Dissemination of Multidrug-Resistant and mcr-1 Gram-Negative Bacilli in Broilers, Farm Workers, and the Surrounding Environment in Lebanon

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients

Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.

Phenotypic and genotypic characterization of colistin-resistant Escherichia Coli with mcr-4, mcr-5, mcr-6, and mcr-9 genes from broiler chicken and farm environment

BACKGROUND

Colistin is an antibiotic used as a last-resort to treat multidrug-resistant Gram-negative bacterial infections. Colistin had been used for a long time in veterinary medicine for disease control and as a growth promoter in food-producing animals. This excessive use of colistin in food animals causes an increase in colistin resistance. This study aimed to determine molecular characteristics of colistin-resistant Escherichia coli in broiler chicken and chicken farm environments.

RESULTS

Four hundred fifty-three cloacal and farm environment samples were collected from six different commercial chicken farms in Kelantan, Malaysia. E. coli was isolated using standard bacteriological methods, and the isolates were tested for antimicrobial susceptibility using disc diffusion and colistin minimum inhibitory concentration (MIC) by broth microdilution. Multiplex PCR was used to detect mcr genes, and DNA sequencing was used to confirm the resistance genes. Virulence gene detection, phylogroup, and multilocus sequence typing (MLST) were done to further characterize the E. coli isolates. Out of the 425 (94%; 425/453) E. coli isolated from the chicken and farm environment samples, 10.8% (48/425) isolates were carrying one or more colistin-resistance encoding genes. Of the 48 colistin-resistant isolates, 54.2% (26/48) of the mcr positive isolates were genotypically and phenotypically resistant to colistin with MIC of colistin ≥ 4 μg/ml. The most prominent mcr gene detected was mcr-1 (47.9%; 23/48), followed by mcr-8 (18.8%; 9/48), mcr-7 (14.5%; 7/48), mcr-6 (12.5%; 6/48), mcr-4 (2.1%; 1/48), mcr-5 (2.1%; 1/48), and mcr-9 (2.1%; 1/48) genes. One E. coli isolate originating from the fecal sample was found to harbor both mcr-4 and mcr-6 genes and another isolate from the drinking water sample was carrying mcr-1 and mcr-8 genes. The majority of the mcr positive isolates were categorized under phylogroup A followed by phylogroup B1. The most prevalent sequence typing (ST) was ST1771 (n = 4) followed by ST206 (n = 3). 100% of the mcr positive E. coli isolates were multidrug resistant. The most frequently detected virulence genes among mcr positive E. coli isolates were ast (38%; 18/48) followed by iss (23%; 11/48). This is the first research to report the prevalence of mcr-4, mcr-5, mcr-6, mcr-7, and mcr-8 genes in E. coli from broiler chickens and farm environments in Malaysia.

CONCLUSION

Our findings suggest that broiler chickens and broiler farm environments could be reservoirs of colistin-resistant E. coli, posing a risk to public health and food safety.

Co-existence of NDM-, aminoglycoside- and fluoroquinolone-resistant genes in carbapenem-resistant Escherichia coli clinical isolates from Pakistan

Background: To determine the prevalence of antimicrobial-resistant genes in carbapenem-resistant Escherichia coli (CRECO). Methods: A total of 290 carbapenem-resistant bacteria were collected from tertiary care hospitals in Lahore (Pakistan). These isolates were confirmed by VITEK 2 and matrix-assisted laser desorption/ionization time of flight. The minimum inhibitory concentration was performed by VITEK 2. Sequence typing, resistant gene identification, DNA hybridization and replicate typing were also performed. Results: 33 out of 290 (11.3%) were CRECO and carried blaNDM; 69, 18 and 12% were NDM-1, NDM-5 and NDM-7, respectively, with 100% resistance to β-lactams and β-lactam inhibitors. ST405 and ST468 were mostly identified. NDM-ECO carried approximately 50-450 kb of plasmids and 16 (55%) were associated with IncA/C. Conclusion: NDM-1-producing E. coli are highly prevalent in clinical settings.

Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies

Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.

