found responsible for this resistance. The plasmid has been mobilized to an E. coli recipient cell by conjugation and maintained in K. pneumoniae and P. aeruginosa. Subsequently, mcr-1 carriage in E. coli isolates was found in 15% of samples of raw meat, 21% in animals, and 1% in patients with infection. A sub study in China, examining the early emergence of mcr-1 gene found its sporadic occurrence in 2004 and 2006 in and an outbreak of mcr-1 containing E. coli of chicken that began in 2009. The proportion of mcr-1 containing E. coli was found to increase from 5.2% in 2009 to 30% in 2014.
In May 2016, the Department of Defense (DOD) notified stakeholders that its Multidrug-resistant Organism Repository and Surveillance Network (MRSN) at the Walter Reed Institute of Research had identified the first colistin-resistant mcr-1 E. coli in a person in the United States. A US department of Agriculture (USDA) and the Department of Health and Human Services (HHS) search for colistin-resistant bacteria in food animals, retail meats and people also has found colistin-resistant E. coli in a single sample from a pig intestine.
The Department of Defense (DoD) announced in May 2016, the discovery of the first mcr-1 gene found in bacteria in a human in the United States. E. coli bacteria carrying the mcr-1 gene was found in a urine sample from a 49- year old Pennsylvania woman with no recent travel outside of the U.S. Despite some media reports, the Pennsylvania State Health Department investigation has determined that the woman did not have CRE and the bacteria identified was not resistant to all antibiotics (referred to as a pan-resistant infection). The presence of the mcr-1 gene, however, and its ability to share its colistin resistance with other bacteria such as CRE raise the risk that pan-resistant bacteria could develop. The scientists however did determine that the mcr-1 carrying colistin-resistant E. coli was resistant to other antibiotics including ampicillin, streptomycin, sulfisoxazole, and tetracycline. The patient with colistin-resistant E. coli was treated in an outpatient military treatment facility in Pennsylvania.
The Centers for Disease Control and Prevention is part of a coordinated public health response after the Department of Defense (DoD) announced the discovery of the first mcr-1 gene found in bacteria in a human in the United States. CDC is working with DoD, the Pennsylvania Department of Health, local health departments, and others to identify people who have had contact with the patient and take action to prevent local spread.
As of October 2017, CDC has tracked mcr-1 to 27 human samples in 15 states and 2 animal samples in 2 states.
Following the report of the identification of the mcr-1 gene in China, an investigation was launched in December of the same year by the Public Health Agency of Canada. The gene was found retrospectively in three different samples of E. coli (out of 1600 screened) all previously collected for special projects – one from 62 year old Ottawa women (carbapenem-resistance sequencing project, National Microbiology Laboratory), and two in retail ground beef sold in Ontario (Canadian Integrated Program for Antimicrobial Resistance Surveillance, CIPARS). The patient was hospitalized for an abdominal infection in 2011 and had a travel history and it’s likely that she picked up the gene while in Egypt. It was multidrug resistant, OXA-48 producer and colistin resistant (MIC of 4mg/L). The lean ground beef samples were found in samples collected a year apart in different locations, a butcher shop and a retail chain store. Both samples were collected in 2010, predating the samples from China collected between 2011 and 2014. The specimens involved were not the potentially deadly form of the bacteria known as E. coli 0157, but a beneficial garden-variety strain carried on the skin and in the gut of humans and other animals. Both isolates were multidrug resistant remaining susceptible to only the cephalosporins and amikacin, and additionally to gentamicin for one of the isolates. Information about the origin of the ground beef (domestic or imported) was unavailable.
A study looking at the frequency of mcr-1-mediated colistin resistance among E. coli clinical isolates obtained from patients in Canadian hospitals (CANWARD 2008–2015) has suggested that colistin resistance among E. coli human clinical isolates, including resistance mediated by the mcr-1 gene, remains rare in Canada.
In total, 5571 E. coli clinical isolates were obtained over the study years. Twelve isolates (0.2%) were resistant to colistin. The proportion of colistin-resistant isolates varied from 0.0% to 0.5% depending on the study year, and there was no clear trend toward increasing resistance over time. Typically the colistin-resistant isolates remained susceptible to antimicrobials from several
other classes. Two colistin-resistant isolates (0.04%) were found to harbor the mcr-1 gene.
The BC Centre for Disease Control’s (BCCDC) Public Health Laboratory has confirmed a case of mcr-1 E. coli resistance in an individual who returned to British Columbia from China. The patient had traveled to China in November 2015 for 2 weeks, where he required catheterization in a hospital emergency department in Zhejiang Province for acute urinary retention. He experienced acute urinary retention and fever 6 days after catheter removal, requiring another catheter insertion and 3 days of intravenous antimicrobial drugs in Guangdong Province. He denied contact with farm animals, live poultry markets, or undercooked meat. On return to Canada, obstructive urinary tract symptoms persisted, requiring 5 emergency department visits before prostate resection. Urine culture grew E. coli on day 3 post operatively which following further testing was identified to carry mcr-1 gene.
