Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern, with a considerable impact on patients’ health, and substantial healthcare costs. In this study, patients and healthcare workers (HCWs) from six public hospitals in Benin were screened for MRSA. Strains were identified as MRSA using conventional microbiological methods in Benin, and confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in Belgium. Whole-genome sequencing (WGS) was used on the confirmed MRSA isolates, to characterize their genomic content and study their relatedness. Amongst the 305 isolates (304 wound swabs and 61 nasal swabs) that were collected from patients and HCWs, we detected 32 and 15 cases of MRSA, respectively. From this collection, 27 high-quality WGS datasets were obtained, which carried numerous genes and mutations associated with antimicrobial resistance. The mecA gene was detected in all the sequenced isolates. These isolates were assigned to five sequence types (STs), with ST8 (55.56%, n = 15/27), ST152 (18.52%, n = 5/27), and ST121 (18.52%, n = 5/27) being the most common. These 27 isolates carried multiple virulence genes, including the genes encoding the Panton–Valentine leukocidin toxin (48.15%, n = 13/27), and the tst gene (29.63%, n = 8/27), associated with toxic shock syndrome. This study highlights the need to implement a multimodal strategy for reducing the risk of the cross-transmission of MRSA in hospitals.

Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies

“…It is also noteworthy that the WGS-based prediction of AMR based on ARG presence was largely consistent with phenotypic AST results, underscoring the potential of WGS in predicting AMR accurately. Whole genome sequencing has been used by several studies to assess the potential for predicting AMR genes from genomes of pathogens and validating concordances with the phenotypic results [ 19 55 56 ]. In our study, we used five AMR databases to predict AMR genes to prevent the chance of missing any AMR acquired genes or chromosomal point mutation in the genes.…”

“…Moreover, WGS predicted presence of fosB , a fosfomycin resistance gene and point mutations in genes contributing resistance to fosfomycin. We did not perform any phenotypic tests for fosfomycin resistance, however previous studies have used WGS and identified fosB and similar point mutation in S. aureus belonging to ST8, ST5, ST30 [ 56 58 ]. The fosB or related point mutations were not identified in CC97 isolates in our study which agrees with findings from another study [ 58 ].…”