The menace of colistin resistance across globe: Obstacles and opportunities in curbing its spread

Colistin-resistance in bacteria is a big concern for public health, since it is a last resort antibiotic to treat infectious diseases of multidrug resistant and carbapenem resistant Gram-negative pathogens in clinical settings. The emergence of colistin resistance in aquaculture and poultry settings has escalated the risks associated with colistin resistance in environment as well. The staggering number of reports pertaining to the rise of colistin resistance in bacteria from clinical and non-clinical settings is disconcerting. The co-existence of colistin resistant genes with other antibiotic resistant genes introduces new challenges in combatting antimicrobial resistance. Some countries have banned the manufacture, sale and distribution of colistin and its formulations for food producing animals. However, to tackle the issue of antimicrobial resistance, a one health approach initiative, inclusive of human, animal, and environmental health needs to be developed. Herein, we review the recent reports in colistin resistance in bacteria of clinical and non-clinical settings, deliberating on the new findings obtained regarding the development of colistin resistance. This review also discusses the initiatives implemented globally in mitigating colistin resistance, their strength and weakness.

Spread of the mcr-1 colistin-resistance gene in Escherichia coli through plasmid transmission and chromosomal transposition in French goats

Introduction

Colistin-resistance widely disseminated in food-producing animals due to decades of colistin use to treat diarrhea. The plasmid-borne mcr-1 gene has been extensively reported from bovine, swine and chicken worldwide, but smaller productions such as the goat farming sector were much less surveyed.

Methods

We looked for colistin-resistant isolates presenting plasmid-borne genes of the mcr family in both breeding (n=80) and fattening farms (n=5). Localization of the mcr-1 gene was performed using Southern blot analysis coupled to short-read and long-read sequencing.

Results

Only the mcr-1 gene was identified in 10% (8/80) of the breeding farms and four over the five fattening farms. In total, 4.2% (65/1561) of the animals tested in breeding farms and 60.0% (84/140) of those tested in fattening farms presented a mcr-1-positive E. coli. The mcr-1 gene was located either on the chromosome (32.2%) or on IncX4 (38.9%) and IncHI2 (26.8%) plasmids. As expected, both clonal expansion and plasmidic transfers were observed in farms where the mcr-1 gene was carried by plasmids. Tn6330 transposition was observed in the chromosome of diverse E. coli sequence types within the same farm.

Discussion

Our results show that the mcr-1 gene is circulating in goat production and is located either on plasmids or on the chromosome. Evidence of Tn6330 transposition highlighted the fact that chromosomal insertion does not impair the transmission capability of the mcr-1 gene. Only strict hygiene and biosecurity procedures in breeding farms, as well as a prudent use of antibiotics in fattening farms, can avoid such complex contamination pathways.

Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update

Background

Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane.

Results and discussion

Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI₂ conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins.

Conclusion

The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.

Mobile Colistin Resistance (mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks

Background: Pets, especially cats and dogs, represent a great potential for zoonotic transmission, leading to major health problems. The purpose of this systematic review was to present the latest developments concerning colistin resistance through mcr genes in pets. The current study also highlights the health risks of the transmission of colistin resistance between pets and humans. Methods: We conducted a systematic review on mcr-positive bacteria in pets and studies reporting their zoonotic transmission to humans. Bibliographic research queries were performed on the following databases: Google Scholar, PubMed, Scopus, Microsoft Academic, and Web of Science. Articles of interest were selected using the PRISMA guideline principles. Results: The analyzed articles from the investigated databases described the presence of mcr gene variants in pets including mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-8, mcr-9, and mcr-10. Among these articles, four studies reported potential zoonotic transmission of mcr genes between pets and humans. The epidemiological analysis revealed that dogs and cats can be colonized by mcr genes that are beginning to spread in different countries worldwide. Overall, reported articles on this subject highlight the high risk of zoonotic transmission of colistin resistance genes between pets and their owners. Conclusions: This review demonstrated the spread of mcr genes in pets and their transmission to humans, indicating the need for further measures to control this significant threat to public health. Therefore, we suggest here some strategies against this threat such as avoiding zoonotic transmission.

Antibiotic resistance genes in layer farms and their correlation with environmental samples

Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 10⁹- 6.82 × 10¹¹ copies/g. The average abundances of 5 antibiotic resistance genes were above 10¹⁰ copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.

