High Incidence of Escherichia coli Strains Coharboring mcr-1 and blaNDM from Chickens

Rapid Dissemination of blaNDM-5 Gene among Carbapenem-Resistant Escherichia coli Isolates in a Yellow-Feather Broiler Farm via Multiple Plasmid Replicon

Although carbapenems have not been approved for animal use, carbapenem-resistant Escherichia coli (CREC) strains are increasingly being detected in food-producing animals, posing a significant public health risk. However, the epidemiological characteristics of CREC isolates in yellow-feather broiler farms remain unclear. We comprehensively investigated the genetic features of carbapenem-resistance genes among E. coli isolates recovered from a yellow-feather broiler farm in Guangdong province, China. Among the 172 isolates, 88 (51.2%) were recovered from chicken feces (88.5%, 54/61), the farm environment (51.1%, 24/47), and specimens of dead chickens (15.6%, 41/64). All CREC isolates were positive for the blaNDM-5 gene and negative for other carbapenem-resistance genes. Among 40 randomly selected isolates subjected to whole-genome sequencing, 10 belonged to distinct sequence types (STs), with ST167 (n = 12) being the most prevalent across different sources, suggesting that the dissemination of blaNDM-5 was mainly due to horizontal and clonal transmission. Plasmid analysis indicated that IncX3, IncHI2, and IncR-X1-X3 hybrid plasmids were responsible for the rapid transmission of the blaNDM-5 gene, and the genetic surrounding of blaNDM-5 contained a common mobile element of the genetic fragment designated "IS5-△ISAba125-blaNDM-5-bleMBL-trpF-dsbC". These findings demonstrate a critical role of multiple plasmid replicons in the dissemination of blaNDM-5 and carbapenem resistance.

A CRISPR/Cas12a-Based System for Sensitive Detection of Antimicrobial-Resistant Genes in Carbapenem-Resistant Enterobacterales

Antimicrobial-resistant (AMR) bacteria pose a significant global health threat, and bacteria that produce New Delhi metallo-β-lactamase (NDM) are particularly concerning due to their resistance to most β-lactam antibiotics, including carbapenems. The emergence and spread of NDM-producing genes in food-producing animals highlight the need for a fast and accurate method for detecting AMR bacteria. We therefore propose a PCR-coupled CRISPR/Cas12a-based fluorescence assay that can detect NDM-producing genes (blaNDM) in bacteria. Thanks to its designed gRNA, this CRISPR/Cas12a system was able to simultaneously cleave PCR amplicons and ssDNA-FQ reporters, generating fluorescence signals. Our method was found to be highly specific when tested against other foodborne pathogens that do not carry blaNDM and also demonstrated an excellent capability to distinguish single-nucleotide polymorphism. In the case of blaNDM-1 carrying E. coli, the assay performed exceptionally well, with a detection limit of 2.7 × 100 CFU/mL: 100 times better than conventional PCR with gel electrophoresis. Moreover, the developed assay detected AMR bacteria in food samples and exhibited enhanced performance compared to previously published real-time PCR assays. Thus, this novel PCR-coupled CRISPR/Cas12a-based fluorescence assay has considerable potential to improve current approaches to AMR gene detection and thereby contribute to mitigating the global threat of AMR.

Molecular characteristic of mcr-1 gene in Escherichia coli from aquatic products in Guangdong, China

OBJECTIVES

Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study aimed to determine the prevalence of colistin-resistant mcr-like genes in Enterobacteriales in aquatic products, which may be contribute to the transfer of ARGs in water environments.

METHODS

The mcr-1-positive Escherichia coli were recovered from 123 freshwater fish and 34 cultured crocodile cecum samples from 10 farmers' markets in Guangdong, China. Minimum inhibitory concentration (MIC) was determined using the agar dilution method. Genotyping was performed using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Conjugation assay was carried out to investigate the transferability of mcr-1. Genomic information was obtained by whole genome sequencing (WGS) and bioinformatic analysis.

RESULTS

Forty-four mcr-1 positive isolates showed co-resistance to tetracycline, trimethoprim/sulfamethoxazole, and gentamicin, while they were all sensitive to tigecycline, meropenem, and amikacin. They were typed into sixteen PFGE clusters. ST10 and ST117 were the most popular sequence types, followed by ST1114. S1-PFGE verified the presence of the mcr-1 gene on plasmids in sizes of ∼60 kb (n = 1) and ∼240 kb (n = 3). Whole genome sequencing-based analysis identified mcr-1 integrated in IncHI2 plasmid (n = 3), IncI2 plasmid (n = 2), and bacterial chromosome in two copies (n = 1). In addition to mcr-1, they carried several other antibiotic resistance genes, such as blaCTX-M-14, fosA3, and aac(6')-Ib-cr.

CONCLUSION

These data suggest that aquatic products are an important antibiotic resistance reservoir and highlight possible risks regarding food safety.

Fosfomycin resistance mechanisms in Enterobacterales: an increasing threat

Antimicrobial resistance is well-known to be a global health and development threat. Due to the decrease of effective antimicrobials, re-evaluation in clinical practice of old antibiotics, as fosfomycin (FOS), have been necessary. FOS is a phosphonic acid derivate that regained interest in clinical practice for the treatment of complicated infection by multi-drug resistant (MDR) bacteria. Globally, FOS resistant Gram-negative pathogens are raising, affecting the public health, and compromising the use of the antibiotic. In particular, the increased prevalence of FOS resistance (FOS^R) profiles among Enterobacterales family is concerning. Decrease in FOS effectiveness can be caused by i) alteration of FOS influx inside bacterial cell or ii) acquiring antimicrobial resistance genes. In this review, we investigate the main components implicated in FOS flow and report specific mutations that affect FOS influx inside bacterial cell and, thus, its effectiveness. FosA enzymes were identified in 1980 from Serratia marcescens but only in recent years the scientific community has started studying their spread. We summarize the global epidemiology of FosA/C2/L1-2 enzymes among Enterobacterales family. To date, 11 different variants of FosA have been reported globally. Among acquired mechanisms, FosA3 is the most spread variant in Enterobacterales, followed by FosA7 and FosA5. Based on recently published studies, we clarify and represent the molecular and genetic composition of fosA/C2 genes enviroment, analyzing the mechanisms by which such genes are slowly transmitting in emerging and high-risk clones, such as E. coli ST69 and ST131, and K. pneumoniae ST11. FOS is indicated as first line option against uncomplicated urinary tract infections and shows remarkable qualities in combination with other antibiotics. A rapid and accurate identification of FOS^R type in Enterobacterales is difficult to achieve due to the lack of commercial phenotypic susceptibility tests and of rapid systems for MIC detection.

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.

