Plasmid-borne colistin resistance gene mcr-3 in Salmonella isolates from human infections, Denmark, 2009-17

Phenotypic and genotypic antimicrobial resistance correlation and plasmid characterization in Salmonella spp. isolates from Italy reveal high heterogeneity among serovars

Introduction

The spread of antimicrobial resistance among zoonotic pathogens such as Salmonella is a serious health threat, and mobile genetic elements (MGEs) carrying antimicrobial resistance genes favor this phenomenon. In this work, phenotypic antimicrobial resistance to commonly used antimicrobials was studied, and the antimicrobial resistance genes (ARGs) and plasmid replicons associated with the resistances were determined.

Methods

Eighty-eight Italian Salmonella enterica strains (n = 88), from human, animal and food sources, isolated between 2009 and 2019, were selected to represent serovars with different frequency of isolation in human cases of salmonellosis. The presence of plasmid replicons was also investigated.

Results and discussion

Resistances to sulphonamides (23.9%), ciprofloxacin (27.3%), ampicillin (29.5%), and tetracycline (32.9%) were the most found phenotypes. ARGs identified in the genomes correlated with the phenotypical results, with blaTEM-1B, sul1, sul2, tetA and tetB genes being frequently identified. Point mutations in gyrA and parC genes were also detected, in addition to many different aminoglycoside-modifying genes, which, however, did not cause phenotypic resistance to aminoglycosides. Many genomes presented plasmid replicons, however, only a limited number of ARGs were predicted to be located on the contigs carrying these replicons. As an expectation of this, multiple ARGs were identified on contigs with IncQ1 plasmid replicon in strains belonging to the monophasic variant of Salmonella Typhimurium. In general, high variability in ARGs and plasmid replicons content was observed among isolates, highlighting a high level of heterogeneity in Salmonella enterica. Irrespective of the serovar., many of the ARGs, especially those associated with critically and highly important antimicrobials for human medicine were located together with plasmid replicons, thus favoring their successful dissemination.

Prevalence and molecular characterization of mcr-1-positive foodborne ST34-Salmonella isolates in China

Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. 4,[5],12:i:- have become the most common serovars associated with human salmonellosis worldwide. Moreover, the emergence of mcr-carrying S. Typhimurium and S. 4,[5],12:i:- with multidrug resistance (MDR) patterns has posed a threat to public health. In this study, we retrospectively screened 2009-2022 laboratory-preserved strains for the presence of mcr genes. We obtained 16 mcr-1-positive S. Typhimurium and S. 4,[5],12:i:- strains with MDR that belonged to sequence type 34 (ST34). Whole-genome sequencing analysis revealed that the mcr-1 was located on the IncI2 or IncHI2 plasmids. The ISApl1 element downstream of mcr-1 was present in all pig-derived strains. Conjugation experiments confirmed that nine mcr-1-carrying IncHI2 plasmids could not be transferred to Escherichia coli due to loss of the conjugation region. Finally, core genome single nucleotide polymorphism (cgSNP) analyses of the 16 mcr-1-carrying strains and 77 mcr-carrying ST34-Salmonella genome sequences from the NCBI and ENA databases showed that five out of eight clusters contained strains from pig and pig products, revealing pigs and pig products as key reservoirs of mcr-1-positive ST34-Salmonella strains. The transmission of mcr-carrying ST34 Salmonella strains to humans via the pig food chain is a potential cause for public health concern in controlling human salmonellosis.

Evidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34

S. 4,[5],12:i:-, a monophasic variant of S. enterica serovar Typhimurium, is an important multidrug resistant serovar. Strains of colistin-resistant S. 4,[5],12:i:- have been reported in several countries with patients occasionally had recent histories of travels to Southeast Asia. In the study herein, we investigated the genomes of S. 4,[5],12:i:- carrying mobile colistin resistance (mcr) gene in Thailand. Three isolates of mcr-3.1 carrying S. 4,[5],12:i:- in Thailand were sequenced by both Illumina and Oxford Nanopore platforms and we analyzed the sequences together with the whole genome sequences of other mcr-3 carrying S. 4,[5],12:i:- isolates available in the NCBI Pathogen Detection database. Three hundred sixty-nine core genome SNVs were identified from 27 isolates, compared to the S. Typhimurium LT2 reference genome. A maximum-likelihood phylogenetic tree was constructed and revealed that the samples could be divided into three clades, which correlated with the profiles of fljAB-hin deletions and plasmids. A couple of isolates from Denmark had the genetic profiles similar to Thai isolates, and were from the patients who had traveled to Thailand. Complete genome assembly of the three isolates revealed the insertion of a copy of IS26 at the same site near iroB, suggesting that the insertion was an initial step for the deletions of fljAB-hin regions, the hallmark of the 4,[5],12:i:- serovar. Six types of plasmid replicons were identified with the majority being IncA/C. The coexistence of mcr-3.1 and bla_CTX-M-55 was found in both hybrid-assembled IncA/C plasmids but not in IncHI2 plasmid. This study revealed possible transmission links between colistin resistant S. 4,[5],12:i:- isolates found in Thailand and Denmark and confirmed the important role of plasmids in transferring multidrug resistance.

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

Background

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

Results and discussion

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

Conclusion

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

Genomic Characterization of mcr-1-Carrying Foodborne Salmonella enterica serovar Typhimurium and Identification of a Transferable Plasmid Carrying mcr-1, bla CTX-M-14 , qnrS2, and oqxAB Genes From Ready-to-Eat Pork Product in China

Salmonella enterica resistant to colistin, third-generation cephalosporins (3GCs), and fluoroquinolones (FQs) has been deemed a high-priority pathogen by the World Health Organization (WHO). The objective of this study was to characterize 11 mcr-1-harboring Salmonella enterica serovar Typhimurium isolates from raw pork and ready-to-eat (RTE) pork products in Guangzhou, China. All isolates were multi-drug resistant and contained 6–24 antibiotic-resistant genes. The mcr-1 gene was localized in the most conserved structure (mcr-1-orf ) in eight isolates and in mobile structure (ISApl1-mcr-1-orf ) in three isolates. One raw pork isolate SH16SF0850, co-harbored mcr-1, bla_CTX−M−14, and oqxAB genes. One isolate 17Sal008 carried mcr-1, bla_CTX−M−14, qnrS2, and oqxAB genes located on a 298,622 bp IncHI2 plasmid pSal008, which was obtained from an RTE pork product for the first time. The pSal008 was closely related to a plasmid in an S. typhimurium isolate from a 1-year-old diarrheal outpatient in China and was found to be transferable to Escherichia coli J53 by conjugation. Genome sequence comparisons by core-genome Multi Locus Sequence Typing (cgMLST) based on all S. typhimurium isolates from China inferred highly probably epidemiological links between selected pork isolates and no possible epidemiologically links between RTE pork isolate 17Sal008 and other isolates. Our findings indicate that raw pork and pork products are potential reservoirs of mcr-1-harboring S. typhimurium and highlight the necessity for continuous monitoring of colistin, 3GCs, and FQs resistant S. typhimurium from different origins.

Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed

Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.

Analysis of Antimicrobial Resistance in Non-typhoidal Salmonella Collected From Pork Retail Outlets and Slaughterhouses in Vietnam Using Whole Genome Sequencing

Non-typhoidal salmonella (TS) remains a significant health burden worldwide. In Vietnam, pork accounts for 70% of the total meat consumed, and contamination with Salmonella is high. High levels of antimicrobial resistance (AMR) have emerged among porcine NTS and of particular concern is the emergence of colistin resistance, a “last defense” antibioic against multi-drug resistant (MDR) Gram-negative pathogens. This study aimed to investigate the antibiotic susceptibility of 69 NTS isolates collected from the pork retail outlets and slaughterhouses in Vietnam during 2014 a nd 2018/19. Phenotypic testing and whole genome sequencing was used to assess the serotype and AMR gene profiles of the 69 NTS isolates. Seventeen different serotypes were identified, of which S. enterica subsp enterica serotype Typhimurium was the most common followed by S. ser. Rissen, S. ser. London, S. ser. Anatum, and S. ser. Derby. Phenotype AMR was common with 41 (59.4%) isolates deemed MDR. MDR strains were most common in slaughterhouses (83%) and supermarkets (75%) and lowest in traditional markets (38%) and convenience stores (40%). Colistin resistance was identified in 18 strains (15 resistant, three intermediate) with mcr-1 identified in seven isolates (S. ser. Meleagridis, S. Rissen, S. Derby) and mcr-3 in two isolates (S. Typhimurium). This includes the first mcr positive S. Meleagridis to our knowledge. Surprisingly, boutique stores had high levels (60%) of MDR isolates including 5/20 isolates with mcr-1. This study demonstrates that pork from modern retail stores classed as supermarkets or boutique (with pork claiming to be high quality, traceable, environmentally friendly marketed toward higher income consumers) still contained NTS with high levels of AMR.

First Identification and Limited Dissemination of mcr-1 Colistin Resistance in Salmonella Isolates from Jiaxing

ABSTRACT

Salmonella, a major foodborne pathogen, causes severe gastrointestinal disease in people and animals worldwide. Plasmid-borne mcr-1, which confers colistin resistance in Salmonella, has significant epidemiological interest for public health safety. Here, we report the first evidence of mcr-1-mediated colistin resistance in one multidrug-resistant strain, 16062, from 355 Salmonella isolates collected for Jiaxing foodborne pathogen monitoring in Zhejiang Province from 2015 to 2019. In addition to colistin, 16062 displayed multidrug resistance to various antimicrobials (β-lactams, quinolone, sulfonamide, florfenicol, ampicillin, streptomycin, nalidixic acid, aminoglycoside, and trimethoprim-sulfamethoxazole). The mcr-1-carrying IncX4 plasmid (p16062-MCR) in this study shares a conserved structure with other mcr-IncX4 plasmids. We found that other antimicrobial-resistance genes (aac(6')-Ib-cr, aadA1, aadA2, aph(3')-Ia, oqxA, oqxB, sul1, and cmlA1) are located on p16062-cmlA, an atypical IncHI2 plasmid, in isolate 16062. This is the first identification of transferable colistin resistance in a foodborne Salmonella isolate collected in Jiaxing City, the 5-year monitoring of which revealed limited dissemination. By determining the genetic features of the plasmid vehicle, the characteristics of transferable mcr genes circulating in isolates from Jiaxing are now clearer.

HIGHLIGHTS

Plasmid Mediated mcr-1.1 Colistin-Resistance in Clinical Extraintestinal Escherichia coli Strains Isolated in Poland

Objectives: The growing incidence of multidrug-resistant (MDR) bacteria is an inexorable and fatal challenge in modern medicine. Colistin is a cationic polypeptide considered a “last-resort” antimicrobial for treating infections caused by MDR Gram-negative bacterial pathogens. Plasmid-borne mcr colistin resistance emerged recently, and could potentially lead to essentially untreatable infections, particularly in hospital and veterinary (livestock farming) settings. In this study, we sought to establish the molecular basis of colistin-resistance in six extraintestinal Escherichia coli strains.

Methods: Molecular investigation of colistin-resistance was performed in six extraintestinal E. coli strains isolated from patients hospitalized in Medical University Hospital, Bialystok, Poland. Complete structures of bacterial chromosomes and plasmids were recovered with use of both short- and long-read sequencing technologies and Unicycler hybrid assembly. Moreover, an electrotransformation assay was performed in order to confirm IncX4 plasmid influence on colistin-resistance phenotype in clinical E. coli strains.

Results: Here we report on the emergence of six mcr-1.1-producing extraintestinal E. coli isolates with a number of virulence factors. Mobile pEtN transferase-encoding gene, mcr-1.1, has been proved to be encoded within a type IV secretion system (T4SS)-containing 33.3 kbp IncX4 plasmid pMUB-MCR, next to the PAP2-like membrane-associated lipid phosphatase gene.

Conclusion: IncX4 mcr-containing plasmids are reported as increasingly disseminated among E. coli isolates, making it an “epidemic” plasmid, responsible for (i) dissemination of colistin-resistance determinants between different E. coli clones, and (ii) circulation between environmental, industrial, and clinical settings. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.

Whole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs

This study aimed to analyze three ESBL-producing E. coli co-harboring mcr and ESBL genes from a healthy fattening pig (E. 431) and two sick pigs (ECP.81 and ECP.82) in Thailand using Whole Genome Sequencing (WGS) using either Illumina MiSeq or HiSeq PE150 platforms to determine their genome and transmissible plasmids. E. 431 carrying mcr-2.1 and mcr-3.1 belonged to serotype O142:H31 with ST29 sequence type. ECP.81 and ECP.82 from sick pigs harboring mcr-1.1 and mcr-3.1 were serotype O9:H9 with ST10. Two mcr-1.1 gene cassettes from ECP.81 and ECP.82 were located on IncI2 plasmid with 98% identity to plasmid pHNSHP45. The mcr-2.1-carrying contig in E. 431 showed 100% identity to plasmid pKP37-BE with the upstream flanking sequence of IS1595. All three mcr-3.1-carrying contigs contained the ΔTnAs2-mcr-3.1-dgkA core segment and had high nucleotide similarity (85–100%) to mcr-3.1-carrying plasmid, pWJ1. The mobile elements i.e. IS4321, ΔTnAs2, ISKpn40 and IS3 were identified in the flanking regions of mcr-3. Several genes conferring resistance to aminoglycosides (aac(3)-IIa, aadA1, aadA2b, aph(3’’)-Ib, aph(3’)-IIa and aph(6)-Id), macrolides (mdf(A)), phenicols (cmlA1), sulphonamide (sul3) and tetracycline (tet(A) and tet(M)) were located on plasmids, of which their presence was well corresponded to the host’s resistance phenotype. Amino acid substitutions S83L and D87G in GyrA and S80I and E62K in ParC were observed. The bla_CTX-M-14 and bla_CTX-M-55 genes were identified among these isolates additionally harbored bla_TEM-1B. Co-transfer of mcr-1.1/bla_TEM-1B and mcr-3.1/bla_CTX-M-55 was observed in ECP.81 and ECP.82 but not located on the same plasmid. The results highlighted that application of advanced innovation technology of WGS in AMR monitoring and surveillance provide comprehensive information of AMR genotype that could yield invaluable benefits to development of control and prevention strategic actions plan for AMR.

