Clonal dissemination of methicillin-resistant Staphylococcaceae between Algerian sheep farms

Objectives: Sheep farming represents an important economic sector in Algeria, and the potential dissemination of methicillin-resistant Staphylococcaceae (MRS) is a critical veterinary and public health concern. This study aimed to determine the prevalence and types of MRS in ovine in Algeria and characterize them using whole-genome sequencing (WGS) analysis.

Methods: Two hundred sheep from twenty different Algerian farms across three regions were screened for nasal colonization with MRS. The isolates were identified by MALDI-TOF MS, their minimal inhibitory concentration (MIC) was determined by broth microdilution, and the presence of mec gene was confirmed with PCR. The mec-positive isolates were sequenced using Illumina technology to build species specific cgMLST- and single nucleotide polymorphisms (SNPs)-based phylogenies and perform an in-silico screening for antimicrobial resistance genes.

Results: The prevalence of MRS-positive farms was 85% (95% CI, 69.34%-100%) across the sampled farms. Ten distinct Staphylococcaceae species were identified, with Staphylococcus saprophyticus (n=29), Mammaliicoccus lentus (n=24), and Staphylococcus haemolyticus (n=19) being the predominant species. WGS-based phylogeny and SNP analysis (0 to 126 SNPs) revealed that isolates of these three species were highly related, indicating clonal dissemination within and between farms. MRS exhibited a multi-drug resistance pattern, with detection of resistance genes for β-lactams, tetracyclines, fusidic acid, trimethoprim, aminoglycosides, tiamulin and macrolides.

Conclusions: Specific clonal lineages of methicillin-resistant S. saprophyticus, S. haemolyticus, and M. lentus are widespread in Algerian sheep farms. Enhancing hygiene practices on farms is recommended to prevent further dissemination of these resistant strains to animals and humans.