Global distribution and genomic characteristics of carbapenemase-producing Escherichia coli among humans, 2005-2023

The emergence of highly resistant and hypervirulent Escherichia coli ST405 clone in a tertiary hospital over 8 years

The emergence of carbapenem-resistant Escherichia coli (CREC) poses crucial challenges in clinical management, requiring continuous monitoring to inform control and treatment strategies. This study aimed to investigate the genomic and epidemiological characteristics of CREC isolates obtained from a tertiary hospital in China between 2015 and 2022. Next-generation sequencing was used for genomic profiling, and clinical data from patients were integrated into the analysis. ST405 (21.2%), ST167 (20.3%) and ST410 (15.9%) were the most prevalent of the 30 distinct sequence types (STs) identified among the 113 unique CREC isolates. Infections caused by the ST405 CREC clone and severe underlying diseases were associated with higher in-hospital mortality rates, particularly in patients aged ≥65 years. Furthermore, the ST405 clone exhibited a greater number of virulence and resistance genes than non-ST405 CREC clones. The virulence gene eaeX and resistance genes mph(E) and msr(E) were exclusively found in ST405 clones, while other virulence genes (agn43, ipad and malX) and resistance genes (armA, catB3 and arr-3) were more prevalent in this clones. Additionally, ST405 showed higher minimum inhibitory concentrations for both meropenem and imipenem and showed superior growth under the meropenem challenge. Galleria mellonella virulence assays revealed that the ST405 CREC clone was more virulent than other predominant CREC STs. Our findings underscore the clinical threat posed by the ST405 CREC clone, which exhibits both enhanced virulence and extensive drug resistance. These results highlight the urgent need for stringent surveillance and targeted interventions to curb its further dissemination and prevent potential outbreaks.

Companion animals as sources of hazardous critically important antimicrobial-resistant Escherichia coli: Genomic surveillance in Shanghai

This study provides the first comprehensive genomic surveillance of critically important antimicrobial (CIA)-resistant Escherichia coli in companion animals, addressing gaps in the understanding of antimicrobial resistance (AMR) transmission dynamics and the environmental dissemination of hazardous resistance genes within urban ecosystems. A total of 244 CIA-resistant Escherichia coli (CIA-EC) isolates were obtained from 730 anal swabs collected across 11 pet hospitals in Shanghai. High-risk zoonotic clones, such as ST410 and ST405, were identified across multiple districts, with blaNDM-5-positive IncX3 plasmids demonstrating exceptional stability, efficient conjugation, and broad host adaptability. These plasmids significantly amplify the global risk of cross-species blaNDM-5 dissemination. Mobile genetic elements (ISKox3, IS5, ISAba125) further facilitated blaNDM-5 transfer, enhancing the persistence and adaptability of these zoonotic pathogens. Additionally, novel sequence types (ST87, ST12624) exhibited resistance to last-resort antimicrobials, including tigecycline (tet(X4)), exacerbating the public health risks. The findings demonstrate that companion animals serve as critical reservoirs at the human-animal-environment interface, facilitating the environmental spread of hazardous resistance elements such as blaNDM-5-positive IncX3 plasmids. Integrating companion animals into One Health AMR surveillance and implementing antimicrobial stewardship are crucial to mitigating the spread of CIA-resistance determinants and preserving the efficacy of last-resort antimicrobials.

Emergence of a clinical carbapenem-resistant Escherichia coli co-harboring blandm-5 and mcr-1.1 on the same plasmid

OBJECTIVES

Escherichia coli is a major pathogen, and the emergence of carbapenem-resistant E. coli (CREC) significantly restricts clinical treatment options. Polymyxins are considered the last-line treatment for CREC infections; however, the occurrence of polymyxin-resistant CREC, particularly following reports of plasmid-mediated colistin resistance (mcr), poses an increasing challenge.

METHODS

In this study, we identified a polymyxin-resistant CREC strain isolated from the rectal swab of a patient hospitalized in a hematology ward. Antimicrobial susceptibility testings, S1-PFGE, Southern blot analysis, Conjugation Experiment, whole genome sequencing (WGS) and bioinformatic analysis were used to characterize the strain.