Nationwide Assessment of Water Quality in Rivers across Lebanon by Quantifying Fecal Indicators Densities and Profiling Antibiotic Resistance of Escherichia coli

The use of contaminated water has been associated with severe disease outbreaks. Due to widespread pollution with untreated sewage, concerns have been raised over water quality in Lebanon, a country with well-documented challenges in infrastructure. Here, we evaluated the water quality of major rivers in Lebanon by quantifying the densities of fecal indicator bacteria (fecal coliforms and Escherichia coli). Additionally, we assessed the dissemination of antibiotic-resistant E. coli in river water. Composite water samples (n = 132) were collected from fourteen rivers, and 378 E. coli were isolated and analyzed. Fecal coliforms and E. coli were detected in 96.29% and 95.5% of the samples, respectively. Additionally, 73.48–61.3% and 31.81% of the samples exceeded the microbiological acceptability standards for irrigation and the fecal coliform limit for recreational activities, respectively. The E. coli exhibited resistance to ampicillin (40% of isolates), amoxicillin + clavulanic acid (42%), cefepime (4%), cefotaxime (14%), cefalexin (46%), cefixime (17%), doripenem (0.3%), imipenem (0.5%), gentamicin (6%), kanamycin (9%), streptomycin (35%), tetracycline (35%), ciprofloxacin (10%), norfloxacin (7%), trimethoprim-sulfamethoxazole (32%), and chloramphenicol (13%). Notably, 45.8% of the isolates were classified as multidrug resistant (MDR). Our results highlight the need to urgently address fecal pollution and the dissemination of antibiotic resistance in Lebanese rivers.

Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil

Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant mcr-1-producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil). We isolated 490 colistin-resistant Gram-negative rods, of which eight were mcr-1.1-positive Escherichia coli, the only species with this result, indicating a low incidence of the mcr-1 production mechanism among colistin-resistant isolates. All mcr-1.1 positive isolates showed similarly low MICs for colistin and were susceptible to most antibiotics tested. The isolates showed diversity of MLST classification. The eight mcr-1.1-positive E. coli genomes were sequenced. In seven of eight isolates the mcr-1.1 gene is located in a contig that is presumed to be a part of an IncX4 plasmid; in one isolate, it is located in a contig that is presumed to be part of an IncHI2A plasmid. Three different genomic contexts for mcr-1.1 were observed, including a genomic cassette mcr-1.1-pap2 disrupting a DUF2806 domain-containing gene in six isolates. In addition, an IS1-family transposase was found inserted next to the mcr-1.1 cassette in one isolate. An mcr-1.1-pap2 genomic cassette not disrupting any gene was identified in another isolate. Our results suggest that plasmid dissemination of hospital-resident strains took place during the study period and highlight the need for continued genomic surveillance.

WGS Analysis of Clonal and Plasmidic Epidemiology of Colistin-Resistance Mediated by mcr Genes in the Poultry Sector in Lebanon

Poultry and poultry meat are important contributors to the global antimicrobial burden. Unregulated and illegal use of extended-spectrum cephalosporins (ESC) in this sector has long been identified as a major cause of massive spread of ESC-resistant Escherichia coli, and colistin usage is considered a main driver of plasmid-mediated mcr genes dissemination. In Lebanon, the first mcr-1-positive E. coli found in poultry dates back to 2015, followed by a few reports of mcr-1-positive E. coli in poultry, swine, humans, and the environment. On the contrary, a comprehensive picture of the population structure of mcr-1-positive E. coli and mcr-1-bearing plasmids carrying the mcr-1 gene using whole-genome analysis is largely lacking. This study reports the prevalence of mcr-1-positive E. coli in poultry originating from 32 farms across three Lebanese governorates and slaughtered in the same place. We report 27/32 (84.4%) mcr-1 positive farms, leading to a total of 84 non-duplicate E. coli collected, of which 62 presented the mcr-1 gene. Numerous associated resistances were identified, including to ESC through the presence of bla CTX-M or bla CMY genes. The mcr-1 gene was mostly carried by IncX4 (n = 36) and IncI2 (n = 24) plasmids, which are both known for their efficient transfer capacities. A high genetic diversity was detected, arguing for the lack of contamination during the slaughter process. ST744 and ST1011 were the most widely identified clones, which have been both regularly associated to mcr-1-carrying E. coli and to the poultry sector. The wide dissemination of colistin-resistance, coupled to resistances to ESC and numerous other molecules, should urge authorities to implement efficient guidelines for the use of antibiotics in the poultry sector in Lebanon.

