Contribution of whole-genome sequencing to understanding of the epidemiology and control of meticillin-resistant Staphylococcus aureus

Abstract

In recent years, approaches to tracking the spread of methicillin-resistant Staphylococcus aureus (MRSA) as part of outbreak management have used conventional DNA-based methods including pulsed field gel electrophoresis (PFGE) and spa typing. However, when a predominant clone is present, these methods may be insufficiently discriminatory. We conducted a literature search to highlight how whole genome sequencing (WGS) has revolutionised the investigation of outbreaks of MRSA, including intra-hospital spread and MRSA in the community, and to review its future potential. Whole genome sequencing provides enhanced isolate discrimination, as it permits the entire genomic DNA sequence of isolates to be rapidly determined and compared. Many software packages used for the analysis of WGS data are becoming increasingly available. To date WGS has been more sensitive in confirming outbreaks, often persisting for prolonged periods, previously undetected by conventional molecular typing. The evolving dynamic of spread from the community to hospitals, within and between hospitals, and from hospitals to the community, is only becoming clear with WGS studies, and is more complex and convoluted than widely appreciated. Also, WGS can exclude cross-transmission, when isolates are different. The challenges now are to make WGS technology more amenable for routine use and to develop an evidence-based consensus for sequence difference thresholds for isolates that they are deemed part of the same outbreak, including protracted outbreaks. Using such data in a timely way will provide increased sensitivity in detecting cross-transmission events earlier with the potential of preventing outbreaks to positively impact on infection prevention and control.

Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing

“…Our results provided evidence that a strain that seemed related to a cluster by AFLP and MLVA was unrelated using WGS data with 162 allelic cgMLST and 435 wgSNP differences. cgMLST established itself as a reliable and user-friendly tool that can be used for prospective surveillance and comparison between laboratories and differentiate with a higher resolution between relatedness due to transmission events compared to conventional molecular techniques [27,[39][40][41]. In our study, cgMLST confirmed four different genetic lineages and two clusters.…”

Control of Methicillin-Resistant Staphylococcus aureus Strains Associated With a Hospital Outbreak Involving Contamination From Anesthesia Equipment Using UV-C

“…The evolving dynamics of clones spread from the community and hospitals is only becoming clear with the implementation of WGS studies. WGS is also able to exclude cross-transmission when isolates are different (Humphreys and Coleman, 2019). However, the technique is costly and requires trained staff to analyze and interpret the results.…”

Advances of intra‐species molecular typing analysis of aquatic probiotics approved by the Chinese Ministry of Agriculture

“…The challenges now are to make WGS technology more amenable for routine use and to develop an evidence‐based consensus for sequence difference thresholds for isolates that have been deemed to be part of the same outbreak, including protracted outbreaks. Using such data in a timely way would provide increased sensitivity in detecting cross‐transmission events at an earlier stage, with the potential to prevent outbreaks, and have a positive impact on infection prevention and control (Humphreys & Coleman 2019). Recently, the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of WGS was evaluated, and Zheng et al .…”