Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk

Abstract

Five cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.

An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England

“…This situation was also seen during a previous outbreak investigation (Butcher et al . ). In both instances, STEC was isolated from other samples taken from the same farm.…”

“…The PCR‐based method is of improved specificity and sensitivity for STEC compared to the culture‐based methods alone (Butcher et al . ; Hara‐Kudo et al . ).…”

Imported edible leaves collected at retail sale in England during 2017 with an emphasis on betel and curry leaves: microbiological quality with respect toSalmonella, Shiga-toxin-producingE. coli(STEC) and levels ofEscherichia coli

“…The PCR‐based method offers improved specificity and sensitivity for STEC compared with the more traditional methods alone (Butcher et al . ; Hara‐Kudo et al . ).…”

“…; Butcher et al . ); and enumeration of E. coli based on using a surface spread (0·5 ml of a one in 10 homogenate of the food sample was spread over the surface of an agar plate) rather than pour plate technique (International Organisation for Standardisation, ). Tests were performed at all laboratories except for the detection of STEC which was performed at the Porton FW&E laboratory on a subset of the total number of samples.…”

Gastrointestinal infections caused by consumption of raw drinking milk in England & Wales, 1992–2017

“…Since 2015, the use of routine whole genome sequencing (WGS) at PHE has provided unprecedented sensitivity and accuracy in identifying microbiologically linked cases of infection [9, 10]. However, all RDM-associated STEC O157:H7 outbreaks reported to date have been detected through epidemiological links established by local health protection teams prior to the availability of the WGS results [9, 10].…”