Objectives

To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice. Next-generation sequencing has the potential to resolve uncertainties surrounding the route and timing of person-to-person transmission of healthcare-associated infection, which has been a major impediment to optimal management.

Design

The authors used Illumina MiSeq benchtop sequencing to undertake case studies investigating potential outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile.

Setting

Isolates were obtained from potential outbreaks associated with three UK hospitals.

Participants

Isolates were sequenced from a cluster of eight MRSA carriers and an associated bacteraemia case in an intensive care unit, another MRSA cluster of six cases and two clusters of C difficile. Additionally, all C difficile isolates from cases over 6 weeks in a single hospital were rapidly sequenced and compared with local strain sequences obtained in the preceding 3 years.

Main outcome measure

Whole-genome genetic relatedness of the isolates within each epidemiological cluster.

Results

Twenty-six MRSA and 15 C difficile isolates were successfully sequenced and analysed within 5 days of culture. Both MRSA clusters were identified as outbreaks, with most sequences in each cluster indistinguishable and all within three single nucleotide variants (SNVs). Epidemiologically unrelated isolates of the same spa-type were genetically distinct (≥21 SNVs). In both C difficile clusters, closely epidemiologically linked cases (in one case sharing the same strain type) were shown to be genetically distinct (≥144 SNVs). A reconstruction applying rapid sequencing in C difficile surveillance provided early outbreak detection and identified previously undetected probable community transmission.

Conclusions

This benchtop sequencing technology is widely generalisable to human bacterial pathogens. The findings provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection and therefore improve hospital infection control and patient outcomes in routine clinical practice.

Article summary

Article focus

To investigate the prospects of newly available benchtop sequencers to provide rapid whole-genome data in routine clinical practice.

In particular to investigate the potential of such technology for identification of transmission events of healthcare-associated pathogens.

Key messages

We demonstrate benchtop sequencing can enhance hospital infection control through high precision support and rejection of transmission using genetic data.

Whole-genome data provided additional genetic resolution over existing genetic typing strategies.

We also show this technology offers turnaround times of under a week in a format that, in contrast to molecular typing, is organism independent.

Strengths and limitations of this study

The case studies presented provide several good examples of how rapid and precise sequencing could transform identification of transmission of healthcare-associated infection.

Given this is a pilot study, further evaluations of the impact of this technology on hospital infection control are required. However, this study provides a clear rationale for future work undertaking formal comparisons of benchtop sequencing with existing local and national typing schemes.

Background

In the past, strains of Staphylococcus aureus have evolved, expanded, made a marked clinical impact and then disappeared over several years. Faced with rising meticillin-resistant S aureus (MRSA) rates, UK government-supported infection control interventions were rolled out in Oxford Radcliffe Hospitals NHS Trust from 2006 onwards.

Methods

Using an electronic Database, the authors identified isolation of MRS among 611 434 hospital inpatients admitted to acute hospitals in Oxford, UK, 1 April 1998 to 30 June 2010. Isolation rates were modelled using segmented negative binomial regression for three groups of isolates: from blood cultures, from samples suggesting invasion (eg, cerebrospinal fluid, joint fluid, pus samples) and from surface swabs (eg, from wounds).

Findings

MRSA isolation rates rose rapidly from 1998 to the end of 2003 (annual increase from blood cultures 23%, 95% CI 16% to 30%), and then declined. The decline accelerated from mid-2006 onwards (annual decrease post-2006 38% from blood cultures, 95% CI 29% to 45%, p=0.003 vs previous decline). Rates of meticillin-sensitive S aureus changed little by comparison, with no evidence for declines 2006 onward (p=0.40); by 2010, sensitive S aureus was far more common than MRSA (blood cultures: 2.9 vs 0.25; invasive samples 14.7 vs 2.0 per 10 000 bedstays). Interestingly, trends in isolation of erythromycin-sensitive and resistant MRSA differed. Erythromycin-sensitive strains rose significantly faster (eg, from blood cultures p=0.002), and declined significantly more slowly (p=0.002), than erythromycin-resistant strains (global p<0.0001). Bacterial typing suggests this reflects differential spread of two major UK MRSA strains (ST22/36), ST36 having declined markedly 2006–2010, with ST22 becoming the dominant MRSA strain.

Conclusions

MRSA isolation rates were falling before recent intensification of infection-control measures. This, together with strain-specific changes in MRSA isolation, strongly suggests that incompletely understood biological factors are responsible for the much recent variation in MRSA isolation. A major, mainly meticillin-sensitive, S aureus burden remains.

Article summary

Article focus

Multiple infection control interventions in UK hospitals were rolled out in 2005–2010.

Over the same time period, a decline in MRSA isolations has been noted. The relationship between these two events is unclear and was investigated using an observational study in a group of hospitals.

Key messages

MRSA isolation rates from blood culture, surface swabs and samples suggesting invasive disease declined from 2003 onwards, compatible with national trends.

Rates of meticillin-sensitive S aureus changed little by comparison. Analysis of resistance profiles, together with genotyping of archival collections, suggests a differential decline in the two dominant MRSA strains, ST22 and ST36.

MRSA isolation rates were falling before recent intensification of infection-control measures.

This, together with strain-specific changes in MRSA isolation, strongly suggests that incompletely understood biological factors are responsible for the much recent variation in MRSA isolation.

A major, mainly meticillin-sensitive, S aureus burden remains.

Strengths and limitations of this study

A large hospital with trends in MRSA blood culture isolation similar to the national trends was studied, and data are available not only for blood cultures but also for all other samples.

Archival collections of samples and detailed epidemiological and typing data are all available.

The data are observational.