Whole genome characterization of methicillin-resistant Staphylococcus spp. isolates from aquaculture-cultivated shrimps

Abstract

Aquaculture is one of the fastest-growing agricultural sectors which serves as an invaluable source of animal protein. The presence of pathogenic microbes and antimicrobial resistance is a major concern in aquaculture. Aquaculture has been identified as a hotspot for resistant pathogens, but very less details are available on the origin of these pathogens. Here, to better understand the pathogenic incidence and their resistome and virulome, we have sequenced and analysed the genomes of Staphylococcus spp. isolates (n = 12) from shrimps obtained from aquaculture farms in Kerala, India. These isolates were typed as S. aureus (n = 4), S. haemolyticus (n = 3), S. epidermidis (n = 3), S. saprophyticus (n = 1), and S. warneri (n = 1). Comparative genomic analysis of these isolates was done against reference and published Indian Staphylococcus spp. isolates to identify the strain origin and genetic relatedness. Most of the isolates had a very close identity with human isolates, indicating the human origin of these pathogens. Resistome analysis revealed, S. aureus harbouring anti-microbial resistance genes (ARGs) against methicillin, Norfloxacin, Gentamicin, etc. and S. haemolyticus harbouring ARG against methicillin, erythromycin, etc. S. aureus isolates presented quite an extensive virulome and their clustering with human-pathogens displays their potential for pathogenicity. We here, thus, call attention to monitoring the proper implementation of biosecurity measures in aquaculture farms to avoid entry and enrichment of such isolates.