Prevalence and molecular characteristics of mcr-1-positive Escherichia coli isolated from duck farms and the surrounding environments in coastal China

IncI2 plasmid transfer and changes of intestinal microbiota in mice under β-lactam antibiotic pressure

BACKGROUND

β-lactam antibiotics represent the most widely utilized class of antimicrobial agents in livestock and poultry breeding. However, the effects of β-lactam antibiotics on conjugation transfer of IncI2 plasmids and the homeostasis of the mouse intestinal microbiota have not been thoroughly investigated.

RESULTS

The results revealed that the transfer of IncI2 plasmid was the highest for intra-specific E. coli and inter-specific transfer to Salmonella and K. pneumoniae occurred at much lower levels in the absence of β-lactam antibiotic selective pressure. Furthermore, inter-species and intra-species transfer of IncI2 plasmid was enhanced in the presence of sub-MIC levels of amoxicillin/clavulanate and cephalexin whereas ampicillin promoted only inter-species transfer. These results were consistent with in vivo observations where amoxicillin/clavulanate and cephalexin but not ampicillin promoted conjugation. Meanwhile, the intestinal microbiota was also disturbed following antibiotic treatment and Proteobacteria abundance increased while Bacteroides decreased. The gut microbiota could also be partially restored to initial levels after antibiotic cessation for 14 days.

CONCLUSIONS

These findings highlight the potential risk of β-lactam antibiotics in promoting the spread of resistance plasmids and causing disruption to the intestinal microbiota.

One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems

The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.

Antimicrobial peptides: from discovery to developmental applications

Antimicrobial resistance (AMR) has emerged as a significant crisis in global health. Due to their advantageous properties, antimicrobial peptides (AMPs) have garnered considerable attention as a potential alternative therapy to address the AMR crisis. These peptides might disrupt cell membranes or cell walls to exhibit antimicrobial activity, or modulate the immune response to promote recovery from diseases. In recent years, significant progress has been made in the research of AMPs, alongside the emergence of new challenges. This review first systematically summarizes and critically discusses recent advancements in understanding the characteristics and current landscapes of AMPs, as well as their regulatory mechanisms of action and practical applications, particularly those reported or approved within the last 5 years. Additionally, the principles, paths for their identification, and future research trends in AMPs are also analyzed following a discussion of the advantages and disadvantages of AMPs in comparison to conventional antibiotics. Unlike significant prior literature in this field, this report has summarized the latest major discovery methods for AMPs and, more importantly, emphasized their practical applications by supporting various viewpoints using selected examples of AMPs' applications in real-life scenarios. Besides, some emerging hot topics of AMPs, including those derived from gut microbiota and their potential synergistic effects in combating AMR, were profiled. All of these indicate the originality of the report and provide valuable references for future AMP discoveries and applications.

Molecular epidemiology of New Delhi metallo-β-lactamase-producing Escherichia coli in retail market chickens, Shandong, China

Background

The global spread of carbapenem-resistant Escherichia coli is a major public health concern. An investigation of their presence in the human and food chain products would facilitate the elucidation of the route of their food-borne transmission. Thus, the aim of this study was to investigate the prevalence of NDM-positive E. coli isolates in chicken at retail markets in Shandong, China.

Methods

A total of 60 NDM-positive isolates were recovered from 531 E. coli isolates obtained from chickens at the retail market in Shandong. Antimicrobial susceptibility testing and polymerase chain reaction screening were performed to investigate the phenotype and genotype of carbapenemase resistance. Genomic characteristics of the -producing isolates were determined by WGS and bioinformatic analysis.

Results

All of these isolates were multidrug-resistant (MDR), with a majority exhibiting resistance to meropenem, ampicillin, ceftazidime, cefotaxime, florfenicol, sulfamethoxazole/trimethoprim, and tetracycline. Whole genome sequencing (WGS) analysis indicated that these isolates were belonged to 18 distinct sequence types (STs), with the most prevalent STs being ST515 (17/60) and ST69 (11/60). Additionally, WGS analysis revealed that clonal spread of NDM-positive ST69 and ST515 E. coli isolates at markets in different cities in Shandong. Phylogenomic analysis showed that NDM-positive E. coli isolates from chickens were closely related to those of human origin.

