High prevalence of the mcr-1 gene in retail chicken meat in the Netherlands in 2015

Plasmid-mediated colistin resistance from fresh meat and slaughtered animals in the Czech Republic: nation-wide surveillance 2020-2021

The aim of this study was to determine the occurrence of plasmid-mediated colistin resistance in domestic and imported meat and slaughter animals in the Czech Republic during 2020-2021 by using selective cultivation and direct PCR testing. A total of 111 colistin-resistant Escherichia coli isolates with mcr-1 gene were obtained from 65 (9.9%, n = 659) samples and subjected to whole-genome sequencing. Isolates with mcr were frequently found in fresh meat from domestic production (14.2%) as well as from import (28.8%). The mcr-1-positive E. coli isolates predominantly originated from meat samples (16.6%), mainly poultry (27.1%), and only minor part of the isolates came from the cecum (1.7%). In contrast to selective cultivation, 205 (31.1%) samples of whole-community DNA were positive for at least one mcr variant, and other genes besides mcr-1 were detected. Analysis of whole-genome data of sequenced E. coli isolates revealed diverse sequence types (STs) including pathogenic lineages and dominance of ST1011 (15.6%) and ST162 (12.8%). Most isolates showed multidrug-resistant profile, and 9% of isolates produced clinically important beta-lactamases. The mcr-1 gene was predominantly located on one of three conjugative plasmids of IncX4 (83.5%), IncI2 (7.3%), and IncHI2 (7.3%) groups. Seventy-two percent isolates of several STs carried ColV plasmids. The study revealed high prevalence of mcr genes in fresh meat of slaughter animals. Our results confirmed previous assumptions that the livestock, especially poultry production, is an important source of colistin-resistant E. coli with the potential of transfer to humans via the food chain. IMPORTANCE We present the first data on nation-wide surveillance of plasmid-mediated colistin resistance in the Czech Republic. High occurrence of plasmid-mediated colistin resistance was found in meat samples, especially in poultry from both domestic production and import, while the presence of mcr genes was lower in the gut of slaughter animals. In contrast to culture-based approach, testing of whole-community DNA showed higher prevalence of mcr and presence of various mcr variants. Our results support the importance of combining cultivation methods with direct culture-independent techniques and highlight the need for harmonized surveillance of plasmid-mediated colistin resistance. Our study confirmed the importance of livestock as a major reservoir of plasmid-mediated colistin resistance and pointed out the risks of poultry meat for the transmission of mcr genes toward humans. We identified several mcr-associated prevalent STs, especially ST1011, which should be monitored further as they represent zoonotic bacteria circulating between different environments.

Antimicrobial Resistance in Escherichia coli and Its Correlation with Antimicrobial Use on Commercial Poultry Farms in Bangladesh

Antimicrobial resistance is a global concern, posing risks to human and animal health. This research quantified antimicrobial resistance (AMR) in E. coli isolates from poultry fecal and environmental samples in Bangladesh and explored their association with antimicrobial use (AMU). We screened 725 fecal and 250 environmental samples from 94 conventional broilers and 51 Sonali farms for E. coli presence using MALDI-TOF mass spectrometry. AMU data were collected at flock levels, expressed as treatment incidence (TI), while minimum inhibitory concentrations (MIC) for 14 antibiotics were determined on five fecal E. coli isolates per farm and on all environmental isolates. MIC results were interpreted using human clinical breakpoints and EUCAST epidemiological cut-off values (ECOFFs). Acquired resistance against commonly used antimicrobial agents such as ciprofloxacin, tetracycline and ampicillin, was extremely high and predominantly clinically relevant. There was a moderate correlation between fecal and environmental antibiotic resistance index (ARI), but there was no significant correlation between AMU and AMR, suggesting that the observed AMR prevalence is unrelated to current AMU in poultry, but may be due to high historical AMU. A high level of multidrug resistance, including against critically important antimicrobials, was found in both farm types. Therefore, an AMR/AMU surveillance program is urgently needed in the poultry production sector of Bangladesh.

