DNA sequencing helped to limit spread of MRSA in a neonatal unit

BMJ 2012; 345 doi: (Published 14 November 2012) Cite this as: BMJ 2012;345:e7746
  1. Krishna Chinthapalli
  1. 1BMJ

Researchers have used whole genome sequencing to trace the spread of an outbreak of meticillin resistant Staphylococcus aureus (MRSA) in an NHS hospital’s special care baby unit. Prospective sequencing then led them to screen staff and identify the potential source of infection, says a study in Lancet Infectious Diseases.1

Speaking at press briefing on the study, Sharon Peacock, professor of clinical microbiology at the University of Cambridge and one of the study’s authors, said, “Our study indicates the considerable potential of sequencing for the rapid identification of MRSA outbreaks.”

She said that this was the first time she knew that DNA sequencing had been used to follow an outbreak in real time and help to contain it.

Previously her group had shown that whole genome sequencing of MRSA could evaluate the similarity of two strains by looking for mutations, single nucleotide polymorphisms (SNPs), at certain sites. The greater the degree of similarity of SNPs in two specimens, the more closely related they are.

In their current research Julian Parkhill, head of pathogen genomics at the Wellcome Trust Sanger Institute in Cambridge and one of the study’s authors, said that the research team used the sequence of SNPs to “make a family tree” of the MRSA specimens and determine which ones were linked.

The study looked at a spate of infections at the Rosie Hospital, part of Cambridge University Hospitals Foundation Trust, during 2011. Routine microbiology tests isolated MRSA positive cultures in 17 infants over six months. Scientists at the Wellcome Trust Sanger Institute then performed whole genome sequencing and found that 14 infants had MRSA with the same sequence, termed ST2371. They also found this ST2371 sequence in 10 other people with MRSA in the local community. Further investigation showed that nine of these 10 people had been in contact with the original 14 infants.

After two months and a deep clean of the special care baby unit, another infant was infected with ST2371 MRSA. This indicated that the ST2371 MRSA strain had survived the deep clean, the researchers said. Subsequent screening of all 154 staff at the unit found one person positive for ST2371 MRSA, implicating this person as the source of infection before and after the deep clean. No further cases of MRSA were recorded in the unit, said Nick Brown, a microbiologist and coauthor.

The authors proposed that whole genome sequencing could be used to track transmission of MRSA accurately and said that during their investigation standard infection control measures did not detect MRSA transmission to the staff or the community.

Binh An Diep, assistant professor of infectious diseases at the University of California in San Francisco, has written a commentary on the study.2 He said in a statement, “Routine application of whole genome sequencing that is not epidemiologically targeted might yield results that are difficult to interpret, especially during an epidemic.” He added that sequencing should not be used alone, as it could lead to the imposition of contact precautions or isolation measures on the wrong people.

Peacock acknowledged these difficulties, saying, “What we need before this can be introduced into routine care is automated tools that interpret sequence data and provide readily understandable information to healthcare workers. We are currently working on such a system.”

Mark Walport, director of the Wellcome Trust, commented, “This is a dramatic demonstration that medical genomics is no longer a technology of the future—it is a technology of the here and now.”

The UK Health Protection Agency is due to establish its own sequencing service and noted in September that whole genome sequencing “is revolutionising life sciences, including microbiology, and will radically change the way public health microbiology (and other Public Health England) services are delivered in coming years.”


Cite this as: BMJ 2012;345:e7746