Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China

Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period

The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.

Surveillance of Escherichia coli antimicrobial resistance in pig farms in Zhejiang province, China: high prevalence of multidrug resistance and risk-associated genes

OBJECTIVES

The global rise in antimicrobial resistance (AMR) poses a critical threat to public health, with the overuse of antibiotics in livestock being a key driver of this escalating problem. However, research on livestock-associated AMR remains limited, with few systematic monitoring efforts. This study addresses this gap by presenting findings from our surveillance of Escherichia coli resistance in pig farms in Zhejiang Province, China.

METHODS

The minimum inhibitory concentrations were determined via broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence was acquired using both Illumina NovaSeq 6000 platforms. In the plasmid conjugation experiment, sodium azide-resistant E. coli strain J53 served as the recipient. The E. coli genomes were analyzed for AMR genes, multi-locus sequence typing (MLST) types, plasmid types, and virulence genes using the ABRicate.

RESULTS

A total of 51 E. coli strains from 90 fecal samples collected across six farms. Resistance rates for amoxicillin/clavulanic acid and sulfamethoxazole exceeded 90%, while resistance to ampicillin, florfenicol, tetracycline, and trimethoprim/sulfamethoxazole was above 80%. The prevalence of multidrug-resistant strains was 89.24%. Whole-genome sequencing revealed 58 acquired AMR genes and 17 virulence-associated genes, notably including the astA gene. Two strains exhibited meropenem resistance and carried blaNDM-5, located on IncI1-I plasmids. These strains shared an identical genetic context, characterized by an "IS26-IS30-blaNDM-5-bleMBL-dsdD-IS91" structure, which may promote horizontal gene transfer of blaNDM-5. Additionally, six strains harbored the tet(X4) gene.

CONCLUSIONS

Despite ongoing antibiotic reduction efforts, the high prevalence of resistant E. coli in pigs underscores the urgent need for sustained surveillance of AMR in animal populations to mitigate the threat of resistance.

Regression models from portable NIR spectra for predicting the carcass traits and meat quality of beef cattle

The aims of this study were to predict carcass and meat traits, as well as the chemical composition of the 9th to 11th rib sections of beef cattle from portable NIR spectra. The 9th to 11th rib section was obtained from 60 Nellore bulls and cull cows. NIR spectra were acquired at: P1 -center of Longissimus muscle; and P2 -subcutaneous fat cap. The models accurately estimated (P ≥ 0.083) all carcass and meat quality traits, except those for predicting red (a*) and yellow (b*) intensity from P1, and 12th-rib fat from P2. However, precision was highly variable among the models; those for the prediction of carcass pHu, 12th rib fat, toughness from P1, and those for 12th rib fat, a* and b* from P2 presented high precision (R2 ≥ 0.65 or CCC ≥ 0.63), whereas all other models evaluated presented moderate to low precision (R2 ≤ 0.39). Models built from P1 and P2 accurately estimated (P ≥ 0.066) the chemical composition of the meat plus fat, bones and, meat plus fat plus bones, except those for predicting the ether extract (EE) and crude protein (CP) of bones and the EE of Meat plus bones fraction from P2. However, precision was highly variable among the models (-0.08 ≤ R2 ≤ 0.86) of the 9th and 11th rib section. Those models for the prediction of dry matter (DM) and EE of the bones from P1; of EE from P1; and of EE, mineral matter (MM), CP from P2 of meat plus fat plus bones presented high precision (R2 ≥ 0.76 or CCC ≥ 0.62), whereas all other models evaluated presented moderate to low precision (R2 ≤ 0.45). Thus, models built from portable NIR spectra acquired at different points of the 9th to 11th rib section were recommended for predicting carcass and muscle quality traits as well as for predicting the chemical composition of this section of beef cattle. However, it is noteworthy, that the small sample size was one of the limitations of this study.