RESULTS

The strain showed resistance to all tested antimicrobial agents except tigecycline. By bioinformatic analysis, the strain was found to carry one copy of the mcr-1.1 gene and two copies of blaNDM-5 genes. One blaNDM-5 and the mcr-1.1 gene were co-located on a plasmid (pCDE2901_MCR-NDM), while the second blaNDM-5 gene resided on another plasmid (pCDE2901_NDM). The blaNDM-5 gene in pCDE2901_MCR-NDM was likely mobilized from pCDE2901_NDM via a transposon. The plasmid pCDE2901_NDM could successfully transferred from the donor strain CDE2901 to the recipient strain EC600, while the plasmid pCDE2901_MCR-NDM was unable to undergo horizontal transfer despite harboring mobile-associated genes.

CONCLUSIONS

Given the critical role of polymyxins in treating CREC infections, the co-transfer of polymyxin and carbapenem resistance may severely undermine the efficacy of clinical therapies. Strengthened surveillance and monitoring are imperative to curtail the spread of extensively drug-resistant (XDR) pathogens.

Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka

The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were blaOXA, blaGES, blaVEB and blaTEM, whereas blaCTX-M and blaNDM were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1 and ISKpn6-blaKPC-2-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.

Genomic insights into bla AFM-positive carbapenem-resistant Pseudomonas aeruginosa in China

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a global threat; however, the epidemiological characteristics and clinical significance of bla AFM-positive CRPA strains in China remain unclear. In this study, continuous surveillance was conducted from 2018 to 2022 in a hospital in Henan Province, China, and the genomic characteristics of bla AFM-positive CRPA were elucidated. We characterised the genetic features of bla AFM-positive CRPA isolates by antimicrobial susceptibility testing, conjugation assays, whole-genome sequencing, large-scale comparative genomics, and bioinformatic analyses. Among 628 CRPA isolates, one bla AFM-positive multidrug-resistant (MDR) strain, PA19-3158 (ST1123), was identified, with the bla AFM-1 gene located on a novel 518,222 bp megaplasmid. Additionally, big data analysis revealed the genomic characteristics of bla AFM-positive CRPA across China. A total of three different bla AFM gene variants were identified among these isolates, namely bla AFM-1 (44.12%), bla AFM-2 (52.94%), and bla AFM-4 (2.94%). Our findings identified ST463 as the dominant clone among bla AFM-positive CRPA in different regions of China, with some bla AFM-positive CRPA isolates from these regions exhibiting high genetic similarity. Notably, all bla AFM-positive CRPA isolates carried multiple antibiotic resistance genes (ARGs), with approximately 38% co-harboring the carbapenem-resistant gene bla KPC-2 and approximately 47% co-harboring the tigecycline-resistant gene tmexCD-toprJ. Correlation analysis underscored the significant role of mobile genetic elements in facilitating bla AFM gene transfer. These results highlight the critical need for continuous surveillance of bla AFM-positive CRPA in clinical settings to mitigate potential risks.

The pet café is a neglected site for transmission of antimicrobial-resistant Escherichia coli in urban life

The process of urbanization has brought with it several novel lifestyles, but it remains to be seen whether such lifestyles are the potential driver behind the spread of antimicrobial resistance (AMR) in modern society. Hence, this study employs the pet café as a proof of concept to observe how one pathway of AMR transmission occurs within a megacity. A total of 111 samples were collected from consumers, workers, animals and the surrounding environment from three pet cafés in Guangzhou, and 163 bacterial strains were isolated, with Escherichia coli (n=60) being the most dominant species. The sequence type and genomic diversity of E. coli were observed in all three cafés. Notably, 19 highly related ST328 strains were isolated in a single pet café from both workers (skin and faeces) and animals (faeces), suggesting transmission between distinct hosts. The number of SNPs between ST328 E. coli isolated in this study and strains from other provinces in China was minimal, with the possibility of clonal transmission. In terms of AMR, 90% of the isolates exhibited resistance to at least three distinct classes of antimicrobials (multidrug resistance). Multiple antimicrobial resistance genes (ARGs) such as tet(X4) were detected in this study, and plasmid, especially hybrid plasmid, is the main transmission vector of these ARGs. Our findings highlight that the pet café is a neglected site for the transfer of ARGs among Enterobacteriaceae, with a propensity for continuous contamination through either clonal or horizontal transmission of ARGs.

