Genomic characterisation of Campylobacter species in rural Bangladesh

Abstract T14

Presenter: Nikkon Sarker (Child Health Research Foundation)

Author: Nikkon Sarker (1), Bilal Djeghout (2), Nafiz Ahsan (1), Hafizur Rahman (1), Jibon Hossain (1), Nusrat Alam (1), Thanh Le-Viet (2), Gemma Kay (2), Andrew Page (2), Nicol Janecko (2), Alison E. Mather (2,3), John Wain (2), Amira Roess (4), Maksuda Islam (1), Samir K Saha (1), Senjuti Saha (1)

Campylobacter, a causative agent of diarrheal disease, remains a public health challenge in many low- and middle-income countries. However, little is known about the genomic epidemiology of Campylobacter and the transmission patterns in resource-constrained settings because of a lack of systematic surveillance and laboratory capacity. To close this gap, we initiated a longitudinal Campylobacter surveillance study in a rural community in Mirzapur, Bangladesh. We are taking a One Health approach in identifying and characterising Campylobacter among households of expectant mothers and following the mothers and their newborns for a 6-month period utilising culture-based and whole genome sequencing (WGS) technologies. A total of 220 pregnant (third trimester) women were enrolled between December 2020 and March 2021, and baseline sampling included stool from pregnant women, children in the household and animals around the household. A stool sample from the new-born was collected within 14 days of birth. All 1,090 samples (783 human; 307 animal) were screened for Campylobacter jejuni and C. coli using culture and PCR in Bangladesh. Up to two Campylobacter isolates per sample from households with multiple samples testing culture-positive underwent WGS using the Oxford Nanopore Technologies MinION sequencer. Overall, 83 of 1,090 (7.61%) samples were positive for Campylobacter either by PCR and/or by culture. Samples from two households that yielded four C. jejuni isolates from household-1 (child, n=2; chicken, n=2) and three C. jejuni isolates from household-2 (child, n=2; chicken, n=1) by culture were chosen for WGS. No diversity of sequence type (ST) or resistance gene profiles were observed from multiple isolates within a single sample. C. jejuni ST 2315 (chicken) and an unspecified ST (child) was found in one household while ST1035 (child) and unspecified ST (chicken) were found in the other household. Of the seven C. jejuni isolates, six contained one plasmid each (6.5kb to 87kb) with five plasmids carrying blaTEM-1A resistance gene. Three chicken- and one human-derived C. jejuni genomes shared the same resistance gene profile (gyrAT861 mutation; tetO) while the three human-derived C. jejuni genomes contained blaOXA-61; gyrAT861 mutation (n=2) and gyrA_T861 mutation; tetO (n=1). From this dataset, long read sequencing of Campylobacter in Bangladesh revealed within household diversity, and differences between chicken-derived samples from two different households. At completion, this study will contribute to the genomic comparison and epidemiology of Campylobacter present in rural households.

Presenting in Speaking session 3 - Epidemiology and public health