Whole-genome analysis of multidrug-resistant Kluyvera intermedia strain L-40-1 isolated from a pig with respiratory disease.

IMPORTANCE

Kluyvera intermedia (K. intermedia) is an emerging pathogen associated with respiratory disease in pigs. Its multidrug resistance poses a significant threat to livestock health.

OBJECTIVE

This study characterized the resistance phenotype and genotype of K. intermedia L-40-1, isolated from a pig in Jilin Province, China, and investigated the genomic determinants of its antibiotic resistance.

METHODS

16S rRNA sequencing was performed to identify the strain. The resistance phenotype was assessed by determining minimum inhibitory concentrations (MICs), and resistance determinants were characterized by whole-genome sequencing. Comparative genomic analysis against the national center for biotechnology information (NCBI) database of K. intermedia strains was conducted to determine phylogenetic relationships and resistance gene profiles.

RESULTS

L-40-1 exhibited high resistance to β-lactams, cephalosporins, macrolides, aminoglycosides, and sulfonamides. Comparative analysis identified 19 high-frequency resistance genes (e.g., arnT, rsmA, emrR, and acrA). A 159,618 bp plasmid (PYL-8) harbored multiple resistance genes (e.g., sul1, dfrA27, qnrB6, and tet(D)) and transposons (e.g., IS6, IS1, and Tn3), contributing to its multidrug resistance. Chromosomal and plasmid-borne resistance mechanisms were identified.

CONCLUSIONS AND RELEVANCE: K. intermedia L-40-1 uses a combination of chromosomal and plasmid-mediated resistance genes, facilitated by transposons, to confer multidrug resistance. This highlights the need for surveillance of K. intermedia in livestock to mitigate the spread of antibiotic resistance.