Current Update on Intrinsic and Acquired Colistin Resistance Mechanisms in Bacteria

Colistin regained global interest as a consequence of the rising prevalence of multidrug-resistant Gram-negative Enterobacteriaceae. In parallel, colistin-resistant bacteria emerged in response to the unregulated use of this antibiotic. However, some Gram-negative species are intrinsically resistant to colistin activity, such as Neisseria meningitides, Burkholderia species, and Proteus mirabilis. Most identified colistin resistance usually involves modulation of lipid A that decreases or removes early charge-based interaction with colistin through up-regulation of multistep capsular polysaccharide expression. The membrane modifications occur by the addition of cationic phosphoethanolamine (pEtN) or 4-amino-l-arabinose on lipid A that results in decrease in the negative charge on the bacterial surface. Therefore, electrostatic interaction between polycationic colistin and lipopolysaccharide (LPS) is halted. It has been reported that these modifications on the bacterial surface occur due to overexpression of chromosomally mediated two-component system genes (PmrAB and PhoPQ) and mutation in lipid A biosynthesis genes that result in loss of the ability to produce lipid A and consequently LPS chain, thereafter recently identified variants of plasmid-borne genes (mcr-1 to mcr-10). It was hypothesized that mcr genes derived from intrinsically resistant environmental bacteria that carried chromosomal pmrC gene, a part of the pmrCAB operon, code three proteins viz. pEtN response regulator PmrA, sensor kinase protein PmrAB, and phosphotransferase PmrC. These plasmid-borne mcr genes become a serious concern as they assist in the dissemination of colistin resistance to other pathogenic bacteria. This review presents the progress of multiple strategies of colistin resistance mechanisms in bacteria, mainly focusing on surface changes of the outer membrane LPS structure and other resistance genetic determinants. New handier and versatile methods have been discussed for rapid detection of colistin resistance determinants and the latest approaches to revert colistin resistance that include the use of new drugs, drug combinations and inhibitors. Indeed, more investigations are required to identify the exact role of different colistin resistance determinants that will aid in developing new less toxic and potent drugs to treat bacterial infections. Therefore, colistin resistance should be considered a severe medical issue requiring multisectoral research with proper surveillance and suitable monitoring systems to report the dissemination rate of these resistant genes.

Colistin resistance and plasmid-mediated mcr genes in Escherichia coli and Salmonella isolated from pigs, pig carcass and pork in Thailand, Lao PDR and Cambodia border provinces

BACKGROUND

Colistin and carbapenem-resistant bacteria have emerged and become a serious public health concern, but their epidemiological data is still limited.

OBJECTIVES

This study examined colistin and carbapenem resistance in Escherichia coli and Salmonella from pigs, pig carcasses, and pork in Thailand, Lao PDR, and Cambodia border provinces.

METHODS

The phenotypic and genotypic resistance to colistin and meropenem was determined in E. coli and Salmonella obtained from pigs, pig carcasses, and pork (n = 1,619). A conjugative experiment was performed in all isolates carrying the mcr gene (s) (n = 68). The plasmid replicon type was determined in the isolates carrying a conjugative plasmid with mcr by PCR-based replicon typing (n = 7). The genetic relatedness of mcr-positive Salmonella (n = 11) was investigated by multi-locus sequence typing.

RESULTS

Colistin resistance was more common in E. coli (8%) than Salmonella (1%). The highest resistance rate was found in E. coli (17.8%) and Salmonella (1.7%) from Cambodia. Colistin-resistance genes, mcr-1, mcr-3, and mcr-5, were identified, of which mcr-1 and mcr-3 were predominant in E. coli (5.8%) and Salmonella (1.7%), respectively. The mcr-5 gene was observed in E. coli from pork in Cambodia. Two colistin-susceptible pig isolates from Thailand carried both mcr-1 and mcr-3. Seven E. coli and Salmonella isolates contained mcr-1 or mcr-3 associated with the IncF and IncI plasmids. The mcr-positive Salmonella from Thailand and Cambodia were categorized into two clusters with 94%-97% similarity. None of these clusters was meropenem resistant.

CONCLUSIONS

Colistin-resistant E. coli and Salmonella were distributed in pigs, pig carcasses, and pork in the border areas. Undivided-One Health collaboration is needed to address the issue.

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.

Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand

Nontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005–2007 to 11.2% (18/161) during 2014–2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and bla_CTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with bla_CTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.

Global clonal spread of mcr-3-carrying MDR ST34 Salmonella enterica serotype Typhimurium and monophasic 1,4,[5],12:i:- variants from clinical isolates

OBJECTIVES

To investigate the prevalence and transmission of mcr-3 among Salmonella enterica serotype Typhimurium and 1,4,[5],12:i:-.

METHODS

A total of 4724 clinical Salmonella isolates were screened for the presence of mcr-3 in China during 2014-19. The clonal relationship of the mcr-3-positive isolates and their plasmid contents and complete sequence were also characterized based on WGS data from the Illumina and MinION platforms.

RESULTS

We identified 10 mcr-3-positive isolates, and all were MDR, mostly resistant to colistin, cefotaxime, ciprofloxacin, doxycycline and florfenicol. mcr-3 was co-present with blaCTX-M-55-qnrS1 on hybrid ST3-IncC-FII conjugatable plasmids (n = 6) and an ST3-IncC non-conjugatable plasmid (n = 1) and embedded into a pCHL5009T-like IncFII plasmid on the Salmonella chromosome (n = 3). Four distinctive genetic contexts surrounded mcr-3 and all but one were closely related to each other and to the corresponding region of IncFII plasmid pCHL5009T. IS15DI was most likely the vehicle for integration of mcr-3-carrying IncFII plasmids into ST3-IncC plasmids and the chromosome and for shaping the MDR regions. In addition, a phylogenetic tree based on the core genome revealed a unique Salmonella lineage (≤665 SNPs) that contained these 10 mcr-3-positive isolates and another 38 (33 from patients) mcr-3-positive Salmonella from five countries. In particular, most of the 51 mcr-3-positive isolates belonged to ST34 and harboured diverse antibiotic resistance genes (ARGs), including mcr-3-blaCTX-M-55-qnrS1, and possessed similar ARG profiles.

CONCLUSIONS

Our findings revealed global clonal spread of MDR ST34 Salmonella from clinical isolates co-harbouring mcr-3 with blaCTX-M-55 and qnrS1 and a flexibility of mcr-3 co-transmittance with other ARGs mediated by mobile genetic elements.