High prevalence and genomic characteristics of carbapenem-resistant Enterobacteriaceae and colistin-resistant Enterobacteriaceae from large-scale rivers in China

The widespread presence of carbapenem-resistant Enterobacteriaceae (CRE) and mcr-positive Escherichia coli (MCREC) poses a huge threat to both animal and human health. River water environments are vital reservoirs of antibiotic resistance genes, however, the prevalence and characteristics of CRE and MCREC from large-scale rivers in China have not been reported. In the current study, we sampled 86 rivers from four cities in Shandong Province, China in 2021 and analyzed the prevalence of CRE and MCREC. The bla_NDM/bla_KPC-2/mcr-positive isolates were characterized with methods including PCR, antimicrobial susceptibility testing, conjugation, replicon typing, whole-genome sequencing and phylogenetic analysis. We found that the prevalence of CRE and MCREC in 86 rivers was 16.3% (14/86) and 27.9% (24/86), respectively and eight rivers carried both mcr-1 and bla_NDM/bla_KPC-2. A total of 48 Enterobacteriaceae isolates (10 ST11 Klebsiella pneumoniae with bla_KPC-2, 12 bla_NDM-positive E. coli and 26 MCREC carrying only mcr-1) were obtained in this study and 47 displayed multidrug resistance (MDR). Notably, 10 of the 12 bla_NDM-positive E. coli isolates also harbored the mcr-1 gene. The bla_KPC-2 gene was located within mobile element ISKpn27-bla_KPC-2-ISKpn6 on novel F33:A-:B- non-conjugative MDR plasmids in ST11 K. pneumoniae. The dissemination of bla_NDM was mediated by transferable MDR IncB/O plasmids or IncX3 plasmids while mcr-1 was primarily disseminated by highly similar IncI2 plasmids. Notably, these waterborne IncB/O, IncX3 and IncI2 plasmids were all highly similar to previously identified plasmids from animal and human isolates. A phylogenomic analysis revealed that the CRE and MCREC isolates from water environments might be derived from animals and trigger infections in humans. The high prevalence of CRE and MCREC in large-scale environmental rivers is alarming and needs sustained surveillance due to the potential risk for transmission to humans via the food chain (irrigation) or direct contact.

Persistence and molecular epidemiology of blaNDM-positive Gram-negative bacteria in three broiler farms: A longitudinal study (2015-2021)

Although carbapenems have not been approved for animal use, bla_NDM-positive bacteria (NPB) are increasingly being detected in farm animals. It is important to investigate the routes and underlying mechanisms of evolution and transmission of animal-borne NPB. In this study, NPB recovered from chicken feces and environmental samples in three adjacent broiler farms were investigated. We found that 13.0% of Escherichia coli strains recovered from chicken feces during the period 2015-2016 carried the bla_NDM gene. In 2017-2021, however, as many as 55.8% chicken and environmental samples collected during the breeding period were found to harbor NPB. Importantly, such strains were detectable in samples from farmland (10.3%, 8/78), vegetable fields (7.3%, 3/41), and environment of chicken farms (25.6%, 41/160) which had been left vacant for a long period of time. Intriguingly, different sequence types of NPB became dominant in different years. Both clonal dissemination of NPB and horizontal transmission of bla_NDM-bearing plasmids were observed among different farms and among the environment niches inside and outside the farm houses. Worryingly, transmission of NPB and bla_NDM-bearing plasmids between these farms and other places was also observed. All in all, our results suggested the persistence of NPB in chickens and farm environments, presumably due to extensive contamination by exogenous materials and transmission of NPB within the farm system. These events were aggravated by the increase in antibiotic usage and poor sanitary conditions in the farm houses. Stringent control measures should be implemented to arrest transmission of animal-borne NPB to the environment and the community.

Drug resistance analysis of three types of avian-origin carbapenem-resistant Enterobacteriaceae in Shandong Province, China

Animal-derived Enterobacteriaceae bacteria such as Escherichia coli (E. coli), Proteus mirabilis (P. mirabilis), and Klebsiella pneumoniae (K. pneumoniae) are important food-borne zoonotic bacilli that exist widely in the broiler-breeding industry. Although carbapenem antibiotics are considered to be the last line of defense against multidrug-resistant bacteria, carbapenem-resistant Enterobacteriaceae (CRE) break through them. In our study, we therefore, examined the prevalence of CRE and characteristics of antimicrobial resistance in 6 conventional broiler-fattening farms in Shandong Province, China. Our study revealed isolation rates of 3.57% (6/168) for carbapenem-resistant E. coli, 10% (5/50) for carbapenem-resistant P. mirabilis, and 3.03% (1/33) for carbapenem-resistant K. pneumoniae. All 12 CRE bacterial strains showed varying degrees of resistance to 27 antibiotics in 8 classes and were multidrug-resistant. The rate of the strains containing bla_NDM genes, at 91.67% (11/12), was especially high. Among other results, the carrying rate of integrons in CRE bacteria was 91.67% (11/12), and 2 strains carried both class I and class II integrons, which accelerated the lateral transmission of resistant bacteria. Our first-ever finding of the 3 CRE bacteria E. coli, P. mirabilis, and K. pneumoniae on the same broiler farm suggests that poultry-derived CRE strains may pose a risk to humans. Moreover, our findings from surveillance can inform current understandings of the prevalence and characteristics of multidrug-resistant CRE in Shandong Province and, in turn, help to curb threats to food safety and public health and better prevent and control infectious zoonotic diseases.

Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis

Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.

NDM-5-Producing Escherichia coli Co-Harboring mcr-1 Gene in Companion Animals in China

Carbapenem and colistin are important antibiotics for the treatment of infections caused by multidrug-resistant Gram-negative pathogens. Here, we isolated the blaNDM-5-harboring Escherichia coli in companion animals in healthy or diseased companion animals from veterinary clinics in six cities in China from July to November 2016. A total of 129 rectal swabs of healthy or diseased dogs and cats were collected from veterinary clinics in six different cities in China, and the isolates were subjected to carbapenem and colistin susceptibility testing. Resistance genes were confirmed using PCR. Conjugation experiments were conducted to determine the transferability of antibiotic resistance genes (ARGs) in the strains. The isolated rate of blaNDM-5-harboring E. coli strains was 3.88% (five strains). These five strains were multidrug resistant to at least three antibiotics and corresponded to four sequence types including ST101. The blaNDM-5 gene was located on 46 kb IncX3 plasmids in these five strains, and the genetic contexts were shared and were nearly identical to the K. pneumoniae plasmid pNDM5-IncX3 from China. In addition, one strain (CQ6-1) co-harbored blaNDM-5-encoding-IncX3 plasmid along with a mcr-1-encoding-IncX4 plasmid, and their corresponding genetic environments were identical to the blaNDM-5-IncX3 and mcr-1-IncX4 hybrid plasmid reported previously from the same area and from the same clinic. The results indicated that the similar genetic contexts were shared between these isolates from companion animals, and the IncX3-type plasmids played a key role in the spread of blaNDM-5 among these bacteria.