Susceptibility testing indicated a possible extended-spectrum β-lactamase producer and showed resistance to ampicillin, cefazolin, ceftriaxone, gentamicin, ciprofloxacin, and trimethoprim/sulfamethoxazole ; intermediate resistance to tobramycin; and susceptibility to amoxicillin/clavulanate, piperacillin/tazobactam, ertapenem, meropenem, and nitrofurantoin.
ADDITIONAL MCR GENES
A novel plasmid-mediated colistin resistance gene in porcine and bovine colistin-resistant E. Coli that did not contain mcr-1 has been identified in Belgium. The 1617bp long phosphoethanolamine transferase encoding gene shares 76.7% nucleotide homology to mcr-1. PCR screening identified higher prevalence of mcr–2 than mcr-1 in porcine E. coli in Belgium. Possible source of colistin resistance especially among isolates which do not have mcr-1. Harbored on IncX4 plasmid within IS1595 which indicates likely origins in Moraxella species.
- Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016
A third mobile colistin gene, mcr–3 has been characterized in porcine colistin- resistant E. coli. It coexists with 18 additional resistance determinants in a 261kb IncHI2-type plasmid pWJ1 and shows 45% and 47% nucleotide sequence identity to mcr-1 and mcr–2. Deduced amino acid sequence of mcr-3 shows identity to phosphoethanolamine transferse found in other Enterobacteriaceae and in Aeromonas species. mcr-3 has been found in samples of clinical infections as well as environmental sources.
RESERVOIR AND TRANSMISSION
Since its discovery in China in 2015, the reservoir of mcr-1 gene has been expanding. Initially found in bacteria of the gut in food animals and in food samples, now worryingly in human patients. Recently, mcr-1 gene has been shown to be present in healthy human microbiome. Adding another layer of complexity to the rapidly evolving epidemiology of plasmid-mediated colistin resistance in the community companion animals have recently been shown to serve as a reservoir of colistin-resistant E. coli as well.
Evidence suggest that the spread of mcr-1 is from animals to humans. Its discovery in the healthy human microbiome indicates that gene might have been in China longer than originally thought and that it has spread from the animals to healthy human gut. The healthy human gut is regarded as an antibiotic resistance gene reservoir and a site with high horizontal gene transfer potential. Colonization with mcr-1-positive organisms is not surprising, but it is none-the-less concerning because it suggests that mcr-1 may follow the same rapid pattern of spread that has already been observed for other plasmid-borne mechanisms of resistance, such as the K. pneumoniae Carbapenemase (KPC) and the New Delhi Metallo Beta-Lactamase (NDM).
mcr-1 gene has demonstrated natural interspecies spread within the Enterobacteriaceae. In addition, in vitro transmission to P. aeruginosa has been shown through experimental models. The spread of mcr-1 has been linked to agricultural use of colistin, indicating that transmission between animals and humans may take place. In response to these findings the Chinese government has now banned use of colistin in animal feed. Possible transmission of mcr-1–harboring E. coli between companion animals and human has been observed.
Challenges in laboratory testing and reporting of colistin susceptibility.
- Related to specific physiochemical properties of this antimicrobial agent
- Relative lack of clinical data to correlate with isolate MICs
- Large size and amphipathic hampers performance of disc diffusion and agar gradient diffusion
- Cationic nature increases adsorption of these agents to plastic surfaces and leads to inaccurate MICs
- Currently no US FDA-cleared test methods for polymyxin B susceptibility are available, no interpretive breakpoints exists
CDC recommendations for detection of colistin resistance
- using a validated broth microdilution method and reporting the MIC values with no interpretation or sending it to a reference laboratory
- not necessary to test isolates that are intrinsically resistant to colistin (e.g. Proteus, Providencia, Morganella, and Serratia)
- ETest has been used by some researchers but its limitation is that it may underestimate the actual MIC
Joint Clinical and Laboratory Standards Institute (CLSI)–European Committee on Antimicrobial Susceptibility Testing Polymyxin Breakpoints Working group has been established to help guide colistin susceptibility testing.
European Committee on Antimicrobial Susceptibility Testing (ECAST) breakpoints for interpretation of colistin MICs for the Enterobacteriaceae have been established and define colistin resistance as MIC ≥ 4 μg/mL
The Clinical and Laboratory Standards Institute (CLSI) has re-evaluated colistin interpretive criteria, and upcoming changes will be outlined in the M100 Performance Standards for Antimicrobial Susceptibility Testing to be published in 2017.
Detection of mcr-1 gene
CDC advices confirming the presence of mcr-1 mediated colistin resistance
- In Enterobacteriaceae isolates with an colistin MIC of 4 µg/ml or greater
- In Enterobacter spp. with elevated colistin MICs of 2 µg/ml or greater.