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe

The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species

Simple Summary

In the era of the COVID-19 global pandemic, antimicrobial resistance is looming as an imminent threat and challenge to human public health. Antimicrobial resistance is a major global threat of increasing concern to human and animal health. It also has implications for both food safety and food security and the economic well-being of millions of humans. Among other zoonotic infectious diseases, antimicrobial resistance in food chain and livestock-associated pathogens such as Salmonella is of great concern. In the present study, the genomic characterization of antimicrobial resistance in food chain and livestock-associated Salmonella was summarized. Several antimicrobial resistance determinants were reported in Salmonella isolated from food chain animals and livestock. Monitoring of antimicrobial resistance in Salmonella in livestock and food chain animals through genomic characterization is significant to control and protect humans from the threat of antimicrobial resistance. Salmonella, a foodborne zoonotic enterobacterium species can transmit antimicrobial resistance from the microbiome of animals to humans. This study summarizes the genomic characterization of antimicrobial resistance in Salmonella species with special focus on resistance against carbapenems and colistin which are the last resort antibiotics used against infections caused by multidrug resistant bacteria. The present review aims to draw attention to prudent use of antibiotics, a good example of the One Health concept.

Abstract

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Prevalence of mobile colistin resistance (mcr) genes in extended-spectrum β-lactamase-producing Escherichia coli isolated from retail raw foods in Nha Trang, Vietnam

The aim of the study was to assess the presence of genes in ESBL-producing E. coli (ESBL-Ec) isolated from retail raw food in Nha Trang, Vietnam. A total of 452 food samples comprising chicken (n = 116), pork (n = 112), fish (n = 112) and shrimp (n = 112) collected between 2015 and 2017 were examined for the prevalence of ESBL-Ec. ESBL-Ec were detected in 46.0% (208/452) of retail food samples, particularly in 66.4% (77/116), 55.4% (62/112), 42.0% (47/112) 19.6% (22/112) of chicken, pork, fish and shrimp, respectively. Sixty-five out of the 208 (31.3%) ESBL-Ec isolates were positive for mcr genes including mcr-1, mcr-3 and both mcr-1 and mcr-3 genes in 56/208 (26.9%), 1/208 (0.5%) and 8/208 (3.9%) isolates, respectively. Particularly, there was higher prevalence of mcr-1 in ESBL-Ec isolates from chicken (53.2%, 41/77) in comparison to shrimp (22.7%, 5/22), pork (11.3%, 7/62) and fish (6.4%, 3/47). mcr-3 gene was detected in co-existence with mcr-1 in ESBL-Ec isolates from shrimp (9.1%, 2/22), pork (8.1%, 5/62) and fish (2.1%, 1/47) but not chicken. The 65 mcr-positive ESBL-Ec (mcr-ESBL-Ec) were colistin-resistant with the MICs of 4-8 μg/mL. All mcr-3 gene-positive isolates belonged to group A, whereas phylogenetic group distribution of isolates harboring only mcr-1 was B1 (44.6%), A (28.6%) and D (26.8%). PFGE analysis showed diverse genotypes, although some isolates demonstrated nearly clonal relationships. S1-PFGE and Southern hybridization illustrated that the mcr-1 and mcr-3 genes were located either on chromosomes or on plasmids. However, the types of mcr genes were harbored on different plasmids with varied sizes of 30-390 kb. Besides, the ESBL genes of CTX-M-1 or CTX-M-9 were also detected to be located on plasmids. Noteworthy, co-location of CTX-M-1 with mcr-1 or mcr-3 genes on the same plasmid was identified. The conjugation experiment indicated that the mcr-1 or mcr-3 was horizontally transferable. All mcr-ESBL-Ec isolates were multidrug resistance (resistance to ≥3 antimicrobial classes). Moreover, β-Lactamase-encoding genes of the CTX-M-1 (78.5%), CTX-M-9 (21.5%), TEM (61.5%) groups were found in mcr-ESBL-Ec. The astA gene was detected in 27 (41.5%) mcr-ESBL-Ec isolates demonstrating their potential virulence. In conclusion, mcr-1 and mcr-3 genes existed individually or concurrently in ESBL-Ec isolates recovered from retail raw food in Nha Trang city, which might further complicate the antimicrobial-resistant situation in Vietnam, and is a possible health risk for human.

Complete Genome Sequences for 36 Canadian Salmonella enterica Serovar Typhimurium and I 1,4,[5],12:i:- Isolates from Clinical and Animal Sources

Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:– from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.

Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:– from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.

Colistin and its role in the Era of antibiotic resistance: an extended review (2000-2019)

Increasing antibiotic resistance in multidrug-resistant (MDR) Gram-negative bacteria (MDR-GNB) presents significant health problems worldwide, since the vital available and effective antibiotics, including; broad-spectrum penicillins, fluoroquinolones, aminoglycosides, and β-lactams, such as; carbapenems, monobactam, and cephalosporins; often fail to fight MDR Gram-negative pathogens as well as the absence of new antibiotics that can defeat these "superbugs". All of these has prompted the reconsideration of old drugs such as polymyxins that were reckoned too toxic for clinical use. Only two polymyxins, polymyxin E (colistin) and polymyxin B, are currently commercially available. Colistin has re-emerged as a last-hope treatment in the mid-1990s against MDR Gram-negative pathogens due to the development of extensively drug-resistant GNB. Unfortunately, rapid global resistance towards colistin has emerged following its resurgence. Different mechanisms of colistin resistance have been characterized, including intrinsic, mutational, and transferable mechanisms.In this review, we intend to discuss the progress over the last two decades in understanding the alternative colistin mechanisms of action and different strategies used by bacteria to develop resistance against colistin, besides providing an update about what is previously recognized and what is novel concerning colistin resistance.

A Multidrug-resistant Monophasic Salmonella Typhimurium Co-harboring mcr-1, fosA3, bla CTX-M-14 in a Transferable IncHI2 Plasmid from a Healthy Catering Worker in China

Background

Polymyxins are currently regarded as a possible last-resort therapy to eradicate multidrug-resistant (MDR) gram-negative bacteria. Meanwhile, the old antimicrobial agent fosfomycin has recently been reintroduced into clinical use for the treatment of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Enterobacteriaceae. This study investigated a multidrug-resistant Salmonella 4,[5],12:i:- strain from a food catering handler, which had the potential to act as a vehicle for transmitting MDR foodborne pathogens.

Methods

A Salmonella 4,[5],12:i:- YZU1189 strain was isolated from the fecal sample of a food catering worker according to the standard protocol of the Salmonella detection method from World Health Organization in 2003. Serotyping of YZU1189 was performed according to the Kauffmann-White scheme. The antimicrobial resistance phenotype of the strain was determined by the agar dilution method according to the instruction from Clinical and Laboratory Standards Institute (CLSI). Plasmid conjugation was performed between the donor strain Salmonella 4,[5],12:i:- YZU1189 and the recipient strain Escherichia coli C600. The genetic locations of mcr-1, bla _CTX-M-14 and fosA3 genes were determined by the whole genome sequence analysis.