First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh

Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4-8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.

Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken

Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.

Genetic analysis of plasmid-encoded mcr-1 resistance in Enterobacteriaceae derived from poultry meat in the Netherlands

Background

Colistin is classified as the highest priority and critically important antimicrobial for human medicine by WHO as it is the last resort agent for treatment of carbapenem-resistant Enterobacteriaceae in humans. Additional research is necessary to elucidate the genetic structure of mcr-1 resistance genes, commonly found on plasmids, using WGS.

Objectives

To map and compare the genetic characteristics of 35 mcr-1-mediated colistin-resistant Enterobacteriaceae isolated from chicken meat to highlight the genetic variation of the mcr-1-containing plasmids.

Methods

Sequencing was performed using Illumina HiSeq2500, Novaseq6000 and ONT’s GridION. GridION data was locally basecalled and demultiplexed using ONT’s Albacore 2.3.4 followed by Porechop 2.3. Quality filtering was performed using Filtlong 2.0. Hybrid Assembly was performed using Unicycler 4.7. Plasmids were compared with reference sequences in plasmid-RefSeq and pATLAS.

Results

A total of 35 mcr-1 positive Enterobacteriaceae were investigated, which resulted in 34 qualitatively robust hybrid assemblies of 2 Klebsiella pneumoniae and 32 Escherichia coli. mcr-1.1 was present in 33/34 isolates. One isolate contained an mcr-1.1-like resistance gene, due to a deletion of one codon. Two mcr-1.1 genes were located on the chromosome, while the majority of the mcr-1 genes were found on IncX4 type plasmids (n = 19). Almost all plasmids identified in this study were highly similar to plasmids found in human-derived strains.

Conclusions

The mcr-1.1-containing plasmids from retail chicken show high sequence similarity to human mcr-1.1 plasmids, suggesting that this may be a contributor to the presence of colistin resistance in humans.

Colistin Resistant mcr Genes Prevalence in Livestock Animals (Swine, Bovine, Poultry) from a Multinational Perspective. A Systematic Review

The objective of this review is to collect and present the results of relevant studies on an international level, on the subject of colistin resistance due to mcr genes prevalence in livestock animals. After a literature search, and using PRISMA guidelines principles, a total of 40 swine, 16 bovine and 31 poultry studies were collected concerning mcr-1 gene; five swine, three bovine and three poultry studies referred to mcr-2 gene; eight swine, one bovine, two poultry studies were about mcr-3 gene; six swine, one bovine and one poultry manuscript studied mcr-4 gene; five swine manuscripts studied mcr-5 gene; one swine manuscript was about mcr-6, mcr-7, mcr-8, mcr-9 genes and one poultry study about mcr-10 gene was found. Information about colistin resistance in bacteria derived from animals and animal product foods is still considered limited and that should be continually enhanced; most of the information about clinical isolates are relative to enteropathogens Escherichia coli and Salmonella spp. This review demonstrates the widespread dispersion of mcr genes to livestock animals, indicating the need to further increase measures to control this important threat for public health issue.

Potential sources and characteristic occurrence of mobile colistin resistance (mcr) gene-harbouring bacteria recovered from the poultry sector: a literature synthesis specific to high-income countries

