Detection, isolation and whole genome sequencing of Campylobacter ureolyticus isolate from non-diarrheal sample in National Microbiology Reference laboratory of Latvia
Objectives Campylobacter ureolyticus is still underdiagnosed in the cases of gastroenteritis and extra-intestinal infections. The traditional approach for Campylobacter sp. identification in the samples of the diarrheal source is biased towards the growth conditions less suitable for the anaerobic and slow- growing Campylobacter ureolyticus. Consequentially, Campylobacter ureolyticus is still considered as an emerging pathogen and the subsequent necessity, implementation and adjustment of the surveillance protocols as well as the development of the more rapid diagnostic assays typically focus on the more common Campylobacter species. Some sporadic cases of extra-intestinal Campylobacter ureolyticus infections have been identified in blood cultures and surgical materials at Riga East University Hospital. This study focused on a recent isolate from an abscess drainage submitted for whole genome sequencing in the National Microbiology Reference Laboratory (NMRL). Materials and Methods The sample underwent anaerobic cultivation on the Shaedler agar with Vitamin K1 and 5% Sheep Blood (Becton Dickinson GmbH, Germany), incubated at 37°C under an anaerobic atmosphere (GENbag anaer, bioMérieux, France). Colonies were identified by MALDI-TOF mass spectrometry (Vitek MS, bioMérieux). DNA was extracted with DNeasy Blood Tissue kit (Qiagen), followed by library preparation with DNAPrep (Illumina, USA) and sequencing on Illumina NovaSeq6000 in 150PE read length configuration (ave. 5 million paired-end reads per sample). Bioinformatic analysis was performed by an in-house pipeline Ardetype v0.1.0-dev (Bodrenko & Vangravs, GitHub), employing Fastp v0.22.0, Shovill v1.1.0, chewBBACA v3.1.2 (cgmlst.org scheme v2023-05-08), 7-gene MLST v2.19.0 (PubMLST v2020-02-24). Results The colonies were identified as Campylobacter ureolyticus and the species identification was subsequently confirmed by ribosomal multilocus sequence typing (rMLST) with 100% support. Conclusions This study demonstrates the NMRL's proficiency in cultivating and genotyping the fastidious bacterium Campylobacter ureolyticus. NMRL contributes to the global knowledge and will share the obtained genomic data with the public sequence depositories for a subsequent improvement of the molecular typing methods for this underrated pathogen.