Genomic epidemiology and zoonotic potential of staphyloccus aureus from pigs and humans in Lusaka province of Zambia.
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Date
2023
Authors
Samutela, Mulemba Tillika
Journal Title
Journal ISSN
Volume Title
Publisher
The University of Zambia
Abstract
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.
Description
Thesis
Keywords
Staphylococcus aureus. , Animal diseases -- Pigs.