Results

Salmonella 4,[5],12:i:- YZU1189 was an ESBL-producing stain isolated from a healthy catering worker. The strain displayed resistance to aminoglycosides, beta-lactams, polymyxins, fosfomycins, phenicols, trimethoprims, sulfonamides, tetracyclines and fluoroquinolones. Whole genome sequence analysis and plasmid conjugation revealed that the strain had a transferable IncHI2 plasmid carrying the mcr-1, bla _CTX-M-14 and fosA3 genes. Sequence homology analysis showed that this plasmid possessed high sequence similarity to previously reported mcr-1, bla _CTX-M-14 and fosA3 positive plasmids in China.

Conclusion

This study reported a the multidrug-resistant Salmonella 4,[5],12:i:- isolate harboring mcr-1, bla _CTX-M-14 and fosA3 from human for the first time in China. The occurrence of mcr-1 and fosA3 genes in the transferable IncHI2 plasmid pYZU1189 from the ESBL-producing Salmonella 4,[5],12:i:- isolate showed a potential threat to public health. Great concern should be taken for the spread of multidrug-resistant ESBL-producing Salmonella isolates from food catering workers to consumers.

Antimicrobial Resistance and Biofilm Formation Capacity of Salmonella enterica Serovar Enteritidis Strains Isolated from Poultry and Humans in Poland

Salmonella enterica ser. Enteritidis (S. enterica ser. Enteritidis) is the most frequently detected serovar in human salmonellosis, and its ability to produce a biofilm and the risk of transmission from animals and food of animal origin to humans are significant. The main aim of the present work was to compare S. enterica ser. Enteritidis strains isolated from poultry and human feces in terms of resistance profiles, prevalence of selected resistance genes, and their potential for biofilm formation, by assessing their biofilm growth intensity, the prevalence and expression of selected genes associated with this phenomenon, and the correlation between increased antimicrobial resistance and biofilm formation ability of the two tested groups of S. enterica ser. Enteritidis. This study showed a difference in antimicrobial resistance (minimal inhibitory concentration value) between S. enterica ser. Enteritidis groups; however, the majority of multidrug-resistant (MDR) strains were isolated from poultry (environmental samples from chicken broilers, turkey broilers, and laying hens). Differences in the prevalence of resistance genes were observed; the most common gene among poultry strains was floR, and that among strains from humans was blaTEM. S. enterica ser. Enteritidis strains isolated from poultry under the tested incubation conditions exhibited better biofilm growth than strains isolated from humans. A higher level of gene expression associated with the production of cellulose was only detected in the S48 strain isolated from poultry. On the other hand, increased expression of genes associated with quorum sensing was observed in two strains isolated from poultry farms and one strain isolated from human feces.

Audacious Hitchhikers: The Role of Travel and the International Food Trade in the Global Dissemination of Mobile Colistin-Resistance (mcr) Genes

Colistin, a last-resort antibiotic, has been used in controlling infections caused by multidrug-resistant Gram-negative bacterial pathogens. However, recent reports showed a global dissemination of mobile colistin-resistance (mcr) genes, genetic elements that encode resistance to colistin, which has raised public health concerns. These mcr genes threaten the effectiveness of colistin and could limit therapy options for complicated infections. Despite global attention, many facets of the molecular epidemiology of mcr remain poorly characterized. Here, we focus on the role of travel and the international food trade in the dissemination of mcr to countries where these genetic elements and/or colistin resistance are relatively limited in prevalence. We present evidence from the literature on the acquisition of mcr during travel, and the carriage of these genes back to travelers’ countries. We also highlight the potential transmission of mcr via imported foods. These observations emphasize the magnitude of efforts that are needed to control the spread of mcr, and further highlight the challenge of antimicrobial resistance and the urgent need for coordinated global action.

Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil

The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.

Molecular Typing, Characterization of Antimicrobial Resistance, Virulence Profiling and Analysis of Whole-Genome Sequence of Clinical Klebsiella pneumoniae Isolates

Klebsiella pneumoniae is one of the most important pathogens concerned with multidrug resistance in healthcare-associated infections. The treating of infections caused by this bacterium is complicated due to the emergence and rapid spreading of carbapenem-resistant strains, which are associated with high mortality rates. Recently, several hypervirulent and carbapenemase-producing isolates were reported that make the situation even more complicated. In order to better understand the resistance and virulence mechanisms, and, in turn, to develop effective treatment strategies for the infections caused by multidrug-resistant K. pneumoniae, more comprehensive genomic and phenotypic data are required. Here, we present the first detailed molecular epidemiology report based on second and third generation (long-read) sequencing for the clinical isolates of K. pneumoniae in the Russian Federation. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as the virulence and plasmid profiling for 36 K. pneumoniae isolates. We have revealed 2 new multilocus sequence typing (MLST)-based sequence types, 32 multidrug-resistant (MDR) isolates and 5 colistin-resistant isolates in our samples. Three MDR isolates belonged to a very rare ST377 type. The whole genome sequences and additional data obtained will greatly facilitate further investigations in the field of antimicrobial resistance studies.

Co-occurrence of mcr-1, mcr-3, mcr-7 and clinically relevant antimicrobial resistance genes in environmental and fecal samples

Multidrug-resistant bacteria harboring different antimicrobial resistance genes (ARGs) have been detected worldwide. The association of plasmid-mediated colistin resistance genes (mcr-like) and other ARGs in bacteria isolated from animals is a huge concern worldwide. Therefore, this study aimed to investigate the presence of mcr-like genes and clinically relevant ARGs as well as plasmids in samples from a zoo. Fecal and environmental (soil and water) samples were collected from a zoo and the DNA of cultivable aerobic bacteria was extracted. ARGs were screened by PCR and the plasmids were detected using the PCR-based replicon typing method. A total of 74 amplicons from 27 ARGs [mcr-1, mcr-3, mcr-7.1, bla_CTX-M-Gp1, bla_CTX-M-Gp2, bla_CTX-M-Gp9, bla_VEB, bla_PER, bla_CMY, tetA, tetB, tetC, aadA, aac(6')-Ib, aph(3')-Ia, ant(2'')-Ia, qnrA, qnrB, qnrS, oqxA, oqxB, sul1, sul2, sul3, cmlA, mefAE, ermB] and 21 amplicons from eight plasmid families (IncY, ColE-like, IncF_repB, IncFIA, IncFIB, IncHI1, IncFIC, IncP) were detected. These findings reinforce that the zoo acts as a reservoir of clinically relevant ARGs, including mcr-like, and call attention to the monitoring studies in the zoo. Therefore, to the best of our knowledge, this is the first report of the world of mcr-1, mcr-3 and mcr-7.1 in environmental samples from the zoo.

The characterization of mobile colistin resistance (mcr) genes among 33 000 Salmonella enterica genomes from routine public health surveillance in England

To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.

