Genomic epidemiology and zoonotic potential of staphyloccus aureus from pigs and humans in Lusaka province of Zambia.

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Samutela, Mulemba Tillika
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The University of Zambia
Pigs have been shown to be a reservoir for Staphylococcus aureus (S. aureus) including methicillin resistant strains which are collectively called Livestock- associated S. aureus (LA-SA) and Livestock-associated Methicillin-resistant S. aureus (LA-MRSA), respectively. These strains significantly colonise and cause infection in farmworkers and other individuals in contact with pigs. These persons are presumably the source of LA-SA transmission to household members and their associates. However, there is sparse information about LA-SA strains circulating in most African countries, including Zambia. This study aimed at determining the genomic epidemiology and zoonotic potential of S. aureus from pigs, farm and abattoir workers in selected districts of Lusaka province of Zambia. It was a cross-sectional study in which a total of 493 pig nasal swabs, 53 hand and nasal swabs each were collected from farm and abattoir workers. Forty-four human clinical isolates from a previous study were also included for selected genotypic investigation. Conventional microbiological methods were used to detect and identify S. aureus while the disc diffusion method was used to determine the antimicrobial susceptibility patterns. Polymerase chain reaction (PCR) with gene specific primers was used to confirm the species identity of S. aureus and detection of antimicrobial resistance and virulence genes. Genetic diversity of the strains was done using spa typing and whole genome sequencing (WGS). The overall prevalence of S. aureus in the study was 33.1%, specifically 37.8% for pigs and 11.8% for humans. The isolates were resistant to several anti-staphylococcal antibiotics including penicillin, tetracycline, and ciprofloxacin, with resistance rates ranging from 18% to 98%. However, the isolates showed considerable susceptibility to chloramphenicol, gentamicin, and co- trimoxazole. All isolates were susceptible to vancomycin. Although the mecA and mecC genes which encode resistance to methicillin were not detected, other resistance genes encoding resistance to tetracyclines (tetM, tetK, and tetL) and to erythromycin (ermB and ermC) were detected using PCR, while WGS showed the presence of other resistance genes which encode resistance to beta-lactams (blaZ), macrolides (vga(A)V), and fluroquinolones (gryA and gyrlA). More virulence genes were detected in silico via WGS compared to using PCR. These virulence genes included the aureolysin gene (aur), hemolysin genes (hlgA, hlgB, and hlgC) and enterotoxin genes (seg, sei, sem, sen, seo and seu). Immune evasion cluster genes (sak and chp) were also detected in some of the isolates from pigs. While several serine like protease genes (splA to F) were detected in both human and pig isolates. Spa typing by both PCR and WGS revealed that most of the isolates belonged to the typical livestock- associated spa types (t1430 being the most common). Typical livestock-associated sequence types ST753 and ST9 were detected in two of the isolates. Novel spa and sequence types were detected among the isolates. Mobile genetic elements (plasmid, transposon and several insertion sequences) associated with the aforementioned resistance and virulence genes were also detected in silico in the isolates. Phylogenetic analysis based on WGS revealed that the isolates clustered together with typical livestock-associated ST398 MRSA isolates and were clonally related. The findings of our study show that LA-SA is present among pigs and workers who work closely with pigs in Zambia and there may be both zoonotic and anthropogenic transmission going on. Furthermore, these isolates pose a high risk to human health as they harbour both resistance and virulence genes which are possibly carried on mobile genetic elements and may thus spread easily. Therefore, continuous monitoring of S. aureus in this sector using a “One health” approach to combat S. aureus infections and prevention of the emergence and spread of antibiotic resistant strains is recommended.
Staphylococcus aureus. , Animal diseases -- Pigs.