Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname

Artur J Sabat,John E Degener,Hajo Grundmann,Alexander W Friedrich,Sandra M Hermelijn,Amadu Juliana,Viktoria Akkerboom

doi:10.1038/srep41050

Abstract

We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.

Highlights

Many human infections are caused by multi-drug resistant bacteria and methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent pathogens in hospitals worldwide
In 2013 it had 504 beds, 23564 total inpatient admissions and 243721 outpatient visits
Healthcare workers who had contact with a MRSA patient (n = 111) were screened using nasal and pharyngeal swabs. Using these interventions the outbreak was halted within a short time and the MRSA isolation at the AZP returned to the background rate

Summary

Introduction

Many human infections are caused by multi-drug resistant bacteria and methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent pathogens in hospitals worldwide. Individuals, who acquire MRSA colonization during a hospital stay, serve as reservoirs for further dissemination in the healthcare settings as well as in the community. The prevention of nosocomial MRSA infections, especially in intensive care units with seriously ill patients, primarily include improved hand hygiene practices, extensive cleaning and disinfection of the hospital environment, and screening for MRSA carriage followed by isolation of documented carriers. A typing method should have a high discriminatory power allowing correct exclusion of epidemiologically unrelated isolates. Typing methods used for epidemiological investigations should be able to discern between genetically very closely related isolates, improving the resolution to near forensic precision. Many different molecular typing methods for discriminating MRSA isolates have been developed. Patient-4+ Patient-5 Patient-6# Patient-7# Patient-8# Patient-8# Patient-9 Patient-10 Patient-11* Patient-9 Patient-12* Patient-11* Patient-11* Patient-11* Nurse+ Patient-13 Nurse+ Nurse+ Patient-9

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Results

Conclusion