A surveillance project in Denmark using whole genome sequencing has found many Campylobacter infections are not sporadic and helped uncover a large outbreak.

The study showed that roughly half of human infections belong to genetic clusters, almost one third of clinical isolates match a chicken source, and most large clusters can be linked to poultry by WGS.

Researchers hope the knowledge and awareness raised will lead to a decrease in the Danish chicken-associated cases of campylobacteriosis in coming years.

Denmark had 5,389 cases in 2019 and 33 percent of conventional chicken meat samples were positive for Campylobacter at slaughter. One third of infections are estimated to be travel-related.

Typing-based surveillance of Campylobacter infections in 2019 enabled detection of large clusters and matched them to retail chicken isolates to react to outbreaks. Surveillance was also able to detect prolonged or reappearing outbreaks to help earlier interventions, according to the study published in the journal Eurosurveillance.

Sample findings
Scientists used WGS on 701 isolates from infected people and 164 from chicken meat. The primary focus was on one area, northern Jutland, but isolates from Funen and Zealand were also included.

Campylobacter isolates from Danish Veterinary and Food Administration control programs were sequenced and compared with clinical isolates. Fresh chicken and beef were sampled at stores in northern Jutland and at distribution centers covering retail chains while organic and free range broilers were sampled at slaughterhouses.

For the WGS-based surveillance, 626 clinical Campylobacter jejuni and Campylobacter coli isolates were collected. Also, 75 isolates from October 2018 through February 2019 were included as a follow-up on an outbreak. The study represented 12.4 percent of all reported cases in 2019.

Campylobacter was detected in 22 percent of 909 retail chicken meat samples. In total, 163 of 852 Danish-produced samples were positive as were 33 of 57 non-Danish samples.
Campylobacter was found in 84 of 123 skin samples from organic and free range broilers. A total of 128 isolates from food samples and 36 isolates from control samples at the slaughterhouse as part of the outbreak investigation were sequenced.

Some strains were only present in chicken meat or people for a few weeks or months, wheras occurrence of other strains fluctuated over time in a way that could be related to the production cycles in each farm.

Outbreak detection
Seventy-two clusters were detected with most being small at between two to four people but 14 large ones involved five to 91 patients.

The largest cluster included 91 people. It was detected at the beginning of surveillance in March 2019, and continued during the whole year, peaking from May to August. A retrospective analysis showed this strain was found in patients in October 2018.

The cluster matched four chicken isolates from retail meat sampled in May and August 2019. These isolates were traced back to a single slaughterhouse belonging to HKScan in Vinderup. An additional 30 isolates were found: 20 from meat samples at the slaughterhouse between late February and August 2019 and 10 from the slaughterhouse environment in late October.

Results supported a link between the outbreak strain and one farm. From August 2019, the slaughterhouse decided that meat from this farm should be frozen to reduce the level of Campylobacter. It also outlined an action plan for optimizing procedures and equipment.

A few cases with the outbreak strain were seen in the beginning of 2020 and it is possible it had spread to multiple farms or other slaughterhouses.

Certain issues identified by researchers included follow-up on each genetic cluster of Campylobacter is not feasible because of the large number, which would require a lot of resources and the time factor, as most cluster types have already disappeared before it is possible to take action.

Also, WGS-based surveillance of human infections without the comparison to food isolates is of limited public health value.