Conclusion

This study provides a new insight into the spread of NDM-positive E. coli isolates from retail chicken, and offers essential data for public health management.

Prevalence, transmission and genomic epidemiology of mcr-1-positive colistin-resistant Escherichia coli strains isolated from international airplane waste, local resident fecal and wastewater treatment plants

The emergence and dissemination of mcr-1-positive Escherichia coli (MCRPEC) represent a critical public health threat. Here, we conducted a prospective analysis of MCRPEC isolates from wastewater treatment plants (WWTPs), local residents' fecal (LRF), and international airplane waste (IAW) to investigate their genetic characteristics and transmission patterns circulating in human-environment domains. The MCRPEC prevalence was 2.43 % in WWTPs, 1.37 % in IAW and 0.69 % in LRF. MCRPEC showed substantial genetic diversity, encompassing 61 sequence types (primarily ST1011, ST101, and ST2705), 7 plasmid types (primarily IncI2), 8 phylogroups (primarily A and B1), 9 mcr-1-flanked lineages (primarily L5), 6 clusters (primarily C2 and C4), diverse serotypes, and 61.95 % transposon-containing strains. The mcr-1 gene co-existed with 46 antibiotic resistance genes (ARGs) and 19 virulence factor genes (VFGs). Notably, 6 IncI2 plasmids carried the blaCTX-M, IS1380, and mcr-1 genes. MCRPEC from WWTPs harbored a greater number of ARGs (56.95 ± 5.99) but fewer VFGs (15.03 ± 6.40) compared to those from human-associated sources (LRF and IAW). ST1011, ST2705, IncHI2, and L7 were prevalent in WWTP-derived MCRPEC, whereas IncX4 and L3 were more common in human-derived MCRPEC. Genetic features such as ST101, ST48, IncI2, L4, L5, C2, and C4 were simultaneously present in strains from LRF, IAW, and WWTPs. Core genetic analyses also showed genetically similar MCRPEC strains across various geographic locations. The findings underscore the extensive dissemination, strong environmental adaptation, and clonal transmission of MCRPEC across diverse reservoirs, reinforcing the urgent need for coordinated multisectoral surveillance of human and environment interfaces to effectively mitigate further transmission.

Convergence of mcr-1 and broad-spectrum β-lactamase genes in Escherichia coli strains from the environmental sector

The mcr-type gene encodes the main plasmid-mediated mechanism of colistin resistance and has been reported in several bacterial species obtained from different sources. Anthropogenic activities in the environment favor the evolution of antimicrobial resistance. Indeed, mcr-1-positive Escherichia coli strains were susceptible to non-polymyxins antimicrobials, but now emerging as multidrug-resistant (MDR) lineages. In this regard, hundreds of surface water and agricultural soil samples were screened for the presence of E. coli carrying the mcr-type genes and mcr-1-positive strains were subjected to in-depth genomic analysis. Almost all colistin-resistant strains were classified as MDR, highlighting those obtained from soils that showed resistance to extended-spectrum cephalosporins and carbapenems. International and high-risk clones of E. coli were identified, with ST10 and ST1720 shared between water and soil samples. Resistome analysis showed a broad resistome (AMR, metal tolerance, and biocide resistance). The mcr-1.1 and mcr-1.26 allelic variants were detected on IncX4 and IncI2 plasmids. Curiously, mcr-1-positive E. coli strains from agricultural soils harbored plasmid-mediated blaCTX-M-1, blaCTX-M-8, or blaKPC-2 genes. Virulome analysis demonstrated traits of a high putative virulence potential, with the presence of extraintestinal pathogenic E. coli. Comparative analysis revealed the persistence and dissemination of plasmid-mediated antimicrobial resistance genes in genetically diversity E. coli strains at the human-animal-environmental interface. These findings demonstrate a possible emerging AMR trend with the convergence of resistance to colistin and broad-spectrum β-lactams in environmental-derived E. coli strains.

Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage

Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.

High prevalence and transmission of blaNDM-positive Escherichia coli between farmed ducks and slaughtered meats: An increasing threat to food safety

The emergence of carbapenem-resistant bacteria especially carbapenem-resistant Escherichia coli (CREC) in food animals poses a serious threat to food safety and public health. Reports about the dissemination of carbapenem-resistant bacteria along the food animal production chain are scattered and mainly focus on swine and chicken. Abuse of antibiotics in duck farms is common especially in China which has the largest duck production industry, however, the CREC transmission between farmed ducks and slaughtered meats remains unclear and the role of slaughterhouse in disseminating CREC among duck meats remains largely unknown. Herein, we collected 251 fecal samples from five typical duck farms along with 125 slaughtered meat samples (25 from each farm) in the corresponding slaughterhouse in Anhui Province, China, in December 2018. All samples were screened for CREC isolates which were analyzed for the presence of carbapenemase genes and colistin resistance gene mcr. The resistance profiles, transferability, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing and phylogenetic analysis of the CREC isolates from both ducks and meats were further characterized. This is the first report presenting the high prevalence of blaNDM-positive CREC isolates in ducks from duck farms (57.8 %) and slaughtered meats (33.6 %) in the corresponding slaughterhouse. Among the 203 blaNDM-positive CREC isolates obtained in this study, 19.2 % harbored mcr-1 and all CREC isolates showed resistance to nearly all currently available antibiotics (except tigecycline). Of note, mcr-1 was found in 17.8 % of the meat-derived CREC carrying blaNDM. Based on the PFGE analysis, clonal spread of blaNDM-positive CREC including some also carrying mcr-1 was found between farmed ducks and slaughtered duck meats even from different farms. Special attention should be paid to the clonal dissemination of meat-derived CREC within the slaughterhouse, which contributed to the high prevalence of blaNDM in slaughtered meats. Additionally, horizontal transmission mainly mediated by transferable blaNDM-5-bearing IncX3 plasmids, untypable blaNDM-1-bearing plasmids and mcr-1-bearing IncHI2 plasmids further facilitated the rapid spread of such multidrug-resistant strains. Notably, the blaNDM-bearing plasmids and mcr-1-bearing plasmids in CREC from meats were highly similar to those from animals and humans. More worryingly, the phylogenomic analysis showed that CREC isolates from both ducks and corresponding meats clustered with previously reported human CREC isolates carrying mcr-1 in different geographical areas including China. These findings further prove that the CREC and resistance plasmids in farmed ducks could transmit to meats even from different farms via the slaughterhouse and then trigger infections in humans. The high prevalence and clonal transmission of CREC isolates including those also carrying mcr-1 between ducks and meats are alarming, and urgent control measures are required to reduce the dissemination of such organisms.

Colistin resistance in ESBL- and Carbapenemase-producing Escherichia coli and Klebsiella pneumoniae clinical isolates in Cambodia

OBJECTIVES

Despite the critical importance of colistin as a last-resort antibiotic, limited studies have investigated colistin resistance in human infections in Cambodia. This study aimed to investigate the colistin resistance and its molecular determinants among Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing (CP) Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) isolated in Cambodia between 2016 and 2020.

METHODS

E. coli (n = 223) and K. pneumoniae (n = 39) were tested for colistin minimum inhibitory concentration (MIC) by broth microdilution. Resistant isolates were subjected to polymerase chain reaction (PCR) for detection of mobile colistin resistance genes (mcr) and chromosomal mutations in the two-component system (TCS).