Understanding the sources, prevalence, phenotypic and genotypic characteristics of mcr gene-harbouring bacteria (MGHB) in the poultry sector is crucial to supplement existing information. Through this, the plasmid-mediated colistin resistance (PMCR) could be tackled to improve food safety and reduce public health risks. Therefore, we conducted a literature synthesis of potential sources and characteristic occurrence of MGHB recovered from the poultry sector specific to the high-income countries (HICs). Colistin (COL) is a last-resort antibiotic used for treating deadly infections. For more than 60 years, COL has been used in the poultry sector globally, including the HICs. The emergence and rapid spread of mobile COL resistance (mcr) genes threaten the clinical use of COL. Currently, ten mcr genes (mcr-1 to mcr-10) have been described. By horizontal and vertical transfer, the mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, and mcr-9 genes have disseminated in the poultry sector in HICs, thus posing a grave danger to animal and human health, as harboured by Escherichia coli, Klebsiella pneumoniae, Salmonella species, and Aeromonas isolates. Conjugative and non-conjugative plasmids are the major backbones for mcr in poultry isolates from HICs. The mcr-1, mcr-3 and mcr-9 have been integrated into the chromosome, making them persist among the clones. Transposons, insertion sequences (IS), especially ISApl1 located downstream and upstream of mcr, and integrons also drive the COL resistance in isolates recovered from the poultry sector in HICs. Genes coding multi-and extensive-drug resistance and virulence factors are often co-carried with mcr on chromosome and plasmids in poultry isolates. Transmission of mcr to/among poultry strains in HICs is clonally unrestricted. Additionally, the contact with poultry birds, manure, meat/egg, farmer's wears/farm equipment, consumption of contaminated poultry meat/egg and associated products, and trade of poultry-related products continue to serve as transmission routes of MGHB in HICs. Indeed, the policymakers, especially those involved in antimicrobial resistance and agricultural and poultry sector stakeholders-clinical microbiologists, farmers, veterinarians, occupational health clinicians and related specialists, consumers, and the general public will find this current literature synthesis very useful.

Inhibition of Antimicrobial-Resistant Escherichia coli Using a Broad Host Range Phage Cocktail Targeting Various Bacterial Phylogenetic Groups

Antimicrobial-resistant (AMR) commensal Escherichia coli is a major reservoir that disseminates antimicrobial resistance to humans through the consumption of contaminated foods, such as retail poultry products. This study aimed to control AMR E. coli on retail chicken using a broad host range phage cocktail. Five phages (JEP1, 4, 6, 7, and 8) were isolated and used to construct a phage cocktail after testing infectivity on 67 AMR E. coli strains isolated from retail chicken. Transmission electron microscopic analysis revealed that the five phages belong to the Myoviridae family. The phage genomes had various sizes ranging from 39 to 170 kb and did not possess any genes associated with antimicrobial resistance and virulence. Interestingly, each phage exhibited different levels of infection against AMR E. coli strains depending on the bacterial phylogenetic group. A phage cocktail consisting of the five phages was able to infect AMR E. coli in various phylogenetic groups and inhibited 91.0% (61/67) of AMR E. coli strains used in this study. Furthermore, the phage cocktail was effective in inhibiting E. coli on chicken at refrigeration temperatures. The treatment of artificially contaminated raw chicken skin with the phage cocktail rapidly reduced the viable counts of AMR E. coli by approximately 3 log units within 3 h, and the reduction was maintained throughout the experiment without developing resistance to phage infection. These results suggest that phages can be used as a biocontrol agent to inhibit AMR commensal E. coli on raw chicken.

From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat

Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.

Prevalence of Colistin-Resistant Bacteria among Retail Meats in Japan

Colistin (CST) is considered the last resort for the treatment of infectious diseases due to multidrug-resistant bacteria. Since the mcr-1 gene has been reported in Enterobacteriaceae isolated from food, animals, and humans in China, the prevalence of CST-resistant bacteria has been of great concern. Here, we investigated the prevalence of CST resistance and plasmid-mediated colistin-resistance genes (mcr) in gram-negative bacteria isolated among retail meats in Japan. CST-resistant bacteria were isolated from 310 domestic retail meats (103 chicken meat, 103 pork, and 104 beef) purchased between May 2017 and July 2018 from retail shops in Japan using CST-containing media and antimicrobial susceptibility testing. The mcr gene was investigated in isolates with a CST minimum inhibitory concentration of ≥1 μg/mL. Excluding the intrinsically CST-resistant isolates, CST-resistant bacteria were isolated from 39 of the total chicken meats (37.9%), 19 of the pork samples (18.4%), and 18 of the beef samples (17.3%). A total of 459 isolates were identified, out of which 99 were CST-resistant. CST resistance (resistance breakpoints: Aeromonas, >4 μg/mL; others, >2 μg/mL) was found in Aeromonas spp. (48/206, 23.3%), Yersinia spp. (5/112, 4.5%), Escherichia coli (23/39, 59%), Citrobacter spp. (4/26, 15.4%), Klebsiella spp. (2/23, 8.7%), Raoultella spp. (2/16, 12.5%), Enterobacter spp. (7/14, 50%), Pseudomonas spp. (1/8, 12.5%), Pantoea spp. (5/7, 71.4%), Ewingella spp. (1/4, 25%), and Kluyvera spp. (1/2, 50%). The mcr gene was detected in 16 isolates: mcr-1 in 14 isolates of E. coli from 10 chicken samples (9.7%), and mcr-3 in two isolates of Aeromonas sobria from pork and chicken samples (each 1.0%). The findings of this study highlight the necessity of surveillance of CST resistance and resistance genes in bacteria that contaminate retail meats.