Enteric pathogenic bacteria and resistance gene carriage in the homeless population in Marseille, France

We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% prevalence of enteric pathogenic bacteria carriage, including Escherichia coli pathotypes (8.7%) and Tropheryma whipplei (0.9%). Only 2 persons carried blaCTX-M-15 resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 to mcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria.

Acquisition of multidrug-resistant bacteria and colistin resistance genes in French medical students on internships abroad

BACKGROUND

Acquisition of multidrug resistant bacteria (MDR) and colistin resistance genes by international travellers has been demonstrated. Studies conducted in medical students during internships abroad are scant.

METHODS

Nasopharyngeal, rectal, and vaginal swabs samples were collected from 382 French medical students before and after travel to investigate the acquisition of MDR bacteria. The bacterial diversity in the samples was assessed by culture on selective media. We also genetically characterised the isolates of MDR bacteria including Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E), methicillin-resistant Staphylococcus aureus (MRSA), and Carbapenemase-producing Enterobacteriacae (CPE) using the real-time polymerase chain reaction method. The samples were collected from 293 students and were investigated for mcr colistin-resistance genes using RT-PCR directly on the samples, followed by conventional PCR and sequencing.

RESULTS

A proportion of 29.3% (112/382) of the participants had acquired ESBL-E and 2.6% (10/382) had acquired CPE. The most common species and ESBL-E encoding gene were Escherichia coli (125/127 isolates, 98.4%) and bla_CTX-M-A (121/127, 95.3%), respectively. A proportion of 6.8% (20/293) of the participants had acquired mcr-1 genes, followed by mcr-3 (1/293, 0.3%) and mcr-8 (1/293, 0.3%). We found that taking part in humanitarian missions to orphanages (aRR = 2.01, p < 0.0001), being in contact with children during travel (aRR = 1.78, p = 0.006), the primary destination of travel being Vietnam (aRR = 2.15, p < 0.0001) and north India (aRR = 2.41, p = 0.001), using antibiotics during travel (aRR = 1.77, p = 0.01), and studying in 2018 (aRR = 1.55, p = 0.03) were associated with the acquisition of ESBL-E. When the primary destination of travel was Vietnam (aRR = 2.74, p < 0.0001) and the year of study was 2018 (aRR = 1.93, p < 0.002), this was associated with acquisition of colistin resistance genes.

CONCLUSION

Medical students are at a potential risk of acquiring ESBL-E, CPE and colistin resistance genes. A number of risk factors have been identified, which may be used to develop targeted preventive measures.

Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: A risk to human health

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

The Mobile Colistin Resistance Gene, mcr-1.1, Is Carried on IncX4 Plasmids in Multidrug Resistant E. coli Isolated from Rainbow Trout Aquaculture

Colistin, a last resort antibiotic, is important for controlling infections with carbapenem-resistant Enterobacteriaceae. The recent emergence of mobile-colistin-resistance (mcr) genes has threatened the effectiveness of colistin. Aquaculture is hypothesized to be a major contributor to the evolution and dissemination of mcr. However, data on mcr in aquaculture are limited. Here, the occurrence of mcr-1 was assessed in Rainbow Trout in Lebanon, a country with developing antimicrobial stewardship and an established use of colistin for medical and farming purposes. mcr-1 was detected in 5 Escherichia coli isolated from fish guts. The isolates were classified as multidrug-resistant and their colistin minimum inhibitory concentration ranged between 16 and 32 μg/mL. Whole genome sequencing analysis showed that mcr-1 was carried on transmissible IncX4 plasmids and that the isolates harbored more than 14 antibiotic resistance genes. The isolates belonged to ST48 and ST101, which have been associated with mcr and can occur in humans and fish. The mcr-1-positive E. coli persisted in 6-day biofilms, but there was a potential fitness cost. Given the status of infrastructure in Lebanon, there is a high potential for the dissemination of mcr via aquatic environments. Urgent actions are needed to control mcr and to enhance antimicrobial stewardship in Lebanon.