Genomic analysis of Proteus mirabilis: Unraveling global epidemiology and antimicrobial resistance dissemination - emerging challenges for public health and biosecurity

Given the escalating public health threat posed byProteus mirabilis(P. mirabilis) and its rapidly evolving drug resistance, it is imperative to elucidate its global epidemiology and resistance mechanisms through a comprehensive genomic lens. As of August 2024, 3,403 high-qualityP. mirabilisgenomes were retrieved from public databases (total 3,752), spanning 58 countries/regions, with the United States showing the highest report rate (52.51 %). Human-derived isolates, particularly from urine (34.47 %), were the primary source. A total of 239 antibiotic resistance genes (ARGs) were identified in P. mirabilis, with β-lactamase and carbapenemase genes being particularly widespread and isolates from China harboring the highest ARG counts. Globally,P. mirabilisisolates were categorized into 17 distinct clusters, with U.S. isolates showing the widest phylogenetic spread. Minimal SNP variations among isolates from different countries and hosts suggest transnational and cross-host clonal propagation. Frequent clonal transmission was also observed among diverse hosts and clinical sources.P. mirabiliscarries numerous integrative and conjugative elements (ICEs), some facilitating ARG dissemination (n = 215). Prophages, though ubiquitous, contributed minimally to ARG spread. Spearman's analysis revealed significant correlations between ARGs and insertion sequences (ISs), replicons, and ICEs. Ancestral state analysis indicated prophages were mainly acquired horizontally, while other mobile genetic elements (MGEs) were largely clonally transmitted. This study provides the first comprehensive genomic analysis ofP. mirabilis's global resistance landscape, highlighting the need to designate it as a novel antimicrobial resistance indicator and implement long-term surveillance.

KpnK48 clone driving hypervirulent carbapenem-resistant Escherichia coli epidemics: Insights into its evolutionary trajectory similar to Klebsiella pneumoniae

AIMS

Hypervirulent and carbapenem-resistant pathogens posed a significant and growing threat to global public health. This study focused on the rapid spread of a hypervirulent carbapenem-resistant E. coli (hv-CREC) subclone and its genomic resembles with hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP), driven by recombination impacting both chromosomal and plasmid gene content.

METHODS

A multicenter molecular epidemiological study was conducted on 653 CREC clinical isolates collected across China (2013-2022), integrated with public genomic data. Pangenome-wide and phylogeographical analyses were performed to uncover recombination events, define the epidemic clone, and trace its evolutionary history. Growth advantage and virulence were evaluated through competition assays and Galleria mellonella infection models.

RESULTS

Sequence types (ST) 167, ST410, ST617, and ST361 collectively accounted for 53.8 % (351/653) of the CREC isolates, with ST167 showing a sharp increase in prevalence after 2017. Among these, subclone named KpnK48 emerged as the primary driver of the increase in ST167 CREC prevalence. Traced to a European origin, KpnK48 rapidly expanded globally, particularly in China. The remarkable success of KpnK48 could plausibly be attributed to enhanced survival and virulence, driven by the acquisition of a ∼492 kb recombinant genomic region which mirrored the genomic architecture underlying the hv-CRKP ST11-K64 clone, reflecting a Klebsiella-like evolutionary path. Additionally, plasmid shift in KpnK48 clone from the prevalent NDM-IncX3 plasmid to Klebsiella-common NDM-IncF plasmid expanded its resistance spectrum and virulence gene repertoire, likely further amplifying its pathogenicity and success.

CONCLUSIONS

The KpnK48 subclone combined the features of hypervirulence and carbapenem resistance, bridging genomic traits of E. coli and K. pneumoniae, signifying a broader evolutionary trend with profound global health implications.

Carbapenem-resistant Morganella morganii carrying blaKPC-2 or blaNDM-1 in the clinic: one-decade genomic epidemiology analysis

