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

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.

MRSA carriage in healthcare personnel in contact with farm animals.

In The Netherlands it has been shown that people in contact with pigs have a higher risk of meticillin-resistant Staphylococcus aureus (MRSA) carriage than the general population. Isolates of closely related spa types, corresponding to multilocus sequence type (MLST) ST398, were found in pig farmers, pig veterinarians and pigs. The objective of this study was to investigate whether contact with pigs and veal calves or other livestock is a risk factor for MRSA carriage in Dutch healthcare workers (HCWs). HCWs at four general hospitals and one university hospital were asked to fill in questionnaires covering contact with animals and to take MRSA cultures of their throat and nares. Cultures of HCWs in contact with livestock were processed with samples from HCWs with no contact with livestock as controls. Seventy-seven of 1721 HCWs (4.4%) reported direct or indirect contact with pigs and/or veal calves and 145 reported contact with other livestock animals. The MRSA carriage rate in the group in contact with pigs and veal calves was 1.7% and in the control group was 0.15%. No carriers were found among HCWs in contact with other livestock. An estimated 3% of hospital staff working in Dutch hospitals serving rural populations belong to a high risk group for MRSA carriage according to the Dutch guidelines. Although MRSA carriage in HCWs in contact with livestock is 10-fold higher than in other HCWs, the difference is not statistically significant.