Prevalence and characteristics of mcr-9-positive Salmonella isolated from retail food in China

Comprehensive Analysis of β-lactam Resistant Non-Typhoidal Salmonella Isolates: Phenotypic and Genotypic Insights from Clinical Samples in Japan

OBJECTIVES

This study examines β-lactam-resistant non-typhoidal Salmonella isolates using phenotypic and genotypic analyses to elucidate resistance mechanisms and epidemiological characteristics.

METHODS

A total of 1663 clinical Salmonella spp. isolates were collected (1994-2016), with 122 exhibiting β-lactam resistance, confirmed via antimicrobial susceptibility testing. Resistance mechanisms were further explored through genotypic analysis by whole genome sequencing, plasmid characterization, and phylogenomic investigations.

RESULTS

All isolates were resistant to at least one β-lactam. Resistance to third-generation cephalosporins was notable, while carbapenem resistance was rare (0.8%). High resistance was observed for minocycline (36.9%) and sulfamethoxazole-trimethoprim (28.7%), whereas resistance to fluoroquinolones (3.3%-5.7%), aminoglycosides (0.8%-8.2%), and tigecycline (8.2%) was low. All isolates remained susceptible to fosfomycin, and 21.3% exhibited multidrug resistance. Genotypic analysis identified diverse serotypes and sequence types, with S. Typhimurium and ST19 being predominant. The most common β-lactamase gene was blaTEM, followed by blaCARB-2, with significant correlations between β-lactam and aminoglycoside resistance genes. Plasmid analysis revealed a high prevalence of plasmid carriage, with IncFII(S) and IncFIB(S) being predominant, strongly associated with antimicrobial resistance genes. Phylogenetic analysis provided insights into the global dissemination of Salmonella, particularly those carrying mcr-9, while clustering analysis revealed shared genetic patterns among isolates sourced from different hosts, highlighting the potential for cross-species transmission.

CONCLUSIONS

These findings underscore the complex interplay of resistance mechanisms and emphasize the need for integrated surveillance and intervention strategies to combat antimicrobial resistance in Salmonella, reinforcing the necessity for ongoing public health efforts.

Global prevalence and transmission of the mcr-9 in Salmonella: A genomic study with insights from Salmonella enterica serovar Thompson isolated from poultry food in China

The plasmid-mediated mcr-9 gene has been widely detected in Salmonella across multiple countries and regions, raising significant concerns for food safety and public health. To investigate the transmission dynamics of mcr-9 in Salmonella, we conducted a comprehensive genomic epidemiological study and explored the potential mechanisms of mcr-9 transmission in poultry-derived S. Thompson in China. This study analyzed 126 mcr-9-positive Salmonella isolates from food in China and genomic data of 1,487 publicly available mcr-9-positive Salmonella collected over the past 40 years from 32 countries and various sources. Two variants, mcr-9.1 and mcr-9.2, were detected, with mcr-9.1 being the most prevalent subtype globally. S. Typhimurium/I 4,[5],12:i:- (23.1 %, 372/1,613) was the dominant lineage of the total collection, followed by S. Saintpaul (15.9 %, 256/1,613), S. Heidelberg (11.4 %, 184/1,613), and S. Thompson (8.6 %, 139/1,613). S. Typhimurium/I 4,[5],12:i:- was widely distributed in North America and Europe, primarily prevalent in humans and swine, whereas S. Thompson was predominantly found in China, mainly prevalent in poultry-related foods and humans. Conjugation experiments were performed on 116 S. Thompson strains from 126 Salmonella isolates. The results showed that 85.3 % (99/116) of the mcr-9-positive plasmids were transferable. The IncHI2-IncHI2A plasmids from three representative donors demonstrated the ability to transfer at varying frequencies to seven Salmonella recipients of different serotypes including Typhimurium, Thompson, Enteritidis, Indiana, Rissen, London, and Derby. Chicken juice matrix significantly increased the proportion of mcr-9-positive S. Thompson conjugants. The inability of mcr-9-positive IncHI2-IncHI2A plasmids to transfer via conjugation may be due to the integration of the plasmid into the chromosome. In addition, the deletion of IS1B-cfdB-fucO-frmR-uvrA-fghA-gloA-frmA-uvrB-flhD-smc-copG-IS26 gene region was observed in the non-conjugative mcr-9-positive plasmids. These findings underscore the importance of ongoing surveillance of mcr-9-positive multidrug-resistant S. Thompson for food safety in China.

Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies

Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.