Prevalence of Genes Involved in Colistin Resistance in Acinetobacter baumannii: First Report from Iraq

Background and Aim: Colistin is increasingly being used as a "last-line" therapy to treat infections caused by multidrug-resistant (MDR) Acinetobacter baumannii isolates, when essentially no other options are available in these days. The aim of this study was to detect genes associated with colistin resistance in A. baumannii. Methods: One hundred twenty-one isolates of A. baumannii were collected from clinical and environmental samples during 2016 to 2018 in Baghdad. Isolates were diagnosed as A. baumannii by using morphological tests, Vitek-2 system, 16SrRNA PCR amplification, and sequencing. Antibiotic susceptibility test was carried out using disk diffusion method. Phenotypic detection of colistin resistance was performed by CHROMagar™ COL-APSE medium and broth microdilution method for the determination of the minimal inhibitory concentration. Molecular detection of genes responsible for colistin resistance in A. baumannii was performed by PCR. Results: Ninety-two (76%) of the 121 A. baumannii isolates were colistin resistant. Twenty-six (21.5%) of the 121 isolates showed positive growth on CHROMagar Acinetobacter base for MDR. PCR detected mcr-1, mcr-2, and mcr-3 genes in 89 (73.5%), 78 (64.5%), and 82 (67.8%) A. baumannii isolates, respectively. Seventy-eight (64.5%) of the 121 isolates harbored the integron intI2 gene and 81 (66.9%) contained intI3 gene. Moreover, 60 (49.6%) of the 121 isolates were positive for the quorum sensing lasI gene. Conclusion: The presence of a large percentage of colistin-resistant A. baumannii strains in Baghdad may be due to the presence of mobile genetic elements, and it is urgent to avoid unnecessary clinical use of colistin.

An overview of colistin resistance, mobilized colistin resistance genes dissemination, global responses, and the alternatives to colistin: A review

Colistin, also known as polymyxin E, is an antimicrobial agent that is effective against a variety of Gram-negative bacilli, especially the Enterobacteriaceae family. Recently, the wide dissemination of colistin-resistance has brought strong attention to the scientific society because of its importance as the last resort for the treatment of carbapenem-resistant Enterobacteriaceae infections and its possible horizontal transmission. The mobilized colistin resistance (mcr) gene was identified as the gene responsible for unique colistin resistance. Indeed, despite many studies that have revealed a pan variation in the existence of this gene, not only for the mcr genes main group but also for its many subgroups, the problem is growing and worsening day after day. In this regard, this review paper is set to review the updated data that has been published up to the end of 2019 third quarter, especially when related to colistin resistance by the mcr genes. It will include the present status of colistin resistance worldwide, the mcr gene dissemination in different sectors, the discovery of the mcr variants, and the global plan to deal with the threat of antimicrobial resistance. In line with global awareness, and to stop antibiotic misuse and overuse, especially in agricultural animals, the study will further discuss in detail the latest alternatives to colistin use in animals, which may contribute to the elimination of inappropriate antibiotic use and to the help in preventing infections. This review will advance our understanding of colistin resistance, while supporting the efforts toward better stewardship, for the proper usage of antimicrobial drugs in humans, animals, and in the environment.

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.

The presence of colistin resistance gene mcr-1 and -3 in ESBL producing Escherichia coli isolated from food in Ho Chi Minh City, Vietnam

Colistin is indicated for the treatment of multidrug-resistant gram-negative bacterial infections. However, the spread of colistin-resistant bacteria harbouring an mcr gene has become a serious concern. This study investigated local foods in Vietnam for contamination with colistin-resistant bacteria. A total of 261 extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli isolates from 330 meat and seafood products were analysed for colistin susceptibility and the presence of mcr genes. Approximately, 24% (62/261) of ESBL- or AmpC-producing E. coli isolates showed colistin resistance; 97% (60/62) of colistin-resistant isolates harboured mcr-1, whereas 3% (2/62) harboured mcr-3. As the result of plasmid analysis of two strains, both plasmids harbouring mcr-3 revealed that plasmid replicon type was IncFII. Sequencing analysis indicated that an insertion sequence was present near mcr-3, suggesting that IncFII plasmids harbouring mcr-3 could be transferred to other bacterial species by horizontal transfer of the plasmid or transfer with some insertion sequence. In conclusion, ESBL-producing E. coli and AmpC-producing E. coli have acquired colistin resistance because 24% of such isolates show colistin resistance and 3% of the colistin-resistant strains harbour mcr-3. We reported the present of the mcr-3-carrying ESBL-producing E. coli isolated from pork in Vietnam.

Emergence and Dissemination of mcr-Carrying Clinically Relevant Salmonella Typhimurium Monophasic Clone ST34

Antibiotic resistance in bacteria is one of the urgent threats to both public and global health. The Salmonella Typhimurium monophasic sequence type 34 (ST34) clone, with its rapid dissemination and resistance to numerous critical antimicrobials, has raised global concerns. Here, we present an updated overview on the emerging infections caused by mobile colistin resistance (mcr)-carrying colistin-resistant ST34 isolates, covering their global dissemination and virulence-associated efficacy. The higher rates of mcr-1-positive ST34 in children in China highlights the increasing threat caused by this pathogen. Most of the ST34 isolates carrying the mcr-1 gene were isolated from animals and food products, indicating the role of foodborne transmission of mcr-1. The emergence of multidrug resistance genes along with various virulence factors and many heavy metal resistance genes on the chromosome and plasmid from ST34 isolates will challenge available therapeutic options. The presence of the colistin resistance gene (mcr-1, mcr-3, and mcr-5) with the multidrug-resistant phenotype in ST34 has spread across different countries, and most of the mcr-1 genes in ST34 isolates were detected in plasmid type IncHI2 followed by IncI2, and IncX4. Together, mcr-carrying S. Typhimurium ST34 may become a new pandemic clone. The fast detection and active surveillance in community, hospital, animal herds, food products and environment are urgently warranted.

mcr-9, an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin

The plasmid-located mcr-9 gene, encoding a putative phosphoethanolamine transferase, was identified in a colistin-resistant human fecal Escherichia coli strain belonging to a very rare phylogroup, the D-ST69-O15:H6 clone. This MCR-9 protein shares 33% to 65% identity with the other plasmid-encoded MCR-type enzymes identified (MCR-1 to -8) that have been found as sources of acquired resistance to polymyxins in Enterobacteriaceae Analysis of the lipopolysaccharide of the MCR-9-producing isolate revealed a function similar to that of MCR-1 by adding a phosphoethanolamine group to lipid A and subsequently modifying the structure of the lipopolysaccharide. However, a minor impact on susceptibility to polymyxins was noticed once the mcr-9 gene was cloned and produced in an E. coli K-12-derived strain. Nevertheless, we showed here that subinhibitory concentrations of colistin induced the expression of the mcr-9 gene, leading to increased MIC levels. This inducible expression was mediated by a two-component regulatory system encoded by the qseC and qseB genes located downstream of mcr-9 Genetic analysis showed that the mcr-9 gene was carried by an IncHI2 plasmid. In silico analysis revealed that the plasmid-encoded MCR-9 shared significant amino acid identity (ca. 80%) with the chromosomally encoded MCR-like proteins from Buttiauxella spp. In particular, Buttiauxella gaviniae was found to harbor a gene encoding MCR-BG, sharing 84% identity with MCR-9. That gene was neither expressed nor inducible in its original host, which was fully susceptible to polymyxins. This work showed that mcr genes may circulate silently and remain undetected unless induced by colistin.