Characterization and Public Health Insights of the New Delhi Metallo-β-Lactamase-Producing Enterobacterales from Laying Hens in China

The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) were isolated from laying hens in China for the surveillance of antibiotic-resistant pathogens, and all were found to be multi-drug resistant bacteria. The genomic analysis of these NDM-positive bacteria revealed the ST167, ST617, and ST410 of the fifteen ST-type E. coli clones and ST37 of the four ST-type K. pneumoniae clones to be the same types as the human-derived strains. Among them, some new clone types were also found. Most of the bla_NDM genes (bla_NDM-1 or bla_NDM-5) were on the IncX3 plasmids (n = 80) and were distributed in E. coli, K. pneumoniae, and E. cloacae, while the remaining bla_NDM-5 genes were harbored in the E. coli ST167 with IncFII plasmids (n = 15). The typeⅠ1 of the eight IncX3 plasmid subtypes was consistent with the human-derived pNDM5_020001 plasmid (accession no. CP032424). In addition, these two plasmids did not affect the growth of the host bacteria and could be reproduced stably without antibiotics. Our study revealed the high genetic propensity of the NDM-positive Enterobacterales from the laying hens and human commensal Enterobacterales, suggesting the potentially enormous risk of its transmission to humans.

Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses

Gram-negative bacteria (GNB) continue to develop resistance against important antibiotics including last-resort ones such as carbapenems and polymyxins. An analysis of GNB with co-resistance to carbapenems and polymyxins from a One Health perspective is presented. Data of species name, country, source of isolation, resistance genes (ARGs), plasmid type, clones, and mobile genetic elements (MGEs) were deduced from 129 articles from January 2016 to March 2021. Available genomes and plasmids were obtained from PATRIC and NCBI. Resistomes and methylomes were analysed using BAcWGSTdb and REBASE whilst Kaptive was used to predict capsule typing. Plasmids and other MEGs were identified using MGE Finder and ResFinder. Phylogenetic analyses were done using RAxML and annotated with MEGA 7. A total of 877 isolates, 32 genomes and 44 plasmid sequences were analysed. Most of these isolates were reported in Asian countries and were isolated from clinical, animal, and environmental sources. Colistin resistance was mostly mediated by mgrB inactivation (37%; n = 322) and mcr-1 (36%; n = 312), while OXA-48/181 was the most reported carbapenemase. IncX and IncI were the most common plasmids hosting carbapenemases and mcr genes. The isolates were co-resistant to other antibiotics, with floR (chloramphenicol) and fosA3 (fosfomycin) being common; E. coli ST156 and K. pneumoniae ST258 strains were common globally. Virulence genes and capsular KL-types were also detected. Type I, II, III and IV restriction modification systems were detected, comprising various MTases and restriction enzymes. The escalation of highly resistant isolates drains the economy due to untreatable bacterial infections, which leads to increasing global mortality rates and healthcare costs. This article is protected by copyright. All rights reserved.

Updates on the global dissemination of colistin-resistant Escherichia coli: An emerging threat to public health

Colistin drug resistance is an emerging public health threat worldwide. The adaptability, existence and spread of colistin drug resistance in multiple reservoirs and ecological environmental settings is significantly increasing the rate of occurrence of multidrug resistant (MDR) bacteria such as Escherichia coli (E. coli). Here, we summarized the reports regarding molecular and biological characterization of mobile colistin resistance gene (mcr)-positive E. coli (MCRPEC), originating from diverse reservoirs, including but not limited to humans, environment, waste water treatment plants, wild, pets, and food producing animals. The MCRPEC revealed the abundance of clinically important resistance genes, which are responsible for MDR profile. A number of plasmid replicon types such as IncI2, IncX4, IncP, IncX, and IncFII with a predominance of IncI2 were facilitating the spread of colistin resistance. This study concludes the distribution of multiple sequence types of E. coli carrying mcr gene variants, which are possible threat to "One Health" perspective. In addition, we have briefly explained the newly known mechanisms of colistin resistance i.e. plasmid-encoded resistance determinant as well as presented the chromosomally-encoded resistance mechanisms. The transposition of ISApl1 into the chromosome and existence of intact Tn6330 are important for transmission and stability for mcr gene. Further, genetic environment of co-localized mcr gene with carbapenem-resistance or extended-spectrum β-lactamases genes has also been elaborated, which is limiting human beings to choose last resort antibiotics. Finally, environmental health and safety control measures along with spread mechanisms of mcr genes are discussed to avoid further propagation and environmental hazards of colistin resistance.

Emergence of IncHI2 Plasmid-Harboring blaNDM-5 from Porcine Escherichia coli Isolates in Guangdong, China

Carbapenem resistance has posed potential harmful risks to human and animals. The objectives of this study were to understand the prevalence of bla_NDM-5 in pigs and investigate the molecular characteristics of NDM-5-producing Escherichia coli isolates in Guangdong province in China. Carbapenem-resistant E. coli isolates were isolated from pigs and obtained using MacConkey plates containing 0.5 mg/L meropenem. Conjugation assay and antimicrobial susceptibility testing were conducted for the isolates and their transconjugants. Whole-genome sequence (WGS) was used to analyze the plasmid genetic feature. A total of five bla_NDM-5-carrying E. coli isolates were obtained in the present investigations. They belonged to five ST types. The bla_NDM-5 genes were found to be in IncX3 and IncHI2 plasmid. The IncX3 plasmid was 46,161 bp in size and identical to other reports. IncHI2 plasmid was 246,593 bp in size and similar to other IncHI2-ST3 plasmids. It consisted of a typical IncHI2 plasmid backbone region and a multiresistance region (MRR). The bla_NDM-5 was closely associated with the IS3000-ISAba125-blaNDM-5-bleMBL-trpF-tat-IS26 unit. We first reported the bla_NDM-5-carrying IncHI2 in E. coli isolates recovered from pigs and revealed the molecular characterization. Continued surveillance for the dissemination of bla_NDM-5 among food-producing animals is required.

IS26 Is Responsible for the Evolution and Transmission of blaNDM-Harboring Plasmids in Escherichia coli of Poultry Origin in China