No commercial screening media exist for mcr-1
- Columbia Colistin- Nalidixic acid Agar (CNA) with 5% sheep blood identified serendipitously mcr-1 gene in an coli from a patient sample however, this method is inadequate for detection of mcr-1.
The presence of mcr-1 gene can be detected using the polymerase chain reaction (PCR) technique. Primers commonly used have been published.
PREVENTION AND TREATMENT
Measures to prevent the acquisition and transmission of bacteria carrying the mcr-1 colistin resistant gene are the same as for prevention of the acquisition and transmission of any antibiotic resistant bacteria and for should focus on proper hand hygiene and proper food safety especially in crowded spaces.
Treatment of mcr-1 carrying bacteria will depends on the type of bacteria and its antibiotic susceptibility pattern. Prompt and proper identification as well as complete antibiotic susceptibility testing is very important to an effective treatment. Although, the presence of mcr-1 gene renders the often last resort drug colistin inactive, it’s important to note that although mcr-1 positive bacteria might often be multi drug not all are pan-resistant and therefore there might still be antimicrobial options available. Empiric treatment should be adjusted accordingly following antibiotic susceptibility testing.
What is the current risk for Canadians from MCR-1?
The risk to Canadians remains very low and people should not be too concerned with it at the present time. mcr-1 is rare in Canada as most cases are likely linked to animals and meats sold in markets in China but it may also be associated to healthcare exposure outside of Canada. On the other hand, physicians and scientists need to be aware of this type of resistance so that proper testing methods and proper screening procedures are available in hospitals and labs so that this type of resistance is not missed.
Microbiology laboratories across Canada have enhanced their vigilance for detection of mcr-1 antibiotic resistant bacteria.
What measures should be taken for a suspected MCR-1 case or contact?
Efforts should be taken to identify close contacts, including household and healthcare contacts, of mcr-1 positive patient to determine whether any of them may have been at risk for transmission of the bacteria.
INFECTION PREVENTION AND CONTROL
Given the discovery of mcr-1 in a person in Pennsylvania, CDC reiterates the importance of measures to prevent transmission of antibiotic resistant bacteria, including those resistant to colistin or carrying the mcr-1 gene. CDC recommends the following:
Infection Prevention: Healthcare providers should follow Standard and Contact Precautions (http://www.cdc.gov/hicpac/2007IP/2007ip_part3.html) for any patients colonized or infected with antibiotic resistant bacteria, including patients who are found to have mcr-1 mediated resistant organisms. Healthcare facilities should follow manufacturers’ instructions for device cleaning and reprocessing.
Laboratory Testing: If laboratories are testing to determine whether colistin can be used clinically, Enterobacteriaceae isolates with a minimum inhibitory concentration (MIC) to colistin of 4 µg/ml or higher should be tested for confirmation and the presence of mcr-1. Thus far, all microorganisms that have contained the mcr-1 gene can safely be tested in a biosafety level-2 (BSL-2) laboratory. Isolates should be sent to CDC for confirmatory testing via the state or local public health department, per the CDC test directory (http://www.cdc.gov/laboratory/specimen-submission/detail.html?CDCTestCode=CDC-10223), if local testing is not available. The results and test method that were used for initial colistin testing should be included with any isolates submitted for confirmatory testing. CDC laboratories are in the process of validating a rapid polymerase chain reaction (PCR) test to detect mcr-1 in bacteria with elevated colistin MICs. It is not necessary to test Enterobacteriaceae with intrinsic colisitin resistance (e.g., Proteus, Providencia, Morganella, and Serratia species). Additionally, since Enterobacter species often have MICs of >=2 mcg/ml to colisitin, they should be sent for mcr-1 testing only if other risk factors exist, such as a recent history of travel outside the United States to a country where mcr-1 has been found to be more common (http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=21403).
Validation of Laboratory Testing: CDC is making test-bacteria with elevated colistin MICs, available to laboratories, researchers, and others through the FDA-CDC Antimicrobial Resistance Bacteria Isolate Bank (http://www.cdc.gov/drugresistance/resistance-bank/) for use in validation of colistin-resistance testing in U.S. clinical laboratories.
Environmental Cleaning: Healthcare facilities should ensure rooms where patients with antibiotic-resistant infections have been placed receive thorough daily and terminal cleaning.
Reporting to Public Health: Healthcare facilities and laboratories should adhere to local reporting requirements for all antibiotic resistant infections. If Enterobacteriaceae with mcr-1 are identified from patients, healthcare facilities and laboratories should notify local or state public health authorities as quickly as possible, and inform clinicians caring for the patient and responsible infection prevention staff.
Preparing food safely: Cook all meat, poultry, and fish to its proper internal temperature to kill bacteria (http://www.foodsafety.gov/keep/charts/mintemp.html), viruses, and other food-borne pathogens, regardless of antibiotic resistance