Carbapenem-resistant Morganella morganii (CRMM) isolates, particularly those producing Klebsiella pneumoniae carbapenemase-2 (KPC-2) or New Delhi metallo-β-lactamase-1 (NDM-1), are increasingly being recognized as causative agents of nosocomial infections. However, systematic phylogeography and genetic characterization of these isolates worldwide are still lacking. Here, through seven years of surveillance of CRMM in a tertiary hospital, we analyzed the genomic characteristics of blaKPC-2- or blaNDM-1-positive CRMM isolates. Furthermore, we conducted a global genomic epidemiological study of Morganella spp. harboring blaKPC or blaNDM using the NCBI database over the past decade. By combining the timeline of isolate collection with the structural analysis of the plasmids, we traced the evolution of the IncL/M plasmid, which acquired the blaKPC-2 gene. Our findings indicate that horizontal transfer of Tn6296 based on IS26 is crucial for the transmission of blaKPC in CRMM isolates. Additionally, the Tn125 transposon appears to have played an important role in early plasmid-mediated dissemination of blaNDM; however, it has been surpassed in recent years by other elements, including IS26 and ISCR. In summary, through phylogeographic analysis of Morganella spp. globally, we elucidated their spatial-temporal distribution and revealed the evolutionary characteristics of KPC- or NDM-producing CRMM isolates as the predominant "epidemic" clone.

IMPORTANCE

Currently, infections attributable to carbapenem-resistant Morganella morganii (CRMM) isolates harboring blaKPC or blaNDM are on the rise, highlighting the increasing severity of acquired antimicrobial resistance. However, systematic phylogeographic and genetic characterization of these isolates worldwide is still lacking. In this study, we elucidated the spatial-temporal distribution and evolutionary trajectory of blaKPC and blaNDM genes within their core genetic environments. We emphasize the necessity of strengthening surveillance and controlling these organisms in clinical settings to prevent the generation of so-called "superbug" isolates.

Fecal carriage and molecular characterization of carbapenem-resistant Enterobacteriaceae from hospitalized children in a tertiary hospital of Shandong, China

BACKGROUND

The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) has emerged as a serious public health problem worldwide, and the data on the fecal carriage of CRE strains in hospitalized children remain limited. This study aimed to investigate the molecular characteristics of intestinal colonization of CRE in hospitalized children in Shandong, China.

METHODS

A retrospective study was conducted from August to November 2023. Antimicrobial susceptibility testing was performed by the broth microdilution method. Carbapenemase genes, drug resistance genes, and plasmid replicon types were detected using multiplex real-time PCR and whole-genome sequencing. Multilocus sequence typing (MLST) was used to determine the genetic relationships between strains.

RESULTS

A total of 20 CRE isolates were identified from 432 fecal samples, with a fecal carriage rate of 4.6%. The CRE isolates predominantly consisted of Escherichia coli (E. coli, n = 13) and Klebsiella strains (n = 6). CRE isolates showed a high resistance rate of 90-100% to seven β-lactam antibiotics. Resistance rates for other antibiotics such as trimethoprim-sulfamethoxazole, tetracycline, azithromycin, ciprofloxacin, chloramphenicol, nalidixic acid, and streptomycin were 90, 85, 85, 80, 75, 75, and 75%, respectively. CRE isolates showed low resistance to amikacin (20%), and none of the isolates were resistant to tigecycline. Additionally, the multidrug resistance rate of CRE isolates was 95%. All CRE strains carried sulfonamide antibiotic and β-lactamase resistance genes, of which the most common β-lactamase resistance genes were bla NDM-1 (n = 9), bla NDM-5 (n = 7) and bla OXA-1 (n = 7). Resistance genes to tetracycline and macrolide antibiotics were also widespread among the strains. The study found that IncFIB and IncFII series plasmids were present in 84 and 42% of the CRE strains, respectively. Additionally, Col, IncFIA, IncC, IncHI2, and IncX series plasmids were also detected. MLST analysis revealed diverse sequence types (STs) among CRE isolates, with ST167 being a common ST among E. coli isolates.

CONCLUSION

This study revealed bla NDM E. coli were the dominant isolates in fecal samples of hospitalized children in Shandong Province, with a broad multidrug resistance to antibiotics, emphasizing that infection control measures need to be taken to limit the spread of these strains.

Epidemiology and Genetic Traits of Carbapenemase-Producing Enterobacterales: A Global Threat to Human Health

Carbapenemase-producing Enterobacterales (CPE) represent an important threat to global health, resulting in an urgent issue in clinical settings. CPE often exhibit a multidrug-resistant (MDR) phenotype, thus reducing the antimicrobial armamentarium, with few antibiotics retaining residual antimicrobial activity against these pathogens. Carbapenemases are divided into three classes (A, B, and D) according to the Ambler classification system. Among these, KPC (class A), NDM, VIM, IMP (class B), and OXA-48-like (class D) represent the most important carbapenemases in terms of diffusion and clinical impact. CPE diffusion has been observed worldwide, with current endemicity in multiple territories around the world. In this context, the clonal spread and plasmid-mediated transmission of carbapenemases have contributed to the global spread of CPE worldwide and to the diffusion of carbapenemases among different Enterobacterales species. In recent years, novel molecules showing excellent in vitro and in vivo activity have been developed against CPE. However, the recent emergence of novel traits of resistance to these molecules has already been reported in several cases, mitigating the initial promising results. This review aims to provide an updated description of the major classes of carbapenemases, their global distribution, and future perspectives to limit the diffusion of CPEs.

