Research and analysis

HPR volume 12 issue 31: news (24 August)

Updated 21 December 2018

Implementing pathogen genomics: a case study

Public Health England has been working to implement whole genome sequencing techniques since 2012 and its National Infection Service has adopted a whole genome sequencing (WGS) strategy to enhance the control of communicable diseases nationally and to help PHE meet its regional, national and international obligations in infectious disease control.

‘Implementing pathogen genomics: a case study’ is a new 30-page description of how WGS has been adopted by one of NIS’s reference laboratories, the Gastrointestinal Bacteria Reference Unit (GBRU) [1]. It describes, in particular, how sequencing has facilitated recent GBRU investigations of outbreaks of Escherichia coli (from unpasteurised milk) and Salmonella Enteritidis (from contaminated eggs and from mice being used to feed reptiles).

The GBRU was an early adopter of the centralised WGS service established at PHE Colindale in 2012 to 2013 and now uses WGS as the routine typing tool for 5 major GI pathogens: salmonella, shigella, listeria, campylobacter and E. coli.

NIS’s central WGS service was one of the first in the UK to be accredited for its WGS services relating to bacteria and viruses. It now provides a service for a wide range of pathogens of national importance.

The case study on GBRU outlines the extensive development process undertaken by PHE to establish the central WGS service and the transformation of a national bacteriology reference laboratory into a genomics-led service. This includes changes in workflows, working practices and revisions to analytical procedures as services have migrated to using WGS for pathogen typing, surveillance and outbreak investigation.

Reference

1. PHE website. Implementing pathogen genomics: a case study.

MERS-CoV case in England

PHE is working with NHS England to manage a case of Middle East Respiratory Syndrome (MERS) in an air traveller recently returned to the UK from the Middle East [1]. This includes following up appropriate contacts.

The case was hospitalised and no further possible cases had been identified among travellers on the same flight from Saudi Arabia, as at 23 August. Nevertheless, because pilgrims are expected to be returning from the Hajj religious festival in the country over the coming days, PHE Centre Health Protection Teams have been asked to be prepared to support follow up with returning travellers exhibiting respiratory symptoms. In such situations, HPTs should refer to the MERS-CoV Possible Case Algorithm for the assessment of putative cases [2].

MERS is a viral respiratory disease caused by a novel coronavirus first identified in Saudi Arabia in 2012. Between 2012 and June 2018, 2,229 confirmed cases had been reported to the WHO, the majority coming from that country.

References

1. ”“MERS-CoV case in England”, PHE press release, 23 August 2018.
2. PHE website. Investigation and public health management of possible cases of MERS-CoV.

Infection reports in this issue of HPR

Measles, mumps and rubella: laboratory confirmed cases in England 2018

There were 421 laboratory confirmed measles cases in England between April and June this year bringing the total for the first two quarters of 2018 to 686. PHE declared a national measles incident in May. Although the World Health Organization Regional Office for Europe has confirmed that the UK maintained its measles and rubella elimination status in 2017, the recent outbreaks are a warning against complacency: the UK remains vulnerable to importations leading to spread among communities with low MMR coverage, and in age groups with very close mixing.

It is essential for the maintenance of the UK’s elimination status that vaccination coverage with two doses of the MMR vaccine in children under the age of 5 years is improved; also that catch-up vaccines are offered to older children and young adults who missed the opportunity to be vaccinated at an earlier age.

The most up to date (provisional) measles figures for England are regularly published on PHE’s Measles outbreaks across England webpage.

A decrease in mumps activity in England was observed this quarter with 139 laboratory confirmed mumps infections compared to the 275 cases reported in the previous quarter, in line with usual seasonal trends. No rubella cases were reported this quarter.

Laboratory-confirmed hepatitis A and C (England and Wales), January to March 2018.

Acute hepatitis B (England): annual report for 2017.