Complete Genetic Analysis of Plasmids Carrying mcr-1 and Other Resistance Genes in Avian Pathogenic Escherichia coli Isolates from Diseased Chickens in Anhui Province in China

Antimicrobial resistance associated with colistin has emerged as a significant concern worldwide, threatening the use of one of the most important antimicrobials for treating human disease. This study aimed to investigate the prevalence of colistin-resistant avian-pathogenic Escherichia coli (APEC) and shed light on the possibility of transmission of mcr-1 (mobilized colistin resistance)-positive APEC. A total of 72 APEC isolates from Anhui Province in China were collected between March 2017 and December 2018 and screened for the mcr-1 gene. Antimicrobial susceptibility testing was performed using the broth dilution method. Pulsed-field gel electrophoresis, Southern blot analysis, and conjugation assay were performed to determine the location and conjugative ability of the mcr-1 gene. Whole-genome sequencing and analysis were performed using Illumina MiSeq and Nanopore MinION platforms. Three APEC isolates (AH25, AH62, and AH65) were found to be positive for the mcr-1 gene and showed multidrug resistance. The mcr-1 genes were located on IncI2 plasmids, and conjugation assays revealed that these plasmids were transferrable. Notably, strains AH62 and AH65, both belonging to ST1788, were collected from different places but carried the same drug resistance genes and shared highly similar plasmids. This study highlights the potential for a possible epidemic of mcr-1-positive APEC and the urgent need for continuous active monitoring.

IMPORTANCE In this study, three plasmids carrying mcr-1 were isolated and characterized from APEC isolates from Anhui Province in China. The mcr-1 genes were located on IncI2 plasmids, and these plasmids were transferrable. These three IncI2 plasmids had high homology with the plasmids harbored by pathogenic bacteria isolated from other species. This finding showed that IncI2 plasmids poses a risk for the exchange of genetic material between different niches. Although colistin has been banned for use in food-producing animals in China, the coexistence of the broad-spectrum β-lactamase and mcr-1 genes on a plasmid can also lead to the stable existence of mcr-1 genes. The findings illustrated the need to improve the monitoring of drug resistance in poultry systems so as to curb the transmission or persistence of multidrug-resistant bacteria.

Quantitative Analysis of Colistin-Resistant Escherichia coli in Retail Meat from Local Vietnamese Markets

The spread of drug-resistant bacteria via food has contributed to the dissemination of resistant bacteria among humans. However, the status of food contamination with resistant bacteria, particularly the quantitative level of resistant bacteria in food, has not yet been well elucidated. In this study, the abundance of colistin-resistant Escherichia coli in meat samples was quantified to understand the origin of the contamination of meat available in local Vietnamese markets. Fifteen samples each of chicken and pork meat purchased from local Vietnamese markets were assessed for the presence of colistin-resistant E. coli with the mobile colistin resistance gene, mcr. The results showed that 40% (6/15) and 66% (10/15) of the pork and chicken meat samples, respectively, were contaminated with colistin-resistant E. coli. The median quantitative levels of colistin-resistant E. coli in the contaminated pork and chicken samples were 1.8 × 10⁴ and 4.2 × 10³ CFU/g, respectively. The results of phylogenetic analysis of isolates from a chicken meat sample showed that the contaminated colistin-resistant E. coli was a mix of multiple phylogenetical clones of bacteria that may have multiplied during sale. This is the first study to quantify the abundance of colistin-resistant E. coli in meat samples.

Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken

Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.

Prevalence and Genetic Characterization of mcr-1-Positive Escherichia coli Isolated from Retail Meats in South Korea

The spread of plasmid-mediated colistin resistance has posed a serious threat to public health owing to its effects on the emergence of pandrug-resistant bacteria. In this study, we investigated the prevalence and characteristics of mcr-1-positive Escherichia coli isolated from retail meat samples in Korea. In total, 1,205 E. coli strains were isolated from 3,234 retail meat samples in Korea. All E. coli strains were subjected to antimicrobial susceptibility testing and were examined for the presence of mcr-1 gene. All mcr-1-positive E. coli (n = 10, 0.8%) from retail meat were subjected to pulse-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). The transferability of mcr-1 gene was determined by conjugation assays. The mcr-1-positive strains exhibited diverse clonal types. Our mcr-1 genes were located in plasmids belonged to the IncI2 (n = 1) and IncX4 (n = 8) types, which were reported to be prevalent in Asia and worldwide, respectively. Most mcr-1 genes from mcr-1-positive strains (9/10) were transferable to the recipient strain and the transfer frequencies ranged from 2.4 × 10^-3 to 9.8 × 10^-6. Our data suggest that the specific types of plasmid may play an important role in spreading plasmid-mediated colistin resistance in Korea. Furthermore, our findings suggest that the retail meat may be an important tool for disseminating plasmid-mediated colistin resistance.

The effective design of sampling campaigns for emerging chemical and microbial contaminants in drinking water and its resources based on literature mining

As well as known contaminants, surface waters also contain an unknown variety of chemical and microbial contaminants which can pose a risk to humans if surface water is used for the production of drinking water. To protect human health proactively, and in a cost-efficient way, water authorities and drinking water companies need early warning systems. This study aimed to (1) assess the effectiveness of screening the scientific literature to direct sampling campaigns for early warning purposes, and (2) detect new aquatic contaminants of concern to public health in the Netherlands. By screening the scientific literature, six example contaminants (3 chemical and 3 microbial) were selected as potential aquatic contaminants of concern to the quality of Dutch drinking water. Stakeholders from the Dutch water sector and various information sources were consulted to identify the potential sources of these contaminants. Based on these potential contamination sources, two sampling sequences were set up from contamination sources (municipal and industrial wastewater treatment plants), via surface water used for the production of drinking water to treated drinking water. The chemical contaminants, mycophenolic acid, tetrabutylphosphonium compounds and Hexafluoropropylene Oxide Trimer Acid, were detected in low concentrations and were thus not expected to pose a risk to Dutch drinking water. Colistin resistant Escherichia coli was detected for the first time in Dutch wastewater not influenced by hospital wastewater, indicating circulation of bacteria resistant to this last-resort antibiotic in the open Dutch population. Four out of six contaminants were thus detected in surface or wastewater samples, which showed that screening the scientific literature to direct sampling campaigns for both microbial and chemical contaminants is effective for early warning purposes.

Colistin-Resistant Enterobacteriaceae Isolated From Process Waters and Wastewater From German Poultry and Pig Slaughterhouses

