No 6 - 2020

The criteria for when you need to be tested for infection with corona virus have been adjusted

The new corona virus outbreak is still developing within China. On this backdrop, Statens Serum Institut (SSI) and the Danish Health Authority (DHA) have decided to heighten the preparedness level to prevent spreading of infection with new corona virus in Denmark. Even so, the SSI and the DHA assess that the probability that we will see human-to-human spreading of the infection in Denmark remains limited. Furthermore, there are strong indications that the new virus may also cause mild symptoms and that the mortality associated with the virus is lower than that of SARS.

The Danish Health Authority has therefore updated its guidelines on handling of new corona virus (2019-nCoV). Importantly, the case definition stipulating when 2019-nCoV should be suspected has been changed. The geographical risk area has been extended to comprise all of mainland China. Additionally, patients with acute onset of symptoms of infection of the upper airways and fever (≥38 degrees Celsius) should also be suspected of corona virus. Previously, only persons with signs of severe lower airway infections should be suspected of corona virus.

Patients who meet the case definition or present with other symptoms and clinical findings that may cause suspicion of 2019-nCoV infection must still be conferred with the infectious medicine on-call doctor at either Hvidovre Hospital or Skejby Hospital. The on-call doctor decides if the patient should be referred for admission to an isolation ward for acute 2019-nCoV testing. The SSI has established a 24-hour preparedness service ensuring that testing of the new virus may be completed and results given within approx. four hours.

The guidelines also include guidance on how the risk of infection from a suspected or confirmed case may be classified as either low or high risk, based on the proximity or intensity of the contact experienced. The Danish Patient Safety Authority informs contacts and initiates any quarantine measures warranted under the Danish Epidemic Act.

The SSI will continue updating its outbreak web page on corona virus on a daily basis.

(T.G. Krause, P.H. Andersen, Department of Infectious Disease Epidemiology and Prevention)

Offer of free whooping cough vaccination for pregnant women extended until end of April 2020

The whooping cough epidemic continues, and January 2020 has recorded the highest number seen since the epidemic started: 829 laboratory-confirmed cases. Therefore, upon recommendation from the Danish Health Authority, the Danish Minister of Health has decided to extend the temporary offer of free whooping cough vaccination for pregnant women in their third trimester. The offer remains valid until 30 April 2020. Offering vaccination is recommend in connection with the routinely performed pregnancy examination in Week 32, but the vaccine (diTekiBooster) may be given until one week before the expected date of delivery.

It is expected that the SSI will be able to provide vaccines to all pregnant women comprised by the offer.

(F. Kristensen Lomholt, P.H. Andersen, Department of Infectious Disease Epidemiology and Prevention)

Campylobacter infections, 2018-19

The detailed 2018-19 annual report is available here.

The number of registered disease cases caused by Campylobacter spp increased in 2018 and 2019 alike. In 2018, a total of 4,547 cases (79 per 100,000) were recorded, and 2019 saw 5,389 cases (93 per 100,000), which is the highest number ever recorded. As previously described, EPI-NEWS 15/18, the introduction of PCR diagnostics on faeces material affects the number of positive cases recorded. This should be taken into account when assessing the trend in increases and decreases in the number of campylobacter infections. Even so, the high number of infections in 2019 compared with 2018 cannot be accounted for by reference to diagnostic changes and likely reflects a large outbreak, as described below.

For a long period of time, campylobacter infections have remained the most frequent cause of bacterial gastrointestinal infections in Denmark, and they currently constitute an important public health problem. Researchers have so far assumed that Campylobacter - as opposed to Salmonella - only rarely causes outbreaks. Even so, in recent years, whole-genome sequencing (WGS) of isolates has shown that minor outbreaks and accumulation of patients with the same genetic type of Campylobacter (a cluster) are more common than previously assumed. The clusters and outbreaks are, however, difficult to detect, as they easily “blend into” a context of a very high number of cases, and because whole-genome sequencing is not performed routinely on all human isolates.

Genetic monitoring of campylobacter infections

In 2019, Statens Serum Institut (SSI) initiated ongoing monitoring of campylobacter infections based on whole-genome sequencing of Campylobacter jejuni and C. coli isolates. Upon agreement with the three departments of clinical microbiology (DCMs), all campylobacter isolates from culture-positive patients in 2019 were submitted from DCM Aalborg along with a monthly sample from DCM Odense and DCM Slagelse (approx. 25% of their annual campylobacter cases). Furthermore, the SSI received a minor number of isolates from other DCMs. The isolates were whole-genome sequenced and analysed to detect genetic clusters of Campylobacter and therefore possible outbreaks. This was done in the same manner as the already established WGS-based monitoring of infections with Salmonella, Listeria monocytogenes and Shiga-toxin-producing E. coli (STEC).