Genetic and Biochemical Mechanisms for Bacterial Lipid A Modifiers Associated with Polymyxin Resistance

Polymyxins are a group of detergent-like antimicrobial peptides that are the ultimate line of defense against carbapenem-resistant pathogens in clinical settings. Polymyxin resistance primarily originates from structural remodeling of lipid A anchored on bacterial surfaces. We integrate genetic, structural, and biochemical aspects of three major types of lipid A modifiers that have been shown to confer intrinsic colistin resistance. Namely, we highlight ArnT, a glycosyltransferase, EptA, a phosphoethanolamine transferase, and the AlmEFG tripartite system, which is restricted to EI Tor biotype of Vibrio cholerae O1. We also discuss the growing family of mobile colistin resistance (MCR) enzymes, each of which is analogous to EptA, and which pose great challenges to global public health.

Effectiveness of BOX-PCR in Differentiating Genetic Relatedness among Salmonella enterica Serotype 4,[5],12:i:- Isolates from Hospitalized Patients and Minced Pork Samples in Northern Thailand

Salmonella enterica Serotype 4,[5],12:i:-, a monophasic variant of S. Typhimurium, with high virulence and multidrug resistance is distributed globally causing pathogenicity to both humans and domesticated animals. BOX-A1R-based repetitive extragenic palindromic-PCR (BOX)-PCR proved to be superior to three other repetitive element-based PCR typing methods, namely, enterobacterial repetitive intergenic consensus (ERIC)-, poly-trinucleotide (GTG)₅-, and repetitive extragenic palindromic (REP)-PCR (carried out under a single optimized amplification condition), in differentiating genetic relatedness among S. 4,[5],12:i:- isolates from feces of hospitalized patients (n=12) and isolates from minced pork samples of S. 4,[5],12:i:- (n=6), S. Typhimurium (n=6), and Salmonella Serogroup B (n=4) collected from different regions of northern Thailand. Construction of phylogenetic trees from amplicon size patterns allowed allocation of Salmonella isolates into clusters of similar genetic relatedness, with BOX-PCR generating more unique clusters for each serotype than the other three typing methods. BOX-, (GTG)₅-, and REP-PCR indicated significant genetic relatedness between S. 4,[5],12:i:- isolates 1 and 9 from hospitalized patients and S. 4,[5],12:i:- isolate en 29 from minced pork, suggesting a possible route of transmission. Thus, BOX-PCR provides a suitable molecular typing method for discriminating genetic relatedness among Salmonella spp. of the same and different serotypes and should be suitable for application in typing and tracking route of transmission in Salmonella outbreaks.

Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human

A colistin-resistant Salmonella enterica 4, [5],12:i:- sequence type (ST) 34 harbouring mcr-3.1 was recovered from a patient who travelled to China 2 weeks prior to diarrhoea onset. Genomic analysis revealed the presence of the mcr-3.1 gene located in the globally disseminated IncHI2 plasmid, highlighting the intercontinental dissemination of the colistin-resistant S. enterica 4, [5],12:i:- ST34 pandemic clone.

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.

Emergence of blaCTX-M-55 associated with fosA, rmtB and mcr gene variants in Escherichia coli from various animal species in France

Objectives

In Asian countries, blaCTX-M-55 is the second most common ESBL-encoding gene. blaCTX-M-55 frequently co-localizes with fosA and rmtB genes on epidemic plasmids, which remain sporadic outside Asia. During 2010-13, we investigated CTX-M-55-producing Escherichia coli isolates and their co-resistance to fosfomycin, aminoglycosides, fluoroquinolones and colistin as part of a global survey of ESBLs in animals in France.

Methods

blaCTX-M-55, fosA, rmtB and plasmidic quinolone and colistin resistance genes were characterized by PCR, sequencing and hybridization experiments. Plasmids were classified according to their incompatibility groups and subtypes. Genotyping was performed by MLST and repetitive extragenic palindromic sequence-based PCR.

Results

Twenty-one E. coli isolates from bovines (n = 16), dogs (n = 2), horses (n = 2) and a monkey harboured blaCTX-M-55, were MDR and belonged to ST744 (n = 9) and 10 other clones. blaCTX-M-55 was mostly located on IncF (n = 19), but also on IncI1 (n = 2) plasmids. On IncF33:A1:B1 plasmids, blaCTX-M-55 co-localized with the rmtB and aac(6')-Ib genes and in one isolate with the fosA3 allele. Ten IncF46:A-:B20 plasmids, which were found in different clones from unrelated animals, also carried the mcr-3 gene. blaCTX-M-55-carrying IncF18:A-:B1 plasmids were found in different animal species from distinct locations and periods, and one additionally carried the fosA4 gene. One isolate harboured the mcr-1 gene, which did not co-localize with blaCTX-M-55.

Conclusions

A large diversity of E. coli clones and plasmid types supported the spread of blaCTX-M-55, together with atypical resistance genes, in various animal species in France. fosA and rmtB genes are emerging among animals in Europe and this issue is of concern for public health.

Molecular mechanisms related to colistin resistance in Enterobacteriaceae

Colistin is an effective antibiotic for treatment of most multidrug-resistant Gram-negative bacteria. It is used currently as a last-line drug for infections due to severe Gram-negative bacteria followed by an increase in resistance among Gram-negative bacteria. Colistin resistance is considered a serious problem, due to a lack of alternative antibiotics. Some bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacteriaceae members, such as Escherichia coli, Salmonella spp., and Klebsiella spp. have an acquired resistance against colistin. However, other bacteria, including Serratia spp., Proteus spp. and Burkholderia spp. are naturally resistant to this antibiotic. In addition, clinicians should be alert to the possibility of colistin resistance among multidrug-resistant bacteria and development through mutation or adaptation mechanisms. Rapidly emerging bacterial resistance has made it harder for us to rely completely on the discovery of new antibiotics; therefore, we need to have logical approaches to use old antibiotics, such as colistin. This review presents current knowledge about the different mechanisms of colistin resistance.

Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes

Background and aimPlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.

Plasmid-Mediated Colistin Resistance in Salmonella enterica: A Review

Colistin is widely used in food-animal production. Salmonella enterica is a zoonotic pathogen, which can pass from animal to human microbiota through the consumption of contaminated food, and cause disease, often severe, especially in young children, elderly and immunocompromised individuals. Recently, plasmid-mediated colistin resistance was recognised; mcr-like genes are being identified worldwide. Colistin is not an antibiotic used to treat Salmonella infections, but has been increasingly used as one of the last treatment options for carbapenem resistant Enterobacteria in human infections. The finding of mobilizable mcr-like genes became a global concern due to the possibility of horizontal transfer of the plasmid that often carry resistance determinants to beta-lactams and/or quinolones. An understanding of the origin and dissemination of mcr-like genes in zoonotic pathogens such as S. enterica will facilitate the management of colistin use and target interventions to prevent further spread. The main objective of this review was to collect epidemiological data about mobilized colistin resistance in S. enterica, describing the mcr variants, identified serovars, origin of the isolate, country and other resistance genes located in the same genetic platform.

