STEC - report on disease occurrence 2014-2018

Annual report on Shiga toxin-producing E. coli (STEC) and haemolytic uraemic syndrome (HUS), 2014-2018

In Denmark, STEC infection (also known as VTEC infection) is monitored at Statens Serum Institut (SSI) via two systems: a) Clinical notification by the treating physician to the Danish Patient Safety Authority and to the Department of Infectious Disease Epidemiology and Prevention at the SSI via Form 1515, and b) the laboratory notification system to which the diagnostic laboratories report cases to the SSI. In the two systems, a total of 1,609 cases of STEC infection were reported in the 2014-2018 period. Eleven persons had the same STEC type for more than six months. Eight persons had more than one STEC type verified. Among 1,294 STEC isolates submitted to the SSI, 1,179 could be verified and/or further characterised at the SSI.

In a total of 13 of 37 DNA eluates for which no isolate could be determined at the local department of clinical microbiology (DCM), the eluate could be determined by PCR at the SSI. A total of 162 of 1,438 cases were reported to the Department of Infectious Disease Epidemiology and Prevention at the SSI without concurrent reporting to the laboratory notification system, Figure 1.

The number of persons found to have become infected by STEC nearly doubled from 281 in 2014 to 495 in 2018. The largest increase was observed from 2017 to 2018, Figure 1 and Table 1. In 2018 an incidence of 8.6/100,000 inhabitants was seen with the highest incidence being recorded in East and West Jutland.

Geographical distribution

Table 1 presents the number of STEC cases recorded in 2018, the average for 2014-2017, and the number of cases per 100,000 inhabitants per area and in total. In 2014-2017, the average number of cases per 100,000 inhabitants was 4.9; varying from 2.3 to 11 for the respective areas. By 2018, the incidence had increased to 8.6, varying from 2.8 to 15 per 100,000 inhabitants in the various areas, apart from the island of Bornholm where no cases were observed in 2018. Table 1 also shows that the number of STEC cases has increased in the majority of areas, except East Zealand and Funen.

Funen has experienced a high STEC incidence throughout the period, which may probably be explained by the fact that all diarrhoea patients are tested for STEC at the DCM at Odense University Hospital. The number of detected STEC cases more than quadrupled in East and West Jutland (The Central Denmark Region) in the period. The Central Denmark Region is serviced by DCM Skejby which, as from June 2018, introduced STEC screening by PCR in all stool samples with diarrhoea. The remaining DCMs employ as a minimum the diagnostic criteria recommended by the Danish Society for Microbiology (DSCM).

A high number of STEC infections was seen in the summer period from June to September. The unusually high number of cases in the summer and autumn of 2018, Figure 2, was due to the combination of the above-mentioned introduction of STEC screening of all samples from patients with diarrhoea at DCM Skejby and an O26 outbreak, described below.

Country of infection

A total of 1,018 (63%) of the notified STEC cases were recorded as having been acquired in Denmark, 19% abroad, whereas in 18% of the cases, no information was provided about the place of infection (see table in the corresponding issue of EPI-NEWS).

Distribution by age and sex

Figure 3 presents the number of STEC cases in the 2014-2018 period per 100,000 inhabitants, by sex and age groups. The median age for the period overall was 23 years, and 528 (33%) were children below the age of 8 years, which in part reflects that the DSCM recommends that stool samples from this age group are tested for STEC. The share of 0-7-year-olds declined from 40% in 2014 to 28% in 2018 after DCM Skejby introduced STEC testing of stool samples from persons above seven years of age. Girls/women accounted for 53%-58% of annual cases.

O groups

Bacteria isolates were available for 1,179 STEC cases (73%). For some patients, an O group could not be determined. This was the case because of the growing use of ever more sensitive PCR diagnostics, which does not always allow for culture of isolates for typing after a positive PCR signal, and/or because the isolate was not submitted for typing with the SSI. This has also affected the share of diagnosed cases with STEC O157, which has remained more or less constant at 14%-15% for several years, but which declined to 8% in 2018, Table 2.