Due to the high prevalence of colistin-resistant Enterobacteriaceae in poultry and pigs, process waters and wastewater from slaughterhouses were considered as a hotspot for isolates carrying plasmid-encoded, mobilizable colistin resistances (mcr genes). Thus, questions on the effectiveness of wastewater treatment in in-house and municipal wastewater treatment plants (WWTPs) as well as on the diversity of the prevailing isolates, plasmid types, and their transmissibility arise. Process waters and wastewater accruing in the delivery and unclean areas of two poultry and two pig slaughterhouses were screened for the presence of target colistin-resistant bacteria (i.e., Escherichia coli, Klebsiella spp., Enterobacter cloacae complex). In-house and municipal WWTPs (mWWTPs) including receiving waterbodies were investigated as well. Samples taken in the poultry slaughterhouses yielded the highest occurrence of target colistin-resistant Enterobacteriaceae (40.2%, 33/82), followed by mWWTPs (25.0%, 9/36) and pig slaughterhouses (14.9%, 10/67). Recovered isolates exhibited various resistance patterns. The resistance rates using epidemiological cut-off values were higher in comparison to those obtained with clinical breakpoints. Noteworthy, MCR-1-producing Klebsiella pneumoniae and E. coli were detected in scalding waters and preflooders of mWWTPs. A total of 70.8% (46/65) of E. coli and 20.6% (7/34) of K. pneumoniae isolates carried mcr-1 on a variety of transferable plasmids with incompatibility groups IncI1, IncHI2, IncX4, IncF, and IncI2 ranging between 30 and 360 kb. The analyzed isolates carrying mcr-1 on transferable plasmids (n = 53) exhibited a broad diversity, as they were assigned to 25 different XbaI profiles. Interestingly, in the majority of colistin-resistant mcr-negative E. coli and K. pneumoniae isolates non-synonymous polymorphisms in pmrAB were detected. Our findings demonstrated high occurrence of colistin-resistant E. coli and K. pneumoniae carrying mcr-1 on transferrable plasmids in poultry and pig slaughterhouses and indicate their dissemination into surface water.

Genomic background of a colistin-resistant and highly virulent MCR-1-positive Escherichia coli ST6395 from a broiler chicken in Pakistan

The convergence of high virulence and multidrug resistance (MDR) in Gram-negative pathogens circulating at the human-animal interface is a critical public health issue. We hereby report the genomic characteristics and virulent behavior of a colistin-resistant Escherichia coli, serotype ONT:H26, belonging to ST6395, isolated from a healthy broiler in Pakistan. This strain harbored multiple antimicrobial resistance genes, including mcr-1.1 and blaCARB-2, besides cma (colicin M) and astA [heat-stable enterotoxin 1 (EAST1) toxin] virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that MCR-1-positive E. coli ST6395 killed 96.4% of the larvae at 18 hour post-infection. Interplay between resistance and virulence in clinically important pathogens could be a potential threat, representing a serious challenge to global public health.

Farm animals and aquaculture: significant reservoirs of mobile colistin resistance genes

Colistin resistance has attracted substantial attention after colistin was considered as a last-resort drug for the treatment of infections caused by carbapenem-resistant and/or multidrug-resistant (MDR) Gram-negative bacteria in clinical settings. However, with the discovery of highly mobile colistin resistance (mcr) genes, colistin resistance has become an increasingly urgent issue worldwide. Despite many reviews, which summarized the prevalence, mechanisms, and structures of these genes in bacteria of human and animal origin, studies on the prevalence of mobile colistin resistance genes in aquaculture and their transmission between animals and humans remain scarce. Herein, we review recent reports on the prevalence of colistin resistance genes in animals, especially wildlife and aquaculture, and their possibility of transmission to humans via the food chain. This review also gives some insights into the routine surveillance, changing policy and replacement of polymyxins by polymyxin derivatives, molecular inhibitors, and traditional Chinese medicine to tackle colistin resistance.

Molecular epidemiology of mcr gene group

Colistin and polymyxin B are the “last reserve” antimicrobials for the treatment of extensively drug-resistant Gram-negative bacterial infections. The rapidly increasing prevalence of polymyxin resistance mediated by the mcr gene localized on plasmid DNA currently poses a high epidemiological threat. In order to control a distribution of mcr genes, it is necessary to develop highly accurate, highly sensitive and easy-to-use diagnostic tools. This paper provides a review of the most relevant studies on the molecular epidemiology as well as current approaches to microbiological and molecular detection of mcr group genes.