Carbapenem-resistant Enterobacteriaceae are some of the most important pathogens responsible for nosocomial infections, which can be challenging to treat. The bla_NDM carbapenemase genes, which are expressed by New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli isolates, have been found in humans, environmental samples, and multiple other sources worldwide. Importantly, these genes have also been found in farm animals, which are considered an NDM reservoir and an important source of human infections. However, the dynamic evolution of bla_NDM genetic contexts and bla_NDM-harboring plasmids has not been directly observed, making it difficult to assess the extent of horizontal dissemination of the bla_NDM gene. In this study, we detected NDM-1 (n = 1), NDM-5 (n = 24), and NDM-9 (n = 8) variants expressed by E. coli strains isolated from poultry in China from 2016 to 2017. By analyzing the immediate genetic environment of the bla_NDM genes, we found that IS26 was associated with multiple types of bla_NDM multidrug resistance regions, and we identified various IS26-derived circular intermediates. Importantly, in E. coli strain GD33, we propose that IncHI2 and IncI1 plasmids can fuse when IS26 is present. Our analysis of the IS26 elements flanking bla_NDM allowed us to propose an important role for IS26 elements in the evolution of multidrug-resistant regions (MRRs) and in the dissemination of bla_NDM. To the best of our knowledge, this is the first description of the dynamic evolution of bla_NDM genetic contexts and bla_NDM-harboring plasmids. These findings could help proactively limit the transmission of these NDM-producing isolates from food animals to humans. IMPORTANCE Carbapenem resistance in members of the order Enterobacterales is a growing public health problem that is associated with high mortality in developing and industrialized countries. Moreover, in the field of veterinary medicine, the occurrence of New Delhi metallo-β-lactamase-producing Escherichia coli isolates in animals, especially food-producing animals, has become a growing concern in recent years. The wide dissemination of bla_NDM is closely related to mobile genetic elements (MGEs) and plasmids. Although previous analyses have explored the association of many different MGEs with mobilization of bla_NDM, little is known about the evolution of various genetic contexts of bla_NDM in E. coli. Here, we report the important role of IS26 in forming multiple types of bla_NDM multidrug resistance cassettes and the dynamic recombination of plasmids bearing bla_NDM. These results suggest that significant attention should be paid to monitoring the transmission and further evolution of bla_NDM-harboring plasmids among E. coli strains of food animal origin.

The Emergence and Molecular Characteristics of New Delhi Metallo β-Lactamase-Producing Escherichia coli From Ducks in Guangdong, China

This study aimed to determine the prevalence and transmission characteristics of New Delhi metallo β-lactamase (NDM)-producing Escherichia coli from ducks in Guangdong, China. In this study, a total of 28 NDM-producing E. coli isolates were recovered from 88 unduplicated diseased duck samples (31.8%) from veterinary clinics in Guangzhou, Foshan, Qingyuan, and Huizhou. Two variants, bla _NDM-1 and bla _NDM-5, were detected and the latter was present in 89.6% of the isolates (25/28). Multilocus sequence typing (MLST) analysis indicated that these E. coli isolates possessed six distinct STs, and ST156 was the most prevalent followed by ST648, ST746, ST354, ST10, and ST162. In addition, phylogenomic analysis found that two of the isolates that were recovered from a single sample possessed different genomes, and the bla _NDM-carrying IncX3 plasmids may be horizontal transfer between E. coli isolates in the intestinal tracts of ducks. Whole-genome sequencing (WGS) analysis further revealed that bla _NDM co-existed with other 25 types of antimicrobial resistance genes (ARGs), of which 16 ARGs were highly prevalent with detection rates >50%, and a high incidence of coproducing bla _NDM and mcr-1 E. coli isolates (22/88, 25.0%) was detected in ducks. This study underscores the importance of surveillance for bla _NDM-harboring microbes in ducks.

Molecular epidemiology of carbapenemase-producing Escherichia coli from duck farms in south-east coastal China

OBJECTIVES

To determine the dissemination and molecular characteristics of NDM-producing Escherichia coli strains from duck farms in south-east coastal China and their threats to human health.

METHODS

A total of 232 NDM-producing E. coli were recovered from 1505 samples collected from 25 duck farms and their surrounding environments in five provinces in China. Resistance genes were confirmed using PCR. Genomic characteristics of the carbapenemase-producing isolates were determined by WGS and bioinformatic analysis.

RESULTS

The rate of NDM-positive E. coli detected in samples from the five provinces ranged from 3.7% to 28.5%. There was substantial variation in the prevalence of NDM-positive E. coli from different duck farms in each province studied. Three variants (blaNDM-1, blaNDM-4 and blaNDM-5) were found in 232 NDM-positive E. coli; blaNDM-5 (94.8%, 220/232) was the most prevalent. WGS analysis indicated that ST746, ST48, ST1011 and ST167 E. coli isolates were prevalent in the current study and poultry was likely the primary reservoir for NDM-positive ST746 and ST48 E. coli in China. Phylogenomic analysis showed that NDM-positive E. coli isolates from ducks were closely related to those of human origin. In addition, WGS analysis further revealed that blaNDM co-existed with other antibiotic resistance genes, conferring resistance to nine classes of antimicrobials.

CONCLUSIONS

This study revealed that ducks farm in China are an important reservoir for NDM-positive E. coli and STs of the isolates showed obvious distinctive diversities in geographical distribution. The distribution and spread of NDM-positive E. coli in duck farms poses a threat to public health.

Emergence of blaNDM-9-bearing tigecycline-resistant Klebsiella aerogenes of chicken origin

OBJECTIVES

The aim of this study was to characterise a tigecycline-resistant bla_NDM-9-bearing Klebsiella aerogenes strain (HNHF1) of chicken origin.

METHODS

Strain HNHF1 was characterised by phenotypic antimicrobial susceptibility testing, PCR, conjugation assays, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), whole-genome sequencing and bioinformatics analysis.

RESULTS

The bla_NDM-9 gene was located on an IncHI2 plasmid (pHNHF1_NDM-9) carrying various antimicrobial resistance genes. Moreover, the genetic context ΔISAba125-bla_NDM-9-ble_MBL-trpF is similar to other bla_NDM-bearing genetic contexts. TA cloning experiments showed that tet(A) variants may play a partial role in high-level tigecycline resistance in HNHF1.

CONCLUSION

This is the first report of a tigecycline-resistant bla_NDM-9-bearing IncHI2 plasmid in a K. aerogenes ST4 isolate of animal origin, which poses a great threat to public health. Further comprehensive surveillance is needed.

Perspective on Clinically-Relevant Antimicrobial Resistant Enterobacterales in Food: Closing the Gaps Using Genomics

Antimicrobial resistance is one of the most important public health concerns—it causes 700,000 deaths annually according to the World Health Organization (WHO). Enterobacterales such as E. coli and Klebsiella pneumoniae, have become resistant to many relevant antimicrobials including carbapenems and extended spectrum cephalosporins. These clinically relevant resistant Enterobacterales (CRRE) members are now globally distributed in the environment including different food types (meats, produce, dairy). Unlike known foodborne pathogens, CRRE are not usually part of most food surveillance systems. However, numerous reports of CRRE highlight the importance of these bacteria in food and have been shown to contribute to the overall crisis of antimicrobial resistance. This is especially important in the context of carriage of these pathogens by immuno-compromised individuals. CRRE infections upon consumption of contaminated food could colonize the human gastrointestinal tract and eventually be a source of systemic infections such as urinary tract infections or septicemia. While different aspects need to be considered to elucidate this, whole genome sequencing along with metadata could be used to understand genomic relationships of CRRE obtained from foods and humans, including isolates from clinical infections. Once robust scientific data is available on the role of CRRE in food, countries could move forward to better survey and control CRRE in food.

