Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission

Summary

Background

In order to study the micro-epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) effectively, the molecular typing method used must be able to distinguish between different MRSA strains. Pulsed-field gel electrophoresis (PFGE) can detect small genetic differences but is limited in its potential to distinguish isolates within a major lineage. Whole-genome sequencing (WGS) provides sufficient resolution to support or exclude links between otherwise indistinguishable isolates, but lacks the practical utility of conventional typing methods.

Aim

To explore the utility of WGS in a hierarchical approach with PFGE to help establish possible sources of MRSA cross-transmission in the intensive care setting.

Methods

Possible transmission routes from donor to recipient via the hands of staff, the air or environmental surfaces were identified. Focused molecular typing used PFGE to explore these transmission hypotheses. WGS was applied when an acquisition event involved a common PFGE pulsotype.

Findings

Thirty-eight of the 78 acquisition events could not be explored as clinical isolates were not available. PFGE excluded all potential donors from 26 of the remaining 40 acquisition events, but did identify a probable source in 14 new colonizations. Within the hypotheses tested, PFGE supported links between patients occupying the same bay, the same bed space, adjacent isolation rooms and different wards. When a patient source was not identified, PFGE implicated the ward environment and the hands of staff. However, WGS disproved three of these transmission pathways.

Conclusion

WGS can complement conventional typing methods by confirming or refuting possible MRSA transmission hypotheses. Epidemiological data are crucial in this process.

Introduction

In the 1990s, the rapid and uncontrolled spread of two epidemic meticillin-resistant strains of Staphylococcus aureus (EMRSA-15 and EMRSA-16) within and between UK hospitals led to MRSA becoming the leading cause of UK healthcare-associated infection.¹ In 2003–2004, MRSA bacteraemia cases peaked at 7700 and reducing this burden became a priority for the Government and the National Health Service.¹

Improvements in infection prevention and control (IPC) including hand hygiene compliance, MRSA screening and decolonization programmes, antibiotic stewardship, environmental cleaning, mandatory reporting of MRSA bloodstream infections and the introduction of organizational targets resulted in the number of MRSA bacteraemias in the four years to 2008 decreasing by more than half.2, 3 However, the exact role of each of these interventions remains uncertain.

Knowledge about the relative contribution and clinical importance of the different modes of MRSA transmission is required to target IPC measures effectively. However, information detailing the spread of specific MRSA strains from patient to patient is limited.

Typing systems such as pulsed-field gel electrophoresis (PFGE) are often used in the investigation of MRSA outbreaks to determine the genetic relatedness of MRSA isolates. This process can determine which of the suspected transmission hypotheses are likely to be correct, and therefore inform IPC measures. It is essential that there are relevant and robust epidemiological data (including data from environmental samples if these are to be considered) to inform this interpretation.⁴ A difficult issue with many typing systems, including PFGE, is their inability to subtype MRSA sufficiently to differentiate between isolates during an outbreak and/or to demonstrate potential cross-infection, especially if a clone is often present. Whole-genome sequencing (WGS) provides a possible means to detect minor variations down to the level of single nucleotide variants (SNVs),⁵ and thus has the capacity to be more discriminatory than conventional epidemiological typing, and has the potential to track MRSA spread over short time periods.

In a study involving 1065 patients, WGS indicated that just five of 22 new MRSA acquisitions were transmissions from other colonized patients.⁶ It was concluded that patient-to-patient transmission rarely accounted for S. aureus acquisition in an intensive care unit (ICU). However, the study also highlighted the size and, by implication, the cost of any study designed to investigate MRSA transmission, particularly in a non-outbreak setting.

Between April 2007 and April 2008, the authors conducted a prospective, randomized crossover study to investigate the impact of enhanced cleaning on contamination of the near-patient environment and patient acquisition of MRSA.⁷ Over the course of 12 months, 2654 patients were admitted to two UK ICUs, and 22,646 samples were collected from environmental surfaces (N = 18,596), the air (N = 859) and the hands of staff (N = 4191). Enhanced cleaning reduced both environmental contamination and hand carriage, but had no significant effect on patient acquisition of MRSA.

To explore the possible sources of MRSA cross-transmission (including the environment), WGS was used in a hierarchical approach with PFGE to examine a subset of the 2007–2008 study isolates in more detail.