Rapid Simultaneous Detection of the Clinically Relevant Carbapenemase Resistance Genes blaKPC, blaOXA48, blaVIM and blaNDM with the Newly Developed Ready-to-Use qPCR CarbaScan LyoBead

Antibiotic resistance, in particular the dissemination of carbapenemase-producing organisms, poses a significant threat to global healthcare. This study introduces the qPCR CarbaScan LyoBead assay, a robust, accurate, and efficient tool for detecting key carbapenemase genes, including blaKPC, blaNDM, blaOXA-48, and blaVIM. The assay utilizes lyophilized beads, a technological advancement that enhances stability, simplifies handling, and eliminates the need for refrigeration. This feature renders it particularly well-suited for point-of-care diagnostics and resource-limited settings. The assay's capacity to detect carbapenemase genes directly from bacterial colonies without the need for extensive sample preparation has been demonstrated to streamline workflows and enable rapid diagnostic results. The assay demonstrated 100% specificity and sensitivity across a diverse range of bacterial strains, including multiple allelic variants of target genes, facilitating precise identification of resistance mechanisms. Bacterial strains of the species Acinetobacter baumannii, Citrobacter freundii, Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized as reference material for assay development (n = 9) and validation (n = 28). It is notable that the assay's long shelf life and minimal operational complexity further enhance its utility for large-scale implementation in healthcare, food safety, and environmental monitoring. The findings emphasize the necessity of continuous surveillance and the implementation of rapid diagnostic methods for the effective detection of resistance genes. Furthermore, the assay's potential applications in other fields, such as toxin-antitoxin system research and monitoring of resistant bacteria in the community, highlight its versatility. In conclusion, the qPCR CarbaScan LyoBead assay is a valuable tool that can contribute to the urgent need to combat antibiotic resistance and improve global public health outcomes.

Neglected class A carbapenemases: Systematic review of IMI/NmcA and FRI from a One Health perspective

Carbapenemase-producing Enterobacterales are pathogens classified as a critical priority by the World Health Organization and a burden on human health worldwide. IMI, NmcA, and FRI are under-detected class A carbapenemases that have been reported in the human, animal and environmental compartments, particularly these last 5 years. Bacteria producing these carbapenemases have been mostly identified in digestive carriage screenings, but they are also involved in severe infections, such as bacteremia. Their increasing detection in wild fauna and natural environments confirms their ubiquitous nature. Indeed, they have been especially found in aquatic ecosystems and in many animals living in close association with them. Therefore, the hydric compartment is suspected to be the main reservoir of IMI carbapenemases. Although they are almost confined to Enterobacter cloacae complex species, some variants are plasmid-encoded and may diffuse to other bacterial species that are more virulent or more adapted to humans. Furthermore, their association with other resistance mechanisms, such as Extended Spectrum Beta-Lactamases, leaves only few therapeutic options and raises concerns about the environmental spread of Multi-Drug-Resistant bacteria. These carbapenemase might be responsible of "mixed" outbreaks of CPE with a community origin and a possible secondary nosocomial spread. Therefore, more studies from a One Health perspective are needed to identify as many primary environmental (aquatic) reservoirs as possible, as well as secondary distribution routes (directly from the environment, via the food chain or animals…) which may also become secondary reservoirs for these carbapenemases, in order to implement measures to combat this potential emerging threat to humans. This review summarizes the main characteristics of the IMI, NmcA, and FRI carbapenemases, covering their detection, epidemiology, genetic environment, and associated resistance genes using a One Health approach.