RESULTS

Eighteen isolates (10 K. pneumoniae and 8 E. coli) revealed colistin resistance with a rate of 5.9% in E. coli and 34.8% in K. pneumoniae among ESBL isolates, and 1% in E. coli and 12.5% in K. pneumoniae among CP isolates. The resistance was associated with mcr variants (13/18 isolates, mcr-1, mcr-3, and mcr-8.2) and TCS mutations within E. coli and K. pneumoniae, with the first detection of mcr-8.2 in Cambodia, the discovery of new mutations potentially associated to colistin resistance in the TCS of E. coli (PhoP I47V, PhoQ N352K, PmrB G19R, and PmrD G85R) and the co-occurrence of mcr genes and colistin resistance conferring TCS mutations in 11 of 18 isolates.

CONCLUSIONS

The findings highlight the presence of colistin resistance in ESBL- and CP- Enterobacteriaceae involved in human infections in Cambodia as well as chromosomal mutations in TCS and the emergence of mcr-8.2 in E. coli and K. pneumoniae. It underscores the need for continuous surveillance, antimicrobial stewardship, and control measures to mitigate the spread of colistin resistance.

Epidemiology and genetic characterization of tet(X4)-positive Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from raw meat in Chengdu City, China

The rapid spread of mobile tigecycline resistance presents a significant public health threat, particularly with the increasing prevalence of tet(X4)-positive Enterobacterales across various species. This study aimed to investigate the epidemic features and transmission dynamics of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) through the analysis of 206 raw meats, including pork (n = 182), beef (n = 16), duck (n = 5), and chicken (n = 3). These samples were collected from schools, markets, and restaurants in Chengdu City, China. A total of 25 isolates were obtained from 13 administrative regions. All isolates exhibited resistance to tetracycline, tigecycline, ampicillin, chloramphenicol, and florfenicol. Over half of the isolates also demonstrated resistance to streptomycin (80 %), sulfamethoxazole/trimethoprim (72 %), ciprofloxacin (64 %), and ampicillin/sulbactam (56 %). Among these strains, 14 distinct sequence types (STs) were identified, revealing evidence of inter-regional clonal spread, notably among 9 K. pneumoniae ST3393. Phylogenetic analysis revealed the presence of two K. pneumoniae ST5 closely resembling hypervirulent K. pneumoniae from Jiangsu. Importantly, 12 isolates were capable of transferring tigecycline resistance to Escherichia coli J53. Further plasmid analysis showed that the tet(X4)-harboring plasmids in K. pneumoniae could be classified into four types, primarily belonging to the IncFIA(HI1)/HI1A/HI1B hybrid plasmid (n = 16) and IncFII plasmid (n = 7), which significantly contributed to the cross-species dissemination of tet(X4). In summary, this study highlights the prevalence of MDR tet(X4)-positive K. pneumoniae in Chengdu, driven predominantly by clonal expansion and plasmid-mediated horizontal gene transfer. These findings emphasize the importance of continuous surveillance of tet(X4)-positive K. pneumoniae in raw meat and the implementation of effective measures to control their spread.

Emergence and Genomic Features of a mcr-1 Escherichia coli from Duck in Hungary

Plasmids carrying high-risk resistance mechanisms in pathogenic E. coli have gained particular attention in veterinary medicine, especially since the discovery of the colistin resistance gene, mcr-1. Here, we provide the first evidence of its emergence and describe the complete mcr-1 plasmid sequence of a multi-resistant avian pathogenic E. coli (APEC) strain from waterfowl in Hungary. Whole-genome sequencing analysis and core-genome MLST were performed to characterize the genome structure of the mcr-1 plasmid and to reveal the phylogenetic relation between the Hungarian duck strain Ec45-2020 and the internationally circulating mcr-1-positive E. coli strains from poultry and humans. Results showed that plasmid pEc45-2020-33kb displayed a high level of genome identity with mcr-1 plasmids of IncX4 type widespread among human, animal and food reservoirs of enteric bacteria of public health. The mcr-1-positive E. coli strain Ec45-2020 belongs to the ST162 genotype, considered as one of the globally disseminated zoonotic genotypes of MDR E. coli. In accordance with international findings, our results underline the importance of continuous surveillance of enteric bacteria with high-risk antimicrobial resistance genotypes, including neglected animals, such as waterfowls, as possible reservoirs for the colistin resistance gene mcr-1.