Plasmid-Determined Colistin Resistance in the North African Countries: A Systematic Review

We have conducted a systematic review to update available information on plasmid-mediated colistin resistance (mobilized colistin resistance [mcr]) genes in North African countries. We have searched the articles of PubMed, Scopus, and Web of Science databases reporting plasmid-mediated colistin resistance bacteria isolated in North African countries. After searching and selection, 30 studies that included 208 mcr-positive isolates were included. Different mcr-positive strains frequencies were recorded and ranged from 2% in clinical isolates to 12.3% in environmental samples. Escherichia coli was the predominant species recorded and these microorganisms showed high resistance to ciprofloxacin and cotrimoxazole. IncHI2 plasmids are probably the key vectors responsible for the dissemination of mcr genes in these countries. This review highlighted that the mcr-positive isolates are circulating in different ecological niches with different frequencies. Therefore, actions should be implemented to prevent the dissemination of the mcr genes within and outside of these countries, such as microbiological and molecular surveillance programs and restriction use of colistin in farming.

Wildlife Carnivorous Mammals As a Specific Mirror of Environmental Contamination with Multidrug-Resistant Escherichia coli Strains in Poland

In recent decades, the number of studies on the occurrence of resistant strains in wildlife animals has increased significantly, but data are still fragmentary. The aim of this study was to evaluate drug resistance of Escherichia coli strains isolated from wild carnivorous mammals, common in Poland. Selective media with antimicrobials (tetracycline, kanamycin, chloramphenicol, and cefotaxime) were used for isolation. Of 53 isolates shown to be distinct by the amplification of DNA fragments surrounding rare restriction site-fingerprinting method, 77.8% were multidrug-resistant (multidrug-resistant). All strains were resistant to ampicillin and many of them also exhibited resistance to tetracycline (76.2%), sulfamethoxazole (57.1%), streptomycin and kanamycin (49.2%), chloramphenicol (30.1%), and nalidixic acid (46%). In most cases, the phenotypic resistance profile was confirmed by detection of relevant genes mostly occurring in strains isolated from livestock animals and humans. Extended-spectrum β-lactamase-producing strains were detected in one mink and three martens. The strains were carriers of bla_TEM-1, bla_TEM-135, and bla_CTX-M-15 genes. Our research confirmed a high carrier rate of MDR E. coli, even more than one MDR strain in a single individual; therefore, wider monitoring in this group of animals should be considered.

Occurrence and Characteristics of Mobile Colistin Resistance (mcr) Gene-Containing Isolates from the Environment: A Review

The emergence and spread of mobile colistin (COL) resistance (mcr) genes jeopardize the efficacy of COL, a last resort antibiotic for treating deadly infections. COL has been used in livestock for decades globally. Bacteria have mobilized mcr genes (mcr-1 to mcr-9). Mcr-gene-containing bacteria (MGCB) have disseminated by horizontal/lateral transfer into diverse ecosystems, including aquatic, soil, botanical, wildlife, animal environment, and public places. The mcr-1, mcr-2, mcr-3, mcr-5, mcr-7, and mcr-8 have been detected in isolates from and/or directly in environmental samples. These genes are harboured by Escherichia coli, Enterobacter, Klebsiella, Proteus, Salmonella, Citrobacter, Pseudomonas, Acinetobacter, Kluyvera, Aeromonas, Providencia, and Raulotella isolates. Different conjugative and non-conjugative plasmids form the backbones for mcr in these isolates, but mcr have also been integrated into the chromosome of some strains. Insertion sequences (IS) (especially ISApl1) located upstream or downstream of mcr, class 1–3 integrons, and transposons are other drivers of mcr in the environment. Genes encoding multi-/extensive-drug resistance and virulence are often co-located with mcr on plasmids in environmental isolates. Transmission of mcr to/among environmental strains is clonally unrestricted. Contact with the mcr-containing reservoirs, consumption of contaminated animal-/plant-based foods or water, international animal-/plant-based food trades and travel, are routes for transmission of MGCB.