Global phylogeography and antibiotic resistance characteristics of Morganella: An epidemiological, spatial, comparative genomic study

Morganella morganii has been recognized as an important opportunistic pathogen that is becoming increasingly prevalent worldwide. However, the current global evolutionary dynamics and emergence of ARGs remain obscure. The present study determined the global distribution, genomic classification, phylogeny, and monitor longitudinal resistome changes. During 1900-2024, a total of 1027 non-duplicate Morganella genomes have been reported from 49 countries. The countries with the highest number were China (433), the USA (143), and France (74). Through ANI distance analysis and core genome phylogeny, Morganella was reclassified into six species: M. morganii, M. sibonii, M. chanii, M. laugraudii, M. kristinii, M. psychrotolerans. Further analysis using cgMLST identified 87 distinct genetic clusters and 737 singleton strains, indicating a high level of multi-locus sequence type diversity and local clonal outbreaks. Bayesian evolutionary analysis revealed the most recent common ancestor year and potential global transmission routes. A total of 195 ARGs were carried by Morganella isolates, with each genome containing between 2 and 544 ARGs. The most common ARGs were associated with resistance to the following drug-classes: aminoglycosides, beta-lactam, chloramphenicol, sulfamides, and tetracycline. Twenty-one carbapenemase-encoding genes were identified in 22 countries, with blaNDM-1, blaKPC-2, blaIMP-27, blaOXA-48, blaNDM-5, blaNDM-7, and blaVIM-1 being the most prevalent. Positive correlations were observed between ARGs and mobile genetic elements, like plasmids, ISs, and Tns, indicating frequent mobilization of certain ARGs by different mobile genetic elements (p < 0.05). In conclusion, Morganella isolates that are showing an upward trend in resistance and infection rates warrant a reclassification of their taxonomy and continuous monitoring for resistance.

Antimicrobial resistance genes and associated mobile genetic elements in Escherichia coli from human, animal and environment

The global rise of antimicrobial resistance (AMR) poses a significant threat to human health. The environment plays an essential role in transmission of antimicrobial resistance genes (ARGs) between human and animal. Bacterial communities harbour diverse ARGs, carried by mobile genetic elements (MGEs) like plasmids and insertion sequences (ISs). Here, a total of 2199 Escherichia coli (E. coli) whole genome sequences from human, animal, bird and environment were retrieved globally to investigate ARG prevalence and assess their genetic framework. The study highlights how the genetic background including plasmids, IS elements and transposons surrounding ARGs influences their transmission potential. The maximum number of ARGs was found in United Kingdom followed by USA, majorly in human hosts. However, IS-associated ARGs were most prevalent in bird hosts. ARGs like aph(6)-ld, aph(3″)-lb, blaCTX-M, blaNDM were widespread across all hosts. Tn2 was the most prevalent, majorly carried by IncFIB plasmids. The IS26 and ISVsa3 carried diverse ARGs, primarily linked to aminoglycoside and β-lactam resistance. The combinations like mph(A)_IS6100 and blaNDM-5_IS5 showed fixed IS-ARG associations. ARGs like blaNDM, blaCTX-M variants displayed strong association with IS elements. The study highlights possible mechanism of transmission due to close proximity of AMR genes to MGEs, offering promising strategies to combat AMR by predicting and addressing future resistance determinants.

Dynamics of antimicrobial resistance and genomic characteristics of foodborne Vibrio spp. in Southern China (2013-2022)

Vibrio spp., known as significant marine pathogens, have become more prevalent due to global warming. Antibiotics released into the environment drive Vibrio resistance. The increasing consumption of seafood leads to more interactions between Vibrio and humans. Despite this concerning trend, there remains a lack of large-scale surveillance for Vibrio contamination across various types of food. This study isolated 4027 Vibrio strains, primarily comprising V. parahaemolyticus and V. alginolyticus, in 3581 fresh shrimp and meat products from 2013 to 2022. The Vibrio strains showed increased resistance to important antibiotics, especially β-lactams used to treat foodborne bacterial infections. Whole genome sequencing of 591 randomly chosen strains showed a strong correlation between antibiotic resistance and genotypes in Vibrio. Notably, various ESBL genes have evolved over the past 8 years, with blaVEBs being the most dominant. Additionally, carbapenemase genes, such as blaNDM-1, have become increasingly prevalent in recent years. Various mobile genetic elements, including IncQ and IncA/C plasmids, recoverable in Vibrio, facilitate the transmission of crucial β-lactamase genes. These data provide insights into the evolutionary traits of antimicrobial resistance in foodborne Vibrio strains over a decade. Policymakers should consider these findings when devising appropriate strategies to combat bacterial antimicrobial resistance and safeguard human health.

