Genomic characterization of tigecycline-resistant tet(X4)-positive E. coli in slaughterhouses

Towards identification of new genetic determinants for post-weaning diarrhea in piglets

Post-weaning diarrhea in pigs is a considerable challenge in the pig farming industry due to its effect on animal welfare and production costs, as well as the large volume of antibiotics, which are used to treat diarrhea in pigs after weaning. Previous studies have revealed loci on SSC6 and SSC13 associated with susceptibility to specific diarrhea causing pathogens. This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biological determinants for diarrhea susceptibility. With the present work, we revealed a new locus for diarrhea resistance on SSC16. Furthermore, studies of metabolomics in the same pigs revealed one metabolite associated with diarrhea.

Emergence of plasmid-mediated tigecycline resistance tet(X4) gene in Enterobacterales isolated from wild animals in captivity

Background

Over the past few decades, antimicrobial resistance (AMR) has emerged as a global health challenge in human and veterinary medicine. Research on AMR genes in captive wild animals has increased. However, the presence and molecular characteristics of tet(X)-carrying bacteria in these animals remain unknown.

Methods

Eighty-four samples were collected from captive wild animals. tet(X) variants were detected using polymerase chain reaction and the isolates were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. All isolated strains were subjected to antimicrobial susceptibility testing and whole-genome sequencing. The virulence of an Escherichia coli strain carrying enterotoxin genes was assessed using a Galleria mellonella larval model.

Results

We isolated two tet(X4)-positive E. coli strains and one tet(X4)-positive Raoultella ornithinolytica strain. Antimicrobial susceptibility tests revealed that all three tet(X4)-carrying bacteria were sensitive to the 13 tested antimicrobial agents, but exhibited resistance to tigecycline. Notably, one tet(X4)-carrying E. coli strain producing an enterotoxin had a toxic effect on G. mellonella larvae. Whole-genome sequencing analysis showed that the two tet(X4)-carrying E. coli strains had more than 95% similarity to tet(X4)-containing E. coli strains isolated from pigs and humans in China.

Conclusion

The genetic environment of tet(X4) closely resembled that of the plasmid described in previous studies. Our study identified tet(X4)-positive strains in wildlife and provided valuable epidemiological data for monitoring drug resistance. The identification of enterotoxin-producing E. coli strains also highlights the potential risks posed by virulence genes.

Emergence of plasmid-mediated high-level tigecycline resistance gene tet(X4) in Enterobacterales from retail aquatic products

The spread of antimicrobial-resistant microbes and genes in various foods poses a significant threat to public health. Of particular global concern is the plasmid-mediated tigecycline resistance gene tet(X4), which, while identified in various sources, has not hitherto been reported in aquatic products. This study aimed to investigate the occurrence and characterization of tigecycline-resistant strains from aquatic products. A total of 73 nonrepetitive seafood samples were purchased from 26 farmers' markets to detect tigecycline-resistant strains. Of these, nine Escherichia coli strains (comprising two ST58, one ST195, ST10, ST48, ST88, ST877, ST1244, ST14462) and one Citrobacter meridianamericanus, recovered from nine (12.33 %, 9/73) seafood samples (fish, n = 7; shrimp, clam and crab, n = 1 respectively), were positive for the tet(X4). Notably, phylogenetic analysis showed that E. coli ST195, a common ST carrying tet(X4), has a close phylogenetic relationship (23∼48 SNPs) with 32 tet(X4)-harboring E. coli ST195 isolates (isolated from pigs, animal foods, vegetable, and humans) deposited in NCBI database. Additionally, E. coli ST58 was closely (2 SNPs) related to one tet(X4)-positive E. coli strain from retail vegetables documented in the NCBI database. Whole genome sequencing and bioinformatic analysis revealed that tet(X4) genes were located on IncX1 (7 E. coli) or hybrid plasmid IncFIA(HI1)/IncHI1B(R27)/IncHI1A (2 E.coli and one C. meridianamericanus). These plasmids displayed high homology with those of plasmids from other sources deposited in GenBank database. These findings underscore the role of epidemic clones and plasmids in driving the dissemination of tet(X4) gene within Enterobacterales of aquatic products origin. To the best of our knowledge, this is the first report of tet(X4)-positive Enterobacterales from aquatic products. The pervasive propagation of tet(X4) gene facilitated by epidemic plasmids and clones across food animals, food products, humans, and the environment presents a serious threat to public health.

Decoding the enigma: unveiling the molecular transmission of avian-associated tet(X4)-positive E. coli in Sichuan Province, China

Tigecycline is considered one of the "last resort antibiotics" for treating complex infections caused by multidrug-resistant (MDR) bacteria, especially for combating clinical resistant strains that produce carbapenemases. However, the tet(X4) gene, which carried by different plasmids can mediate high levels of bacterial resistance to tigecycline, was first reported in 2019. Here, we report the emergence of the plasmid-mediated tet(X4) in avian environment of Sichuan Province. A total of 21 tet(X4)-positive Escherichia coli (E. coli) strains were isolated and identified from avian samples in selected regions, with an isolation rate of 1.6% (21/1,286), and all of them were MDR strains. Multilocus Sequence Typing (MLST) method was used to classify the 21 tet(X4)-positive E. coli into the ST206, ST761, ST155, ST1638, ST542, and ST767 types, which also belong to the 3 phylogenetic subgroups A, B1, and C. Tet(X4) is located on mobile plasmids that can be efficiently and stably propagated. The results of fitness cost experiments showed that tet(X4)-positive plasmids may incur some fitness cost to host bacteria, but different tet(X4)-positive plasmids bring about differential fitness costs. Whole-genome sequencing further confirmed the tet(X4) gene can be located on IncX1-type plasmids and the core genetic structures are ISVsa3-rdmc-tet(X4) or rdmc-tet(X4)-ISVsa3, the former is a 7 copies tandem repeat structure. In this study, we isolated and identified tet(X4)-positive E. coli from the avian origin in Sichuan, analyzed the mobility of the tet(X4) by conjugational transfer and S1-PFGE, and evaluated the biological characteristics of the tet(X4)-positive plasmid using the results of conjugational frequency, plasmid stability, and fitness costs. Finally, combined with the third-generation whole-genome sequencing analysis, the molecular transmission characteristics of the tet(X4) were preliminarily clarified, providing a scientific basis for guiding veterinary clinical use in this area, as well as risk assessment and prevention of the transfer and spread of tigecycline resistant strains or genes.