Detection of mcr-1-harbouring Escherichia coli by quantum dot labelling of synthetic small peptides mimicking lipopolysaccharide receptors

Overuse of antibiotics and the emergence of multidrug-resistant bacteria has made colistin the last line of defence against complex infections. In previous studies, MCR-1-mediated colistin resistance was mainly detected through PCR or antimicrobial susceptibility testing. However, intuitive detection methods for phenotype are rarely reported. In this study, two small peptide antibodies were constructed for immunofluorescence detection of mcr-1-harbouring Escherichia coli: one was a small peptide labelled with a quantum dot antibody; and the other was a small peptide labelled with a fluorescein isothiocyanate (FITC) antibody. Whether using FITC or quantum dots, colistin-resistant bacteria in the sample could be qualitatively detected. The assembled antibodies achieved the desired goals in terms of sensitivity, specificity, precision and repeatability. The non-specific problem of sandwich antigen recognition of lipid A binding to small peptides in modified lipopolysaccharide (LPS) was resolved, and this relatively developed immunofluorescence technique standardised the detection process. Together, in addition to PCR, both fluorescent antibodies can be used for immunofluorescent detection of mcr-1-harbouring E. coli.

Farm to table: colistin resistance hitchhiking through food

Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.

IncHI1 plasmids mediated the tet(X4) gene spread in Enterobacteriaceae in porcine

The tigecycline resistance gene tet(X4) was widespread in various bacteria. However, limited information about the plasmid harboring the tet(X4) gene spread among the different species is available. Here, we investigated the transmission mechanisms of the tet(X4) gene spread among bacteria in a pig farm. The tet(X4) positive Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae and Enterobacter hormaeche were identified in the same farm. The whole genome sequencing (WGS) analysis showed that the K. pneumoniae belonged to ST727 (n = 11) and ST3830 (n = 1), E. cloacae and E. hormaeche belonged to ST524 (n = 1) and ST1862 (n = 1). All tet(X4) genes were located on the IncHI1 plasmids that could be conjugatively transferred into the recipient E. coli C600 at 30°C. Moreover, a fusion plasmid was identified that the IncHI1 plasmid recombined with the IncN plasmid mediated by ISCR2 during the conjugation from strains B12L to C600 (pB12L-EC-1). The fusion plasmid also has been discovered in a K. pneumoniae (K1L) that could provide more opportunities to spread antimicrobial resistance genes. The tet(X4) plasmids in these bacteria are derived from the same plasmid with a similar structure. Moreover, all the IncHI1 plasmids harboring the tet(X4) gene in GenBank belonged to the pST17, the newly defined pMLST. The antimicrobial susceptibility testing was performed by broth microdilution method showing the transconjugants acquired the most antimicrobial resistance from the donor strains. Taken together, this report provides evidence that IncHI1/pST17 is an important carrier for the tet(X4) spread in Enterobacteriaceae species, and these transmission mechanisms may perform in the environment.

Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital

Introduction

Polymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance.

Methods

Polymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome.

Results

Of the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4-256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed.

Discussion

In our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.

The Occurrence and Genomic Characteristics of mcr-1-Harboring Salmonella from Retail Meats and Eggs in Qingdao, China

Salmonella are widely distributed foodborne pathogens and are often associated with food animal products. Colistin resistance mediated by mcr-1 is an increasing threat; however, data on the characteristics of mcr-1-harboring Salmonella among retail foods are still lacking. In this study, retail meats from 24 supermarkets and eggs from nine markets in Qingdao city were investigated to determine the presence and genomic characteristics of mcr-1-harboring Salmonella. We found the retail meats and eggs were highly contaminated by Salmonella, with detection rates of 17.5% (31/177) and 12.3% (16/130), respectively. A total of 76 Salmonella isolates were obtained in this study, and 77.6% showed multidrug resistance (MDR). The MDR proportion of egg isolates (97.5%) was significantly higher than that in meat isolates (55.6%) (p < 0.05). The most prevalent Salmonella serotypes were Typhimurium (56.6%) and Enteritidis (17.1%). Of the 76 Salmonella isolates, 40 possessed mcr-1. All 40 mcr-1-positive isolates were ST34 S. Typhimurium and were from eggs of eight brands. Different mcr-1-harboring isolates existed in the same egg, and some isolates from different egg samples or brands showed clonal relationships. The mcr-1 was located on similar IncHI2/HI2A MDR non-conjugative plasmids lacking transfer region, resulting in the failure of conjugation. The phylogenetic tree using genome sequences showed that the mcr-1-positive isolates from eggs clustered together with mcr-1-positive isolates from chicken and humans in China, revealing that mcr-1-positive egg-borne Salmonella might be derived from chicken and could potentially trigger outbreaks in humans. The high occurrence of mcr-1-harboring Salmonella in fresh eggs is alarming, and there is an urgent need to monitor mcr-1-harboring Salmonella in retail meats and eggs. We report for the first time the role of retail eggs in disseminating mcr-1-positive Salmonella and the risk of transmission of these MDR pathogens from retail food to humans should be evaluated comprehensively.

Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China

Escherichia coli is considered an opportunistic pathogen and an indicator for antimicrobial resistance (AMR) monitoring. Despite many reports on its AMR monitoring, studies based on genome-based analysis of AMR genes are still insufficient. Here, 181 E. coli strains were isolated from anal swab samples collected from pigs and chickens of animal farms located in Eastern China and sequenced through the Illumina platform. The results showed that 87.85% (159/181) of the E. coli isolates were multidrug-resistant (MDR). Ampicillin (AMP)- spectinomycin (SPT)- tetracycline (TET)- florfenicol (FFC)- sulfisoxazole (SF)- trimethoprim/sulfamethoxazole (SXT) was the predominant AMR pattern. By whole-genome sequencing, we found that ST10 (10.49%, 19/181) and ST48 (7.18%, 13/181) were major sequence types. IncFIB and IncX1 were the most prevalent plasmid replicons. The AMR genes bla NDM-5 (1.10%, 2/181), mcr-1 (1.10%, 2/181), tet(X4) (1.10%, 2/181), and cfr (6.08%, 2/181) were also found in these isolates. In addition, among the 169 virulence genes detected, we identified astA (37.02%, 67/181), hlyA (1.66%, 3/181), hlyB (1.66%, 3/181) and hlyD (1.66%, 3/181), which were closely related to heat-stable enterotoxin 1 and α-hemolysin. In addition, there were 33 virulence genes associated with the iron uptake system, and 46 were adhesion-related genes. Our study highlighted the need for routine surveillance of AMR with advanced genomic approaches, providing up-to-date data on the prevalence of AMR for the development and execution of antimicrobial stewardship policy.

Genomic characterization of multidrug-resistance gene cfr in Escherichia coli recovered from food animals in Eastern China

The plasmid-borne cfr gene, mediating multiple drug resistance (MDR), has been observed in many Gram-positive bacteria. The prevalence of cfr and its co-occurrence with additional antimicrobial resistance (AMR) determinants in Escherichia coli is an ongoing issue. Additionally, the prevalence and transfer mechanism of the cfr gene remain partially investigated. Here, eight cfr-positive E. coli strains were screened using PCR from an extensive collection of E. coli (n = 2,165) strains isolated from pigs and chickens in 2021 in China, with a prevalence rate of 0.37%. All of them were MDR and resistant to florfenicol and tetracycline. These strains can transfer the cfr gene to E. coli J53 by conjugation (1.05 × 10⁻¹ – 1.01 × 10⁻⁶). Moreover, the IncX4 plasmid p727A3-62 K-cfr (62,717 bp) harboring cfr in strain EC727A3 was confirmed using Oxford Nanopore Technology. The unknown type plasmid p737A1-27K-cfr (27,742 bp) harboring cfr in strain EC737A1 was also identified. Notably, it was verified by PCR that three of the eight E. coli strains were able to form the cfr-IS26 circular intermediate. It was 2,365 bp in length in strains EC727A3 and ECJHZ21-173, and 2,022 bp in length in EC737A1. Collectively, this study demonstrated that IS26 plays a vital role in transmitting the MDR gene cfr in E. coli via conjugation and provided updated knowledge regarding cfr in E. coli in Eastern China.