Methicillin Resistant Staphylococci Isolated from Goats and Their Farm Environments in Saudi Arabia Genotypically Linked to Known Human Clinical Isolates: a Pilot Study

Abstract

We conducted a pilot whole genome sequencing (WGS) study to characterize the genotypes of nine methicillin resistant staphylococci (MRS) isolates recovered from goats and their farm environments in Eastern Province, Saudi Arabia, between November 2019 to August 2020. Seven out of nine isolates were methicillin resistant Staphylococcus aureus (MRSA), and two were methicillin resistant Staphylococcus epidermidis (MRSE). All MRSA isolates possessed genotypes previously identified to infect humans, including isolates harboring ST6-SCCmec IV-t304 (n = 4), ST5-SCCmec VI- t688 (n = 2) and ST5-SCCmec V-t311 (n = 1). 2 MRSA isolates possessed plasmids that were genetically similar to those identified in S. aureus isolates recovered from humans and poultry. In contrast, plasmids found in three MRSA isolates and one MRSE isolate were genetically similar to those recovered from humans. All MRSA isolates harbored the host innate modulate genes sak and scn previously associated with human infections. The genotypes of MRSE isolates were determined as ST35, a well-known zoonotic sequence type and ST153, which has been associated with humans. However, the MRSE isolates were untypeable due to extra ccr complexes identified in their SCCmec elements. Moreover, we identified in ST153 isolate SCCmec element also harbored the Arginine Catabolic Mobile Element (ACME) IV. All MRS isolates were phenotypically resistant to trimethoprim-sulfamethoxazole, an antibiotic for the decolonization of MRS. Three isolates carried antibiotic resistance genes in their SCCmec elements that were not previously described, including those encoding fusidic acid resistance (fusC) and trimethoprim resistance (dfrC) incorporated in the MRSA SCCmec VI. IMPORTANCE Our findings demonstrate a possible cross-transmission of methicillin resistant staphylococci between goats and their local environments and between goats and humans. Due to ever increasing resistance to multiple antibiotics, the burden of MRS has a significant impact on livestock farming, public health, and the economy worldwide. This study highlights that implementing a holistic approach to whole genome sequencing surveillance in livestock and farm environments would aid our understanding of the transmission of methicillin resistant staphylococci and, most importantly, allow us to implement appropriate infection control and hygiene practices.

Keywords: MRS; MRSA; MRSE; Saudi Arabia; environment; genotypes; goat.

FIG 1

Hierarchy cluster of MRS isolates from goats and farm environments in Eastern Province, Saudi Arabia, showing genomic similarities between S. aureus isolates from different sources. (A) dDDH. (B) Pairwise SNP distance of the core genome containing 2,492,080 nucleotides for S. aureus isolates. (C) Pairwise SNP difference of the core genome containing 2,232,743 nucleotides for S. epidermidis isolates. (D) Gene correlation between isolates.

FIG 2

Hierarchy cluster heatmap of MRS isolates from goats and surrounding farm environments in Eastern Province, Saudi Arabia. (A) Antibiotic resistance phenotype profiles. (B) Genotype resistance phenotypes. Red tiles presence of antibiotic resistance genotype/phenotype; blue tiles absence of antibiotic resistance phenotype/genotype.

FIG 3

Acquired virulence genes of MRSA isolates recovered from goats and their surrounding farm environments in Eastern Province, Saudi Arabia.

FIG 4

Maps of four plasmids isolated from MRS from goats and their surrounding farm environments in Eastern Province, Saudi Arabia.

FIG 5

BLAST analysis of plasmids that had hits from MASH distance analysis showing pSA1, pSA2 and pSA3 were not novel plasmids; however, pSE1 plasmid appeared to be novel due to low similarities to other plasmids on the database. (A) pSA1, (B) pSA2, (C) pSE1, and (D) pSE2.

FIG 6

SCCmec structure found in the MRS isolates recovered from goats and their surrounding farm environments in Eastern Province, Saudi Arabia. (A) SCCmec V found in SA1, (B) SCCmec VI found in SA2 and SA4, (C) SCCmec VI found in SA3, SA5, SA6, SA7. (D) SCCmec with class B mec complex and two class 4, one class 2 ccr complexes and ACME IV element found in SE1. (E) SCCmec IV with an extra class 4 ccr complex found in SE2. DR = direct repeat sequence of the SCCmec attachment sites.