Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission
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.
Section snippets
Methods
The original prospective study was undertaken in the general medical-surgical ICUs of two central London teaching hospitals. Ward layout, patient characteristics, cleaning regimens, study randomization, sampling protocol and primary analyses have been described in full by Wilson et al.7
Primary analysis7
In total, 2645 patients were admitted to intensive care. Of these, 175 (6.6%) patients were positive for MRSA on admission and 78 (2.9%) patients acquired MRSA during their stay, 22 (28.2%) of whom became clinically infected (14 developed a respiratory infection, two developed a wound infection, three developed a line infection and three developed a bacteraemia). MRSA was isolated from the following environmental samples: 191 (1.1%) of 16,868 surfaces within the near-patient environment, 17
Discussion
To study the micro-epidemiology of MRSA effectively, the molecular typing method used must be able to distinguish between different MRSA strains. When used to construct possible transmission pathways, PFGE was, as expected,10 able to detect small genetic differences between many of the strains involved, but its potential to distinguish isolates within a major lineage was more limited. As in previous studies, WGS provided sufficient resolution to support or exclude links between otherwise
Conflict of interest statement
None declared.
Funding sources
The study was supported by a grant from the National Institute for Health Research Central Commissioning Facility (Grant 0410028). A.P.R. Wilson was part-funded by the UCLH/UCL/LSHTM Comprehensive Biomedical Centre. WGS was performed at the Wellcome Trust Centre for Human Genetics (Oxford), and funded by the NIHR Oxford Biomedical Research Centre and the UKCRC Modernising Medical Microbiology Consortium, the latter funded under the UKCRC Translational Infection Research Initiative supported by
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