Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit

Abstract

We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference. In the third level neonatal intensive care unit (NICU) of our hospital, we observed a rise in methicillin-susceptible S. aureus (MSSA) infections in two consecutive years. Traditional MSSA typing methods brought the suspicion of health care workers (HCWs) being repeatedly involved in the outbreak transmission chains. However, as these traditional typing methods fell short in providing definitive answers, we set out to improve the resolution of our outbreak analysis by bacterial whole-genome sequencing (WGS). Neonates have an immature immune system and are susceptible to opportunistic bacterial infections, especially in case of premature birth. Important bacteria involved in outbreaks at NICUs causing neonatal infections are Enterobacteriaceae and S. aureus. Although many studies have emphasized transmission of MRSA (methicillin-resistant S. aureus), its susceptible variant MSSA is, depending on local epidemiology, generally a more frequent cause of neonatal infections 1-3. Neonatal bacterial infections are preceded by bacterial spread which involves both direct transmission by close interaction with visiting parents and HCWs and indirect

Surveillance for Colonization, Transmission, and Infection With Methicillin-Susceptible Staphylococcus aureus in a Neonatal Intensive Care Unit

“…Our findings are consistent with published data on the colonization sites of infants in the NICU setting. 11 , 32 …”

“…Indeed, the role of HCWs as vectors for transmission has been reported numerously. 11 , 37 , 38 Because mandatory screening of HCWs in Germany requires specific approval and compliance, which would only be granted for outbreak investigations, we cannot incorporate S aureus from HCWs in our study. Nevertheless, molecular typing, along with epidemiological patient data and transmission patterns, suggests the involvement of HCWs as a transmission vector and warrants further scrutiny.…”

“… 26 In total, 69 323 polymorphic sites were kept (hqSNV) and clonal groups were defined as genomes distant from less than 20 SNVs (0.03% of the polymorphic sites as suggested by Cremers et al). 11 Minimum spanning tree was calculated using MSTree, version 2, and visualized using Grapetree. 27 …”

“…[7][8][9][10] The colonization and transmission dynamics in newborns in a nonoutbreak setting are not yet fully understood, because most studies focus on transmissions in outbreak settings. 1,11 Commonly, colonization occurs in the postnatal phase and may be acquired through vertical transmission from mother to infant, or from health care workers (HCWs), parents, visitors, or the environment to infant. [12][13][14] In this study, we performed a retrospective analysis of all S aureus colonization and infection events during a 2-year period in the NICU of our tertiary hospital.…”

Centre-specific bacterial pathogen typing affects infection-control decision making

“…WGS provides genomic data, which can be used to find genetic sample-to-sample relations [14–16]. WGS outbreak analysis is more and more applied by hospital Infection Prevention Control (IPC) teams to trace and monitor pathogenic infections [17–20] but also to traceback the source of transmission [21, 22]. Additionally, with WGS, one can detect antimicrobial resistance (AMR) genes and virulence factors, which is a beneficial add-on for clinicians and IPC [11].…”