James-Gzyl, K. E. | bioRxiv Science

bioRxiv2024

Genomic and metabolic characterization of Trueperella pyogenes isolated from domestic and wild animals

Trueperella pyogenes is an important bacterial pathogen implicated in infections such as mastitis, metritis, pneumonia, and liver abscesses in both domestic and wild animals as well as endocarditis and prosthetic joint infections in humans. Understanding the genomic and metabolic features that enable T. pyogenes to colonize different anatomical sites within a host and its inter-kingdom transmission and survival is important for the effective control of this pathogen. We employed whole genome sequencing, phenotype microarrays, and antimicrobial susceptibility testing to identify genomic, metabolic and phenotypic features as well as antimicrobial resistance (AMR) genes in T. pyogenes recovered from different livestock, companion and wildlife animals. For comparative genomic analysis, 83 T. pyogenes genomes, including 60 isolated in the current study and 23 publicly available genomes were evaluated. These genomes represented T. pyogenes strains originated from 16 different body sites of 11 different animal hosts (e.g. bovine, swine, ovine, cervid, bison, equine, chamois, feline). Additionally, 49 T. pyogenes isolates (bovine, ovine, deer, swine and feline) were evaluated for phenotypic antimicrobial resistance using disk diffusion, and for metabolic profiling using the Biology GENIII MicroPlates. We identified that T. pyogenes strains are not host- or body site-specific. The presence of conserved virulence genes (plo and fimA), as well as genotypic and phenotypic AMR may contribute to T. pyogeness ability to cause infections in livestock, wildlife, and pets. Most of the tested isolates metabolized diverse carbon sources and chemical compounds, suggesting that this metabolic versatility may contribute to T. pyogenes survival, competitive advantage, and pathogenic potential. ImportanceTrueperella pyogenes is an important animal pathogen with zoonotic potential, posing a significant health concern to both animals and humans due to its ability to cause infections across different animal host species and tissues. Current understanding of this pathogens adaptability and survival mechanisms is limited. Here, we evaluated the genomic, virulence, metabolic, and antimicrobial resistance characteristics of T. pyogenes recovered from 16 different body sites of 11 different animal hosts (livestock, companion, and wild animals). We identified multiple antimicrobial resistance and virulence genes that may enable T. pyogenes for sustained infection and transmission. Additionally, T. pyogenes strains displayed metabolic versatility which could also contribute to its ability to thrive in diverse environments. Understanding the genomic and metabolic, and antimicrobial resistance characteristics that enable T. pyogenes to colonize different anatomical sites within a host and its transmission between different animal species is important for the effective control of this pathogen.

microbiology↗

bioRxiv2024

Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes

Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications. However, information regarding its effect on the pig gut microbiome and resistome is lacking. Therefore, this study investigated those effects by treating piglets with an intramuscular injection of florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (n =30) and untreated (n = 30) pigs at nine different time points up until 140 days of age and their microbiomes were profiled using both 16S rRNA gene and shotgun metagenomic sequencing. The gut microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an enrichment in Clostridium scindens, Enterococcus faecalis, and Escherichia spp. in the florfenicol-treated piglets and Fusobacterium spp., Pauljensenia hyovaginalis, and Ruminococcus gnavus in the control piglets. In addition to florfenicol resistance genes including floR, fexA, and fexB, florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, peptides, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant Escherichia coli isolated from these piglets were found to carry a plasmid with a floR, along tet(A), aph(6)-Id, aph(3)-Ib, sul2, and blaTEM-1/ blaCMY-2. A plasmid carrying fexB and poxtA was identified in florfenicol-resistant Enterococcus avium, Enterococcus faecium, and E. faecalis isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the gut microbial community in pre-weaned piglets administered florfenicol. ImportanceAntimicrobial use and resistance remain a serious challenge in food-animal production systems. Understanding how specific antimicrobials affect the gut microbiome and resistome is an important step in reducing antimicrobial use and resistance. Florfenicol is an antimicrobial used in swine production, yet very little is known about its effect on the pig gut microbiome and resistome. In this study, we administered florfenicol to piglets at 1 and 7 days of age and characterized their fecal metagenomes through to 140 days of age. Florfenicol altered the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve an Escherichia coli plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. These results demonstrate the potential for certain antimicrobials to co-select for multiple, unrelated antimicrobial resistance genes in pigs.

microbiology↗