Characterization of a colistin-resistant Salmonella enterica 4,[5],12:i:- harbouring mcr-3.2 on a variant IncHI-2 plasmid identified in Canada

We have identified a Salmonella enterica serotype 4,[5],12:i:- containing a mcr-3.2 in a patient who travelled to Thailand 1 month prior to the identification of it in Canada. The isolate was multidrug resistant, but remained susceptible to the carbapenems, amikacin and piperacillin/tazobactam. The mcr-3.2 was carried on a 261 Kb variant of the IncHI2 pWJ1. This report provides further evidence of the emergence of a ST34 colistin-resistant clone.

Discovery of multi-drug resistant, MCR-1 and ESBL-coproducing ST117 Escherichia coli from diseased chickens in northeast China

An endemic multi-drug resistant ST117 E. coli isolate coproducing MCR-1 and 3 ESBL loci was, for the first time, detected from diseased chicken, Liaoning Province, in Northeast China, from 2011 to 2012. Whole-genome sequencing revealed 5 unique plasmids, namely pHXH-1, pHXH-2, pHXH-3, pHXH-4 and pHXH-5). Among them, pHXH1 and pHXH4 encode ESBL, and pHXH-5 mediates MCR-1 colistin resistance. The results indicate that the potentially-national dissemination of MCR-1-positive pathogens with pan-drug resistance proceeds via food chains.

Molecular Insights into Functional Differences between mcr-3- and mcr-1-Mediated Colistin Resistance

The global emergence of plasmid-mediated colistin resistance genes mcr-1 and mcr-3 has threatened the role of the "last-resort" drug colistin in the defense against infections caused by multidrug-resistant Gram-negative bacteria. However, functional differences between these two genes in mediating colistin resistance remain poorly understood. Protein sequence alignment of MCR-3 and MCR-1 was therefore conducted in Clustal Omega to identify sequence divergence. The molecular recognition of lipid A head group phosphatidylethanolamine and MCR-3 enzyme was studied by homology modeling and molecular docking, with the catalytic mechanism of MCR-3 also being explored. Thr277 in MCR-3 was validated as the key amino acid residue responsible for the catalytic reaction using site-directed mutagenesis and was shown to act as a nucleophile. Lipid A modification induced by the MCR-3 and MCR-1 enzymes was confirmed by electrospray ionization-time of flight mass spectrometry. Far-UV circular dichroism spectra of the MCR-3 and MCR-1 enzymes suggested that MCR-3 was more thermostable than MCR-1, with a melting temperature of 66.19°C compared with 61.14°C for MCR-1. These data provided molecular insight into the functional differences between mcr-3 and mcr-1 in conferring colistin resistance.

Prevalence and Genetic Analysis of mcr-3-Positive Aeromonas Species from Humans, Retail Meat, and Environmental Water Samples

The mobile colistin resistance gene mcr-3 is globally disseminated in both Enterobacteriaceae and Aeromonas species, with the latter potentially serving as a reservoir for this gene. Here, we investigated the prevalence of mcr-3 in rectal swabs from humans, in food-producing animals and their products, and in the aquatic environment, and we investigated the genetic relationships between the mcr-3-positive isolates. An enriched broth screening method was used to detect mcr-3 in samples, and species identification of isolates from positive samples was carried out by matrix-assisted laser desorption ionization-time of flight mass spectrometry and shotgun sequencing. All mcr-3-positive isolates were subjected to antimicrobial susceptibility testing, conjugation, and whole-genome sequencing. Ten Aeromonas isolates, including 2 from human rectal swabs, 1 from pork, 3 from chicken meat, and 4 from the aquatic environment, were positive for mcr-3, but only 2 showed resistance to colistin. In addition to the mcr-3 variants identified previously (the novel variants were termed mcr-3.13 to mcr-3.18), all isolates harbored mcr-3-like genes downstream of the mcr-3 variants. The MCR-3.13 to MCR-3.18 proteins exhibited only 89.2% to 96.1% amino acid identity to the original MCR-3 protein. Whole-genome sequence analysis indicated diversity within the genetic environments of mcr-3-positive Aeromonas isolates and possible transmission between different sources in China and even worldwide. Close relationships between mcr-3-positive and mcr-3-negative Aeromonas isolates suggested that mcr-3 might be common in Aeromonas species, which are not inherent hosts of mcr-3 but may act as an important reservoir of this mobile colistin resistance gene.

Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study

BACKGROUND

Mobilized resistance to colistin is evolving rapidly and its global dissemination poses a severe threat to human health and safety. Transferable colistin resistance gene, mcr-3, first identified in Shandong, China, has already been found in several countries in multidrug-resistant human infections. Here we track the spread of mcr-3 within 13 provinces in China and provide a complete characterization of its evolution, structure and function.

METHODS

A total of 6497 non-duplicate samples were collected from thirteen provinces in China, from 2016 to 2017 and then screened for the presence of mcr-3 gene by PCR amplification. mcr-3-positive isolates were analyzed for antibiotic resistance and by southern blot hybridization, transfer analysis and plasmid typing. We then examined the molecular evolution of MCR-3 through phylogenetic analysis. Furthermore, we also characterized the structure and function of MCR-3 through circular dichroism analyses, inductively coupled plasma mass spectrometry (ICP-MS), liquid chromatography mass spectrometry (LC/MS), confocal microscopy and chemical rescue tests.

FINDINGS

49 samples (49/6497 = 0.75%) were mcr-3 positive, comprising 40 samples (40/4144 = 0.97%) from 2017 and 9 samples (9/2353 = 0.38%) from 2016. Overall, mcr-3-positive isolates were distributed in animals and humans in 8 of the 13 provinces. Three mcr-3-positive IncP-type and one mcr-1-bearing IncHI2-like plasmids were identified and characterized. MCR-3 clusters with PEA transferases from Aeromonas and other bacteria and forms a phylogenetic entity that is distinct from the MCR-1/2/P(M) family, the largest group of transferable colistin resistance determinants. Despite that the two domains of MCR-3 not being exchangeable with their counterparts in MCR-1/2, structure-guided functional mapping of MCR-3 defines a conserved PE-lipid recognizing cavity prerequisite for its enzymatic catalysis and its resultant phenotypic resistance to colistin. We therefore propose that MCR-3 uses a possible "ping-pong" mechanism to transfer the moiety of PEA from its donor PE to the 1(or 4')-phosphate of lipid A via an adduct of MCR-3-bound PEA. Additionally, the expression of MCR-3 in E. coli prevents the colistin-triggered formation of reactive oxygen species (ROS) and interferes bacterial growth and viability.

INTERPRETATION

Our results provide an evolutionary, structural and functional definition of MCR-3 and its epidemiology in China, paving the way for smarter policies, better surveillance and effective treatments.