Occurrence and Transmission of bla NDM-Carrying Enterobacteriaceae from Geese and the Surrounding Environment on a Commercial Goose Farm

We investigated the prevalence and transmission of NDM-producing Enterobacteriaceae in fecal samples of geese and environmental samples from a goose farm in southern China. The samples were cultivated on MacConkey agar plates supplemented with meropenem. Individual colonies were examined for bla _NDM, and bla _NDM-positive bacteria were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. Of 117 samples analyzed, the carriage rates for New Delhi metallo-β-lactamase (NDM)-positive Enterobacteriaceae were 47.1, 18, and 50% in geese, inanimate environments (sewage, soil, fodder, and dust), and mouse samples, respectively. Two variants (bla _NDM-1 and bla _NDM-5, in 4 and 40 isolates, respectively) were found among 44 bla _NDM-positive Enterobacteriaceae; these variants belonged to eight species, and Escherichia coli was the most prevalent (50%). WGS analysis revealed that bla _NDM coexisted with diverse antibiotic resistance genes (ARGs). Population structure analysis showed that most E. coli and Enterobacter sp. isolates were highly heterogeneous, while most Citrobacter sp. and P. stuartii isolates possessed extremely high genetic similarities. In addition, bla _NDM-5-positive ST4358/ST48 E. coli isolates were found to be clonally spread between geese and the environment and were highly genetically similar to those reported from ducks, farm environments, and humans in China. Plasmid analysis indicated that IncX3 pHNYX644-1-like (n = 40) and untypeable pM2-1-like plasmids (n = 4) mediated bla _NDM spread. pM2-1-like plasmids possessed diverse ARGs, including bla _NDM-1, the arsenical and mercury resistance operons, and the maltose operon. Our findings revealed that the goose farm is a reservoir for NDM-positive Enterobacteriaceae The bla _NDM contamination of wild mice and the novel pM2-1-like plasmid described here likely adds to the risk for dissemination of bla _NDM and associated resistance genes.IMPORTANCE Carbapenem-resistant bacteria, in particular NDM-producing Enterobacteriaceae, have become a great threat to global public. These bacteria have been found not only in hospital and community environments but also among food animal production chains, which are recognized as reservoirs for NDM-producing Enterobacteriaceae However, the dissemination of NDM-producing bacteria in waterfowl farms has been less well explored. Our study demonstrates that the horizontal spread of bla _NDM-carrying plasmids and the partial clonal spread of bla _NDM-positive Enterobacteriaceae contribute to the widespread contamination of bla _NDM in the goose farm ecosystem, including mice. Furthermore, we found a novel and transferable bla _NDM-1-carrying multidrug resistance (MDR) plasmid that possessed multiple environmental adaptation-related genes. The outcomes of this study contribute to a better understanding of the prevalence and transmission of bla _NDM-carrying Enterobacteriaceae among diverse niches in the farm ecosystem.

Emergence of the Mobile Colistin Resistance Gene, mcr-1, in Multidrug-Resistant E. coli Isolated from the Fecal Matter of Toddlers in a Community

Colistin is one of the few first-line options for treating complicated infections with certain multidrug-resistant bacteria (1).….

Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru

The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.

Genomic Features of MCR-1 and Extended-Spectrum β-Lactamase-Producing Enterobacterales from Retail Raw Chicken in Egypt

Colistin is considered as a last resort agent for treatment of severe infections caused by carbapenem-resistant Enterobacterales (CRE). Recently, plasmid-mediated colistin resistance genes (mcr type) have been reported, mainly corresponding to mcr-1 producers. Those mcr-1-positive Enterobacterales have been identified not only from human isolates, but also from food samples, from animal specimens and from environmental samples in various parts of the world. Our study focused on the occurrence and characterization of mcr-1-positive Enterobacterales recovered from retail raw chicken in Egypt. From the 345 retail chicken carcasses collected, a total of 20 samples allowed to recover mcr-1-positive isolates (Escherichia coli, n = 19; Citrobacter freundii, n = 1). No mcr-2- to mcr-10-positive isolate was identified from those samples. The colistin resistance trait was confirmed for all those 20 isolates with a positivity of the Rapid Polymyxin NP (Nordmann-Poirel) test. Minimum inhibitory concentrations (MICs) of colistin for all MCR-1-producing isolates ranged between 4 and 16 μg/mL. Noticeably, 9 out of the 20 mcr-1-positive isolates produced an extended-spectrum β-lactamase (ESBL), respectively producing CTX-M-9 (n = 2), CTX-M-14 (n = 4), CTX-M-15 (n = 2), and SHV-12 (n = 1). Noteworthy, the fosA4 gene encoding resistance to fosfomycin was found in a single mcr-1-positive E. coli isolate, in which both genes were located on different conjugative plasmids. The pulsed-field gel electrophoresis (PFGE) patterns were identified, corresponding to 10 different sequence types (STs), highlighting the genetic diversity of those different E. coli. Whole-genome sequencing revealed three major types of mcr-1-bearing plasmids, corresponding to IncI2, IncX4, and IncHI2 scaffolds. The occurrence of MCR-1-producing multidrug-resistant Enterobacterales in retail raw chicken is of great concern, considering the possibility of transmission to humans through the food chain.

Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports

The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively.

The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.

Escherichia coli as Commensal and Pathogenic Bacteria Among Food-Producing Animals: Health Implications of Extended Spectrum β-lactamase (ESBL) Production

Simple Summary

This revision is about the problem of Escherichia coli as a commensal and pathogenic bacterium among food-producing animals and health implications. Escherichia coli may play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tract; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. The majority of E. coli strains are commensals inhabiting the intestinal tract of humans and warm-blooded animals and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. All over the word, antibiotic resistance is commonly detected among commensal bacteria from food-producing animals, raising important questions on the potential impact of antibiotic use in animals and the possible transmission of these resistant bacteria to humans through the food chain. The use, in food-producing animals, of antibiotics that are critically important in human medicine has been implicated in the emergence of new forms of resistant bacteria, including new strains of multidrug-resistant foodborne bacteria, such as extended spectrum β-lactamase (ESBL)-producing E. coli.

Abstract

Escherichia coli are facultative, anaerobic Gram-negative rods with many facets. Within resistant bacterial populations, they play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tracts; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. Thus, the prevalence of antimicrobial resistance in these commensal bacteria (or others, such as enterococci) can be a good indicator for the selective pressure caused by the use of antimicrobial agents, providing an early warning of the emergence of antimicrobial resistance in pathogens. As many as 90% of E. coli strains are commensals inhabiting the intestinal tracts of humans and warm-blooded animals. As a commensal, it lives in a mutually beneficial association with its hosts and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. In humans, it is the prominent cause of enteritis, community- and hospital-acquired urinary tract infection (UTI), septicemia, postsurgical peritonitis, and other clinical infections, such as neonatal meningitis, while, in farm animals, it is more prominently associated with diarrhea. On a global scale, E. coli can be considered the most important human pathogen, causing severe infection along with other major bacterial foodborne agents, such as Salmonella spp. and Campylobacter. Thus, the importance of resistance in E. coli, typically considered a benign commensal, should not be underestimated.