Characterization of mcr-1-Harboring Plasmids from Pan Drug-Resistant Escherichia coli Strains Isolated from Retail Raw Chicken in South Korea

A number of studies from different countries have characterized mcr-1-harboring plasmids isolated from food; however, nothing has been reported about it in South Korea. In this study, we report the characterization of mcr-1 plasmids from pan drug-resistant (PDR) Escherichia coli strains isolated from retail food in the country. Colistin-resistant E. coli strains were isolated from retail raw chicken, and PCR was carried out to detect the mcr-1 gene. Whole genome sequencing of the mcr-1-positive strains was performed for further characterization. The results of whole genome sequencing revealed that all mcr-1 plasmids belonged to the IncI2 type. In addition to the mcr-1 plasmids, all of the isolates also carried additional plasmids possessing multiple antibiotic resistance genes, and the PDR was mediated by resistant plasmids except for fluoroquinolone resistance resulting from mutations in gyrA and parC. Interestingly, the mcr-1 plasmids were transferred by conjugation to other pathogenic strains including enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), Salmonella, and Klebsiella at the frequencies of 10⁻³−10⁻⁶, 10⁻²−10⁻⁵, 10⁻⁴−10⁻⁵, 10⁻⁴−10⁻⁶, and 10⁻⁵−10⁻⁶, respectively. The results showed that mcr-1 plasmids can be easily transmitted to pathogenic bacteria by conjugation.

The rise and spread of mcr plasmid-mediated polymyxin resistance

Polymyxins are important lipopeptide antibiotics that serve as the last-line defense against multidrug-resistant (MDR) Gram-negative bacterial infections. Worryingly, the clinical utility of polymyxins is currently facing a serious threat with the global dissemination of mcr, plasmid-mediated polymyxin resistance. The first plasmid-mediated polymyxin resistance gene, termed as mcr-1 was identified in China in November 2015. Following its discovery, isolates carrying mcr, mainly mcr-1 and less commonly mcr-2 to -7, have been reported across Asia, Africa, Europe, North America, South America and Oceania. This review covers the epidemiological, microbiological and genomics aspects of this emerging threat to global human health. The mcr has been identified in various species of Gram-negative bacteria including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Salmonella enterica, Cronobacter sakazakii, Kluyvera ascorbata, Shigella sonnei, Citrobacter freundii, Citrobacter braakii, Raoultella ornithinolytica, Proteus mirabilis, Aeromonas, Moraxella and Enterobacter species from animal, meat, food product, environment and human sources. More alarmingly is the detection of mcr in extended-spectrum-β-lactamases- and carbapenemases-producing bacteria. The mcr can be carried by different plasmids, demonstrating the high diversity of mcr plasmid reservoirs. Our review analyses the current knowledge on the emergence of mcr-mediated polymyxin resistance.

Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments

Antibiotic resistance genes (ARGs) in the environment are promoted by anthropogenic activities, which cause potential risks to human health. However, large-scale quantitative data on antibiotic resistome from the pristine and anthropogenic environments remains largely unexplored. Here, we used metagenome-wide analysis to investigate the share and divergence in ARG profiles and their potential bacterial hosts between the pristine and gut-associated environments. We found that the abundance of total ARGs in gut-associated environments was significantly higher than the pristine environments (P < 0.001). The mcr-1 and tetX, the genes resistant to the last resort antibiotics (colistin and tigecycline, respectively), were in high abundance (4.57 copies/Gb and 3.39 copies/Gb, respectively) in gut-associated environments, suggesting the ARG pollution caused by anthropogenic antibiotics. Metagenomic assembly-based host-tracking analysis identified Escherichia, Bacteroides, and Clostridium as the predominant bacterial hosts of ARGs in gut-associated environments, while Alteromonas, Vibrio, and Proteobacteria as the predominant bacterial hosts of ARGs in pristine environments. We first described the broad diversity of ARG hosts in different environments using metagenome-wide analysis. Our results revealed the heterogeneous distribution of ARGs and their hosts among different microbial niches in gut-associated environments and the pristine environments.