Molecular Epidemiology of mcr-1-Positive Polymyxin B-Resistant Escherichia coli Producing Extended-Spectrum β-Lactamase (ESBL) in a Tertiary Hospital in Shandong, China

Escherichia coli, a rod-shaped Gram-negative bacterium, is a significant causative agent of severe clinical bacterial infections. This study aimed to analyze the epidemiology of extended-spectrum β-lactamase (ESBL)-producing mcr-1 -positive E. coli in Shandong, China. We collected 668 non-duplicate ESBL-producing E. coli strains from clinical samples at Shandong Provincial Hospital between January and December 2018, and estimated their minimum inhibitory concentrations (MICs) using a VITEK® 2 compact system and broth microdilution. Next-generation sequencing and bioinformatic analyses identified the mcr-1 gene and other resistance genes in the polymyxin B-resistant strains. The conjugation experiment assessed the horizontal transfer capacity of the mcr-1 gene. Of the strains collected, 24 polymyxin B-resistant strains were isolated with a positivity rate of 3.59% and among the 668 strains, 19 clinical strains carried the mobile colistin resistance gene mcr-1, with a positivity rate of approximately 2.8%. All 19 clinical strains were resistant to ampicillin, cefazolin, ceftriaxone, ciprofloxacin, levofloxacin, and polymyxin B. Seventeen strains successfully transferred the mcr-1 gene into E. coli J53. All transconjugants were resistant to polymyxin B, and carried the drug resistance gene mcr-1. The 19 clinical strains had 14 sequence types (STs), with ST155 (n = 4) being the most common. The whole-genome sequencing results of pECO-POL-29_mcr1 revealed that no ISApl1 insertion sequences were found on either side of the mcr-1 gene. Our study uncovered the molecular epidemiology of mcr-1-carrying ESBL-producing E. coli in the region and suggested horizontal transmission mediated by plasmids as the main mode of mcr-1 transmission.

Identification of novel Tet(X6)-Tet(X2) recombinant variant in Elizabethkingia meningoseptica from a bullfrog farm and downstream river in China

Introduction

The dissemination of strains producing tetracyclines monooxygenase Tet(X) from breeding farms to the natural environment poses a potential threat to public health.

Methods

Antimicrobial susceptibility testing and WGS were performed to identify resistance phenotypes and genotypes. Cloning experiments, sequence alignment, and homology modeling were used to characterize the function and formation mechanisms of the recombinant variant. The mobilization potential of Tet(X) was assessed by collinearity analysis, conjugation experiments, and phylogenetic analysis.

Results

Three tet(X)-producing Elizabethkingia meningoseptica strains were isolated from bullfrog breeding ponds, the sewage outlet, and downstream river in Zhejiang Province, China. These strains carry a novel Tet(X) variant, differing from Tet(X6) by seven residues, and possess the ability to degrade tetracyclines. Interestingly, the novel Tet(X) is a recombinant variant formed by homologous recombination of Tet(X6) and the C-terminal of Tet(X2). Further analysis revealed that Tet(X6) formed several Tet(X) variants, including Tet(X5), through homologous recombination. The novel tet(X) gene is located on a circularizable integrative and conjugative element (ICEEmeChn3), with ISwz1 participating in the recombination of its multi-drug resistance region, potentially facilitating the mobilization and recombination of tet(X) in early hosts. These three strains were clonally transmitted and shared a close genetic relationship (SNP < 62) with a clinically-sourced strain isolated from the same province.

Discussion

To our knowledge, this is the first report of homologous recombination between Tet(X) variants with differing activities. These clonal strains provide evidence of the transmission of tet(X)-positive strains from aquaculture sewage to the natural environment, highlighting the need to strengthen the monitoring and management of this emerging farming model.

Characterization of NMCR-3, NMCR-4 and NMCR-5, three novel non-mobile colistin resistance determinants: Implications for MCR-3, MCR-7, and MCR-5 progenitors, respectively

In this study, the progenitors of MCR-3, MCR-7 and MCR-5, namely NMCR-3, NMCR-4 and NMCR-5, were firstly discovered and indicating Aeromonas was a natural reservoir for MCR-3 and MCR-7. Furthermore, different evolutionary models for MCR-3, MCR-7 and MCR-5 were proposed.

Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes

Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.