Letter to the Editor: Escherichia fergusonii Harboring IncHI2 Plasmid Containing mcr-1 Gene-A Novel Reservoir for Colistin Resistance in Brazil

Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii.

Prevalence of avian-origin mcr-1-positive Escherichia coli with a potential risk to humans in Tai'an, China

Multidrug-resistant (MDR) Escherichia coli are responsible for difficult-to-treat infections. We sought to determine the prevalence and characteristics of MDR E. coli strains isolated from poultry and clinical patients in the same geographical region. Eighty-seven E. coli strains were isolated from poultry with perihepatitis lesions at different slaughterhouses, and 356 nonrepetitive E. coli strains were isolated from clinical patients. All samples were continuously collected from October to December 2017 in Tai'an, China. The presence of the mcr-1 gene in the strains was assessed by PCR. The genetic relationships of the polymyxin (POL)-resistant E. coli strains were analyzed by pulsed-field gel electrophoresis and multilocus sequence typing. The results indicate that the POL resistance rate for the E. coli isolates from poultry was 31.03% (27 of 87), whereas the human-origin E. coli isolates were 100% sensitive to POL. The mcr-1 gene and extended-spectrum β-lactamase bla_CTX-M-14 genes were identified in all 27 POL-resistant avian-origin E. coli isolates. Our pulsed-field gel electrophoresis analysis suggested that the 27 strains were represented by 14 pulsotypes, among which there were 3 strains each with A, E, I, and K pulsotypes, and 1 to 2 strains represented by the other 10 pulsotypes. Furthermore, multilocus sequence typing molecular typing identified 16 sequence types, including 4 ST156 strains, 3 ST533 strains, and 1 to 2 strains represented by the remaining 14 sequence types. In summary, the E. coli strains isolated in the Tai'an area all showed the MDR phenotype, the rate of which for poultry was higher than that for humans. No POL-resistant human-origin E. coli strains were identified in the clinical patients. Our study reveals that poultry-derived MDR mcr-1-positive E. coli strains may pose a potential risk to humans, and the surveillance findings presented herein will be conducive to our understanding of the prevalence and characteristics of mcr-1-positive E. coli strains in the Tai'an area.

Retrospective Screening and Analysis of mcr-1 and bla NDM in Gram-Negative Bacteria in China, 2010-2019

Currently, Gram-negative bacteria have developed multidrug and broad-spectrum drug resistance, and the numbers of species and strains carrying mcr or bla_NDM genes are increasing. In this study, mcr-1 and bla_NDM distribution of 12,858 Gram-negative bacteria isolated from wildlife, patients, livestock, poultry and environment in 14 provinces of China from 2010 to 2019 and the antibiotics resistance in regard to polymyxins (polymyxin B and colistin) and carbapenems of positive strains were investigated. A total of 70 strains of 10 species carried the mcr-1 gene, positive rates of patients, livestock and poultry, and environmental strains were 0.62% (36/5,828), 4.07% (29/712), 5.43% (5/92), respectively. Six strains of 3 species carrying the bla_NDM gene all came from patients 0.10% (6/5,828). Two new mcr-1 gene variants (GenBank: MK965883, MK965884) were identified, one of which contains premature stop codon. The drug susceptibility results showed that all mcr-1 carriers were sensitive to carbapenems, among which, 66 strains were resistant and 4 were sensitive to polymyxins. The strains with the bla_NDM gene had different degrees of resistance to carbapenems and were sensitive to polymyxins. The findings that species carrying mcr-1 or bla_NDM genes were limited and mostly normal flora of opportunistic or low pathogenic organisms indicated that transfer of mcr-1 and bla_NDM genes between bacteria was relatively limited in China. The none detection among wildlife compared with other sources supports the speculation that the emergence of and increase in polymyxins and carbapenem-resistant strains was mainly related to the selective pressure of antibiotics.

Novel partners with colistin to increase its in vivo therapeutic effectiveness and prevent the occurrence of colistin resistance in NDM- and MCR-co-producing Escherichia coli in a murine infection model

Objectives

The emergence of NDM- and MCR-1-co-producing Escherichia coli has compromised the use of carbapenems and colistin, which are critically important in clinical therapy, and represents a severe threat to public health worldwide. Here, we demonstrate synergism of colistin combined with existing antibiotics as a potential strategy to overcome XDR E. coli co-harbouring NDM and MCR-1 genes.

Methods

To comprehensively evaluate their combined activity, antibiotic combinations were tested against 34 different E. coli strains carrying both NDM and MCR-1 genes. Antibiotic resistance profiles and molecular characteristics were investigated by susceptibility testing, PCR, MLST, S1-PFGE and WGS. Antibiotic synergistic efficacy was evaluated through in vitro chequerboard experiments and dose-response assays. A mouse model was used to confirm active combination therapies. Additionally, combinations were tested for their ability to prevent high-level colistin-resistant mutants (HLCRMs).

Results

Combinations of colistin with rifampicin, rifabutin and minocycline showed synergistic activity against 34 XDR NDM- and MCR-1-co-producing E. coli strains, restoring, in part, susceptibility to both colistin and the partnering antibiotics. The therapeutic effectiveness of colistin combined with rifampicin or minocycline was demonstrated in a mouse model. Furthermore, colistin plus rifampicin showed significant activity in preventing the occurrence of HLCRMs.

Conclusions

The synergism of colistin in combinations with rifampicin, rifabutin or minocycline offers viable therapeutic alternatives against XDR NDM- and MCR-positive E. coli.

Resistome Profiles, Plasmid Typing, and Whole-Genome Phylogenetic Tree Analyses of BlaNDM-9 and Mcr-1 Co-Harboring Escherichia coli ST617 from a Patient without a History of Farm Exposure in Korea

Recently, a bla_NDM-9 and mcr-1 co-harboring E. coli ST 617 isolate was identified from an asymptomatic carrier in Korea. An 81-year-old female was admitted to a university hospital for aortic cardiac valve repair surgery. Following surgery, she was admitted to the intensive care unit (ICU) for three days, and carbapenem-resistant E. coli YMC/2017/02/MS631 was isolated from a surveillance culture (rectal swab). Antimicrobial susceptibility testing (AST) for colistin was not performed at that time. Upon retrospective study, further AST revealed resistance to all tested antibiotics, including meropenem, imipenem, ceftazidime-avibactam, amikacin, gentamicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colistin, with the exception of tigecycline. Whole genome sequencing analyses showed that this strain belonged to the ST617 serotype O89/162: H10 and harbored three β-lactamase genes (bla_TEM-1B, bla_CTX-M-55, bla_NDM-9), mcr-1, and 14 other resistance genes. Seven plasmid replicon types (IncB, IncFII, IncI2, IncN, IncY, IncR, IncX1) were identified. Horizontal transfer of bla_NDM-9 and mcr-1 from donor cells to the recipient E. coli J53 has been observed. bla_NDM-9 and mcr-1 were carried by IncB and IncI2 plasmids, respectively. To speculate on the incidence of this strain, routine rectal swab screening to identify asymptomatic carriers might be warranted, in addition to the screening of ICU patients.