The first report of emerging mobilized colistin-resistance (mcr) genes and ERIC-PCR typing in Escherichia coli and Klebsiella pneumoniae clinical isolates in southwest Iran

Background: The emergence of the plasmid-mediated mcr colistin-resistance gene in bacteria poses a potential threat for treatment of patients, especially when hospitalized. The aims of this study were to search for the presence of mcr-1 and mcr-2 genes among colistin-resistant Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) isolates from clinical specimens and to determine the fingerprint of strains by enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) method.

Methods: In this study, 712 nonduplicate Enterobacteriaceae isolates from clinical specimens were examined. All of the isolates were subcultured on suitable media, and the isolated colonies were identified by standard biochemical tests. Antimicrobial susceptibility test on 7 antibiotics was performed by disk diffusion method, and minimal inhibitory concentration (MIC) of isolates to colistin was determined by the E-test method. These isolates were typed by ERIC-PCR method, and the presence of mcr-1 and mcr-2 genes was investigated by PCR method.

Results: Out of 712 nonduplicate Enterobacteriaceae, 470 isolates, including 351 (74.7%) E. coli and 119 (25.3%) K. pneumoniae, were detected. The results of antibiogram tests showed that most of the isolates (81.3%) were resistant to ceftazidime; however, the most susceptibility among of E. coli and K. pneumoniae isolates was observed (81.5%) to colistin. The typing results by ERIC-PCR method showed 36 and 23 fingerprint patterns for colistin-resistant E. coli and K. pneumoniae strains, respectively. Among 64 (13.6%) colistin-phenotypically-resistant Enterobacteriaceae, 8 isolates (1.7%) had mcr-1 gene. These 8 isolates were attributed to E. coli and K. pneumoniae with 6 and 2 isolates, respectively. Whereas no isolates carrying the mcr-2 gene was found. These colistin-resistant isolates displayed colistin MIC values >2 μg/ml in the antibiotic concentration by E-test method.

Conclusion: Spreading of Enterobacteriaceae strains harboring plasmid-mediated mcr could fail the colistin-included therapy regimen as the last line of treatment against multidrug-resistant bacterial infections.

The emergence of mcr-1-mediated colistin-resistant Escherichia coli and Klebsiella pneumoniae in domestic and imported turkey meat in the Czech Republic 2017-2018

We investigated the occurrence of plasmid-mediated colistin resistance in Enterobacteriaceae in turkey meat produced in the Czech Republic as well as in turkey meat imported into the Czech Republic from other European Union countries. Seventeen samples of raw turkey meat from the Czech Republic (n = 4), Hungary (n = 2), Poland (n = 6) and Germany (n = 5) were cultured in peptone water at 37 °C overnight and the enriched cultures were tested for the presence of mcr-1-5 genes. PCR-positive enriched cultures were inoculated onto selective agar with colistin (3.5 mg/L). A minimal inhibitory concentration (MIC) of colistin was determined by using the broth microdilution method in PCR-positive isolates. In addition, a macrorestriction analysis was performed using XbaI endonuclease. Of 17 meat samples, 12 samples from Poland (6/6), Germany (3/5) and the Czech Republic (3/4) proved positive for the presence of the mcr-1 gene. Forty-two isolates carrying the mcr-1 gene were obtained: Escherichia coli (n = 39) revealing 32 distinct XbaI profiles and Klebsiella pneumoniae (n = 3) with 2 distinct XbaI profiles. The minimal inhibitory concentration (MIC) of the mcr-1 positive isolates was as follows: 4 mg/L (n = 28), 8 mg/L (n = 12), 32 mg/L (n = 1) and 64 mg/L (n = 1). The high prevalence (70.6%; 12/17 samples) of mcr-1-mediated colistin-resistant Enterobacteriaceae found in the turkey meat samples analysed in this study, builds on previously published evidence that poultry, and their products, represent a substantial risk for the dissemination of plasmid-mediated colistin resistance in Europe.