The majority of the 668 submitted isolates were C. jejuni (93%) and the rest were C. coli. Results from the WGS analysis showed that half of the isolates formed part of a cluster. Isolates were distributed on a large number of small clusters counting 2-4 patients and 14 larger clusters with ≥5 patients. Most of the large clusters counted patients from several regions, which is in line with the typical nationwide distribution of foods in Denmark. This picture of the campylobacter epidemiology was also seen in a project period from 2015 to 2017, when a similar monitoring was in place, based on WGS analyses. However, in contrast to previously, 2019 recorded a remarkably large and prolonged outbreak. A total of 88 patients had a C. jejuni infection with the same clone belonging to sequence type ST122. Patients with this type were distributed across the entire year with more cases in the period from February to August. Large Campylobacter clusters are unusual. Campylobacter is characterised by considerable genetic diversity, and typically any clone only occurs for a limited number of months. The ST122 clone comprised 13% of all WGS-typed campylobacter isolates in 2019.

In the same period, the Danish Veterinary and Food Administration (DVFA) performed WGS on campylobacter isolates from chicken meat. In close collaboration with the DVFA and Denmark's Technical University, the SSI continuously compared Campylobacter genome sequences from patients and chicken meat. Approx. one third of all patients had a campylobacter isolate that was identical to bacteria detected in chicken meat, typically found in 1-3 samples of chicken meat within a few weeks. The prolonged outbreak with the STT122-clone matched simultaneous isolates from chicken meat. The chicken meat was produced at a single abattoir and back-traced to a single producer, even though more producers may have been affected. It is assessed that the continuous source of the ST122-clone in Danish chicken meat contributed to the increased number of campylobacter infections in 2019 compared with the preceding years.
Monitoring based on whole-genome sequencing initiated in 2019 is continued in 2020 with a similar sample of campylobacter from patients diagnosed at four of the country’s DCMs and continuous analyses of samples from chicken meat and other relevant food sources. The objective is to detect larger nationwide outbreaks, enhance our understanding of the contribution of different food sources to the number of infections and, in general, to underpin the efforts made to reduce the number of foodborne campylobacter infections.

Campylobacter, climate and climate change

Since 2000, a total of four very large water-borne campylobacter outbreaks have been recorded, affecting a total of at least 1,300 persons in Denmark. Three of these outbreaks were caused by contaminated drinking water, whereas the fourth outbreak was due to swimming outdoors in contaminated water. All four outbreaks had one factor in common; they occurred shortly after heavy rainfall or actual rain storms - more of which are predicted as the climate changes in years to come.

To elucidate the association between climate and campylobacter, the SSI, in collaboration with colleagues in Finland, Norway and Sweden, has collected detailed data on campylobacter cases and analysed these data in relation to precipitation and temperature data in the period from 2000 to 2015. The results of these analyses were also used to predict how large an effect climate changes may have on the occurrence of campylobacter infections in the four countries.

The study confirms that increasing precipitation - and, in particular rain storms - may cause an increase in the number of campylobacter cases. The results also indicate that heat waves may have the opposite affect, reducing the number of cases after a period with very high temperatures.

Modelled scenarios from The Intergovernmental Panel of Climate Change (IPCC) predict that the temperature in the Nordic countries may increase by an average 4.2°C and that precipitation may increase by 25%, increasing rain storms by 45% by the end of this century. These climate changes were combined with analyses of the dependence of campylobacter on the weather in the Nordic countries, and the results showed that climate change alone may cause a doubling of the number of campylobacter cases in Denmark, Finland, Norway and Sweden by 2090. Additionally, climate changes may mean that the high season for transmitting the infection may be extended – meaning that it will not be limited to the summer months. According to the project’s analyses, the most pronounced effects of climate changes will be observed in Denmark and Norway with a particularly steep increase in the municipalities of West Jutland.

Overall, it is very likely that climate changes will affect the number of campylobacter cases in Denmark. Some areas will be more exposed than others, and it is therefore important to map these areas now and to be attentive to preventive measures in the future, focusing extensively on hygiene.

(K. Gaardbo Kuhn, S. Ethelberg, Department for Infectious Disease Epidemiology and Prevention, E. Møller Nielsen, K. Joensen, M. Torpdahl, Department of Bacteria, Parasites and Fungi)