Global Burden of Colistin-Resistant Bacteria: Mobilized Colistin Resistance Genes Study (1980-2018)

Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1–9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.

Emergence of two Escherichia coli strains co-harboring mcr-1 and bla NDM in fresh vegetables from China

Background

The concurrence of mcr and carbapenemase genes among Enterobacteriaceae has been a great clinical concern. In our study, we aimed to investigate the prevalence of mcr-positive carbapenem-resistant Enterobacteriaceae (CRE) in fresh vegetables and shed light on the possibility of transmission of mcr-positive CRE via fresh vegetables.

Methods

In this study, 712 fresh vegetable samples from 10 provinces in China were collected between May 2017 and Dec 2018 and were screened for mcr and carbapenemase genes. Antibiotic susceptibilities for isolates co-harboring carbapenemase genes and mcr were determined by an agar dilution or a broth microdilution method. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analysis were also performed. Transferability of the carbapenemase/mcr-bearing plasmids was determined by conjugation, replicon typing and S1-PFGE-Southern blotting. The sequences of these plasmids were analyzed by using whole-genome sequencing with Illumina Hiseq platform.

Results

Two E. coli isolates concomitantly carrying mcr-1 and bla_NDM-5/9 from leaf rape and spinach, respectively, were found and both isolates showed multidrug resistance. Notably, mcr-1-positive 690 harboring bla_NDM-5 and 701 carrying bla_NDM-9 belonged to ST156 and ST2847, respectively, similar to the prevalent MLST types of E. coli co-carrying mcr-1 and bla_NDM from avian in our previous study. mcr-1 was on ~33-kb IncX4 plasmid or ~60-kb IncI2 plasmid, while bla_NDM-5/9 was on ~46-kb IncX3 plasmid or ~120-kb untypable plasmid. The plasmids were highly similar to those from animals and clinical patients reported in various countries.

Conclusion:E. coli isolates concomitantly carrying mcr-1 and bla_NDM-5/9 in fresh vegetables may serve as a direct source of pathogens in humans, and such discovery in fresh vegetables emphasizes the importance of prompt surveillance and intervention in limiting the spread of E. coli co-carrying bla_NDM and mcr-1. To our knowledge, this is the first report of Enterobacteriaceae co-carrying bla_NDM and mcr-1 in fresh vegetables.

Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health

Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.

Whole genome sequencing of NDM-1-producing serotype K1 ST23 hypervirulent Klebsiella pneumoniae in China

PURPOSE

The emergence and spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is causing worldwide concern, whereas NDM-producing hvKP is still rare. Here we report the complete genome sequence characteristics of an NDM-1-producing ST23 type clinical hvKP in PR China.

METHODOLOGY

Capsular polysaccharide serotyping was performed by PCR. The complete genome sequence of isolate 3214 was obtained using both the Illumina Hiseq platform and Pacbio RS platform. Multilocus sequence type was identified by submitting the genome sequence to mlst 2.0 and the antimicrobial resistance genes and plasmid replicons were identified using ResFinder and PlasmidFinder, respectively. Transferability of the blaNDM-1-bearing plasmid was determined by conjugation experiment, S1 pulsed-field gel electrophoresis and Southern hybridization.

RESULTS

Isolate 3214 was classified to ST23 and belonged to the K1 capsular serotype. The isolate's total genome size was 6 171 644 bp with a G+C content of 56.39 %, consisting of a 5 448 209 bp chromosome and seven plasmids. The resistome included 18 types of antibiotic resistance genes. Fourteen resistance genes including blaNDM-1 and blaCTX-M-14 were located on plasmids and five also including blaCTX-M-14 were in the chromosome. Plasmid pNDM_3214 carrying blaNDM-1 harboured six types of resistance genes surrounded by insertion sequences and was conjugative. The worldwide pLVPK-like virulence plasmid harbouring rmpA2 and rmpA was also found in this isolate.

CONCLUSION

This study provides basic information of phenotypic and genomic features of ST23 CR-hvKP isolate 3214. Our data highlights the potential risk of spread of NDM-1-producing ST23 hvKP.

Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9

E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS26) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the wzm-wzt genes and in silico serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli.

IMPORTANCEE. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.

Author Video: An author video summary of this article is available.

NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings

New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase able to hydrolyze almost all β-lactams. Twenty-four NDM variants have been identified in >60 species of 11 bacterial families, and several variants have enhanced carbapenemase activity. Klebsiella pneumoniae and Escherichia coli are the predominant carriers of bla _NDM, with certain sequence types (STs) (for K. pneumoniae, ST11, ST14, ST15, or ST147; for E. coli, ST167, ST410, or ST617) being the most prevalent. NDM-positive strains have been identified worldwide, with the highest prevalence in the Indian subcontinent, the Middle East, and the Balkans. Most bla _NDM-carrying plasmids belong to limited replicon types (IncX3, IncFII, or IncC). Commonly used phenotypic tests cannot specifically identify NDM. Lateral flow immunoassays specifically detect NDM, and molecular approaches remain the reference methods for detecting bla _NDM Polymyxins combined with other agents remain the mainstream options of antimicrobial treatment. Compounds able to inhibit NDM have been found, but none have been approved for clinical use. Outbreaks caused by NDM-positive strains have been reported worldwide, attributable to sources such as contaminated devices. Evidence-based guidelines on prevention and control of carbapenem-resistant Gram-negative bacteria are available, although none are specific for NDM-positive strains. NDM will remain a severe challenge in health care settings, and more studies on appropriate countermeasures are required.

Clonal Spread of Escherichia coli ST93 Carrying mcr-1-Harboring IncN1-IncHI2/ST3 Plasmid Among Companion Animals, China

The purpose of this study was to investigate the occurrence of plasmid-mediated colistin resistance gene mcr-1 in Enterobacteriaceae isolates from companion animals in Guangzhou, China. Enterobacteriaceae isolated from 180 samples collected from cats and dogs were screened for mcr-1 by PCR and sequencing. MCR-1-producing isolates were further characterized by multilocus sequence typing and pulsed-field gel electrophoresis (PFGE). Plasmid characterization was performed by conjugation, replicon typing, S1-PFGE, and Southern blot hybridization. Plasmid pHN6DS2 as a representative IncN1-IncHI2/ST3 plasmid from ST93 E. coli was fully sequenced. pHN6DS2-like plasmids were screened by PCR-mapping and sequencing. The mcr-1 gene was detected in 6.25% (8/128) Escherichia coli isolates, of which, five belonged to E. coli ST93 and had identical PFGE patterns, resistance profiles and resistance genes. mcr-1 genes were located on ∼244.4 kb plasmids (n = 6), ∼70 kb plasmids, and ∼60 kb plasmids, respectively. Among them, five mcr-1-carrying plasmids were successfully transferred to recipient by conjugation experiments, and were classified as IncN1-IncHI2/ST3 (∼244.4 kb, n = 4, all obtained from E. coli ST93), and IncI2 (∼70 kb, n = 1), respectively. Plasmid pHN6DS2 contained a typical IncHI2-type backbone, with IncN1 segment (ΔrepA-Iterons I-gshB-ΔIS1294) inserted into the multiresistance region, and was similar to other mcr-1-carrying IncHI2/ST3 plasmids from Enterobacteriaceae isolates of various origins in China. The remaining five mcr-1-bearing plasmids with sizes of ∼244.4 kb were identified to be pHN6DS2-like plasmids. In conclusion, clonal spread of ST93 E. coli isolates was occurred in companion animals in Guangzhou, China.