Whole-genome sequencing

STEC isolates must be submitted continuously to the SSI where isolates have been whole-genome sequenced since 2014. This has produced an increasing number of genetically related isolates and confirmed outbreaks.

In the 2014-2018 period, a total of 55 clusters were found, counting two or more persons with genetically related types. In all, 45 of these clusters included 2-4 patients and eight clusters comprised 5-8 patients. Additionally, the 2016-2018 period recorded a larger cluster counting a total of 15 genetically related cases and an O26:H11 outbreak in 2018 that recorded 38 affected patients.

A total of 45 clusters with genetically related cases distributed on 14 O groups were handled as possible outbreaks. Among these, four serotypes (O157:H7, O26:H11, O103:H2 and O63:H6) caused 181 of 223 (81%) cases, whereas ten other serotypes caused another 42 cases (range: 2-8).

STEC outbreaks

Among the 45 clusters with genetically related cases that were handled as possible outbreaks, the SSI found an epidemiological link between the patients, in the form of shared daycare services and/or secondary infection in the family, in approx. 50% of the cases (18 clusters). In six genetically related clusters, infection from foods possibly occurred. Two serious outbreaks, both occurring in 2018, consisted of seven cases of O111:H8 and 38 cases of O26:H11, respectively. These outbreaks are described below.

In the outbreak caused by O111:H8, five cases could be confirmed by whole-genome sequencing, and an additional two cases probably formed part of the outbreak. One of the confirmed and two probable cases developed HUS - for one of these cases, an isolate was not available. The cases were scattered across Denmark, and none of the patients had travelled abroad during the incubation period. All were interviewed about possible exposures. No common source could be established. Even so, minced beef was an unconfirmed suspicion, as this was the only food that all patients stated that they had ingested. No other countries have reported genetically identical cases, and no new Danish cases have been recorded since 13 September 2018.

The outbreak caused by STEC O26:H11 was comprised by a total of 38 confirmed genetically related cases and one probable case. The patients were scattered all over Denmark with more cases being recorded in or around the largest cities. The age range was from 6 months to 95 years but cases were primarily children aged from 6 months to 3 years of age (79%). Among the 39 cases, 18 were girls/women and 21 boys. Disease onset could be established in 24 cases and occurred from 20 August to 12 November 2018. The majority of the patients attended daycare institutions or other institutions with a shared food service which received a large part of its foods from large catering wholesalers. A review of the purchases made by the involved institutions showed that a beef salami had been provided to most institutions. Beef salami is a known STEC risk product, and no other known risk products were found among the purchased products. The bacterium was not detected in samples collected from the suspected types of beef salami, and it was also not possible to narrow down the source of infection further by use of epidemiologic methods, but the weak suspicion of beef salami was maintained.(link til udbrudsside)

Haemolytic uraemic syndrome (HUS)

HUS is monitored nationally by the SSI via clinical notification by the treating physician using Form 1515. In the period from 2014 to 2018, a total of 55 HUS cases were recorded. The median age of these cases was 6 years, and 50% were between 2½ and 13 years of age (range 0-80 years). A total of 55% (30/55) of the HUS cases were confirmed at the SSI by PCR or isolation of STEC. In 30 HUS cases, in which the STEC virulence genes could be determined, stx2a was the predominant subtype (n = 18) followed by combinations of stx2a + stx1a (n = 9), stx2c (n = 1), stx2a + stx1a + stx2c (n = 1) and stx1a alone (n = 1). The 30 cases were distributed on 10 different O groups, among which the most common was O157 (n = 13) followed by O26 (n = 8).
In 2018, the same trend was seen with more HUS cases being recorded in the O groups of O157 and O26, Figure 4.

In 2018 alone, a total of 21 HUS cases were recorded. This is the highest annual number ever recorded. In all, 75% of theses cases were reported in the period from June to September (n = 16), after which no more cases were reported, Figure 4. The median age of HUS cases in 2018 was 9 years, 50% were 3-15 years of age, as opposed to a median age of 4 years in the 2014-2017 period, when 50% were 2-11 years old.

To see HUS cases by Danish regions and age groups in the 2014-2018 period, please see EPI-NEWS 18/19.