Characteristics of Carbapenem-Resistant Enterobacteriaceae in Ready-to-Eat Vegetables in China

Vegetables harboring bacteria resistant to antibiotics are a growing food safety issue. However, data concerning carbapenem-resistant Enterobacteriaceae (CRE) in ready-to-eat fresh vegetables is still rare. In this study, 411 vegetable samples from 36 supermarkets or farmer's markets in 18 cities in China, were analyzed for CRE. Carbapenemase-encoding genes and other resistance genes were analyzed among the CRE isolates. Plasmids carrying carbapenemase genes were studied by conjugation, replicon typing, S1-PFGE southern blot, restriction fragment length polymorphism (RFLP), and sequencing. CRE isolates were also analyzed by pulsed-field gel electrophoresis (PFGE). Ten vegetable samples yielded one or more CRE isolates. The highest detection rate of CRE (14.3%, 4/28) was found in curly endive. Twelve CRE isolates were obtained and all showed multidrug resistance: Escherichia coli, 5; Citrobacter freundii, 5; and Klebsiella pneumoniae, 2. All E. coli and C. freundii carried bla_NDM, while K. pneumoniae harbored bla_KPC−2. Notably, E. coli with bla_NDM and ST23 hypervirulent Klebsiella pneumoniae (hvKP) carrying bla_KPC−2 were found in the same cucumber sample and clonal spread of E. coli, C. freundii, and K. pneumoniae isolates were all observed between vegetable types and/or cities. IncX3 plasmids carrying bla_NDM from E. coli and C. freundii showed identical or highly similar RFLP patterns, and the sequenced IncX3 plasmid from cucumber was also identical or highly similar (99%) to the IncX3 plasmids from clinical patients reported in other countries, while bla_KPC−2 in K. pneumoniae was mediated by similar F35:A-:B1 plasmids. Our results suggest that both clonal expansion and horizontal transmission of IncX3- or F35:A-:B1-type plasmids may mediate the spread of CRE in ready-to-eat vegetables in China. The presence of CRE in ready-to-eat vegetables is alarming and constitutes a food safety issue. To our knowledge, this is the first report of either the C. freundii carrying bla_NDM, or K. pneumoniae harboring bla_KPC−2 in vegetables. This is also the first report of ST23 carbapenem-resistant hvKP strain in vegetables.

Plasmid-mediated colistin resistance in animals: current status and future directions

Colistin, a peptide antibiotic belonging to the polymyxin family, is one of the last effective drugs for the treatment of multidrug resistant Gram-negative infections. Recent discovery of a novel mobile colistin resistance gene,mcr-1, from people and food animals has caused a significant public health concern and drawn worldwide attention. Extensive usage of colistin in food animals has been proposed as a major driving force for the emergence and transmission ofmcr-1; thus, there is a worldwide trend to limit colistin usage in animal production. However, despite lack of colistin usage in food animals in the USA,mcr-1-positiveEscherichia coliisolates were still isolated from swine. In this paper, we provided an overview of colistin usage and epidemiology ofmcr-1in food animals, and summarized the current status of mechanistic and evolutionary studies of the plasmid-mediated colistin resistance. Based on published information, we further discussed several non-colistin usage risk factors that may contribute to the persistence, transmission, and emergence of colistin resistance in an animal production system. Filling the knowledge gaps identified in this review is critical for risk assessment and risk management of colistin resistance, which will facilitate proactive and effective strategies to mitigate colistin resistance in future animal production systems.

Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review

OBJECTIVES

The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans.

METHODS

We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities.

RESULTS

We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33-67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2-26% in Africa, and 1-15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16-19%.

CONCLUSIONS

The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.

Fitness Advantage of mcr-1-Bearing IncI2 and IncX4 Plasmids in Vitro

The objective of this study was to assess the impact of diverse plasmids bearing colistin resistance gene mcr-1 on host fitness. Forty-seven commensal E. coli isolates recovered from the pig farm where mcr-1 was first identified were screened for mcr-1. mcr-1-bearing plasmids were characterized by sequencing. The fitness impact of mcr-1-bearing plasmids was evaluated by in vitro competition assays. Twenty-seven (57.5%) E. coli isolates were positive for mcr-1. The mcr-1 genes were mainly located on plasmids belonging to IncI2 (n = 5), IncX4 (n = 11), IncHI2/ST3 (n = 8), IncFII (n = 2), and IncY (n = 2). InHI2 plasmids also carried other resistance genes (floR, bla_CTX-M, and fosA3) and were only detected in isolates from nursery pigs. Sequences of the representative mcr-1-bearing plasmids were almost identical to those of the corresponding plasmid types reported previously. An increase in the fitness of IncI2- and IncX4-carrying strains was observed, while the presence of IncHI2, IncFII and IncY plasmids showed a fitness cost although an insignificant fitness increase was initially observed in IncFII or IncY plasmids-containing strains. Acquisition of IncI2-type plasmid was more beneficial for host E. coli DH5α than either IncHI2 or IncX4 plasmid, while transformants with IncHI2-type plasmid presented a competitive disadvantage against IncI2 or IncX4 plasmid containing strains. In conclusion, IncI2, IncX4, and IncHI2 were the major plasmid types driving the dissemination of mcr-1 in this farm. Increased fitness or co-selection by other antimicrobials might contribute to the further dissemination of the three epidemic mcr-1-positive plasmids (IncI2, IncX4, and IncHI2) in this farm and worldwide.

Emergence of mcr-1 in Raoultella ornithinolytica and Escherichia coli Isolates from Retail Vegetables in China

The presence of mcr-1 among Enterobacteriaceae isolates collected from retail vegetables in China between 2015 and 2016 was investigated. Two Raoultella ornithinolytica and seven Escherichia coli strains recovered from lettuce and tomato samples were identified as MCR-1-producers. Similar to isolates from animals and humans, the mcr-1 gene was located on the IncHI2/ST3, IncI2, or IncX4 plasmids. The presence of MCR-1-producing organisms in ready-to-eat food samples represents a serious risk for human health.