Comparative genomics of Helicobacter pullorum from different countries

Abstract

Background Helicobacter pullorum commonly colonized in the gastrointestinal tract of poultry and caused gastroenteritis. This bacterium could be transmitted to humans through contaminated food and caused colitis and hepatitis. Currently, the genetic characteristics of the H. pullorum were not recognized enough. In this study, the genomes of 23 H. pullorum strains from different counties were comparatively analyzed. Among them, H. pullorum 2013BJHL was the first isolated and reported in China. Results The genomes of the studied strains were estimated to vary from 1.55 to 2.03 Mb, with a GC content of ~ 34%. 4064 pan genes and 1267 core genes were obtained from the core-pan genome analysis using the Roary pipeline. Core genome SNPs (cg-SNPs) were obtained using Snippy4 software. Two groups were identified with the phylogenetic analysis based on the cg-SNPs. Some adhesion-related, immune regulation, motility-related, antiphagocytosis-related, toxin-related and quorum sensing related genes were identified as virulence factors. APH(3′)-IIIa, APH(2′’)-If, and AAC(6′)-Ie-APH(2′’)-Ia were identified as antibiotic resistance genes among the H. pullorum genomes. cat, SAT-4 and tetO genes were only identified in 2013BJHL, and tet(C) was identified in MIT98-5489. MIC determination revealed that the 2013BJHL showed acquired resistance to ciprofloxacin, nalidixic acid, tetracycline, gentamicin, streptomycin and erythromycin, only sensitive to ampicillin. The antibiotic resistance genetic determinants on the 2013BJHL genome correlate well with observed antimicrobial susceptibility patterns. Two types of VI secretion system (T6SS) were identified in 52.2% (12/23) the studied strains. Conclusion In this study, we obtained the genetic characteristics of H. pullorum from different sources in the world. The comprehensive genetic characteristics of H. pullorum were first described. H. pullorum showed highly genetic diversity and two sub-types of T6SSs were first identified in H. pullorum. 2013BJHL was found to be multidrug resistant as it was resistant to at least three different antibiotic classes.

Isolation and Genomic Characteristics of Cat-Borne Campylobacter felis sp. nov. and Sheep-Borne Campylobacter ovis sp. nov

“…The minimum inhibitory concentrations (MICs) for 11 antimicrobials (erythromycin, azithromycin, nalidixic acid, ciprofloxacin, gentamicin, streptomycin, chloramphenicol, florfenicol, tetracycline, telithromycin, and clindamycin) at concentrations ranging from 0.02 to 256 µg mL −1 were determined for all isolates using the agar dilution method (ZC-AST-001, Qingdao Sinova Biotechnology Co., Ltd., Qingdao, China) and the gradient strip diffusion method (E-test, bio Mérieux, Nürtingen, Germany) following the manufacturer's instructions, as previously reported [24,25]. The MIC was read as the lowest concentration without visible growth.…”

Genetic characteristics and potential pathogenic agents in Campylobacter upsaliensis based on genomic analysis

“…The minimum inhibitory concentrations (MICs) for a total of eleven antimicrobials, including erythromycin, azithromycin, nalidixic acid, ciprofloxacin, gentamicin, streptomycin, chloramphenicol, florfenicol, tetracycline, telithromycin, and clindamycin, were determined for all isolates in this study. This was achieved using the agar dilution method (ZC-AST-001, Qingdao Sinova Biotechnology, China), as previously reported [ 22 ]. The type strain C. jejuni ATCC 33560 T was employed as a control for comparison.…”

Helicobacter zhangjianzhongii sp. nov., isolated from dog feces

“…The minimum inhibitory concentrations (MICs) for ten antibiotic classes (macrolides, quinolones, aminoglycosides, chloramphenicol, tetracyclines, ketolides, lincosamides, β -lactams, metronidazole, and rifampicin) were determined for isolates using the agar dilution method (ZC-AST-001, Qingdao Sinova Biotechnology Co., Ltd., Qingdao, China) and the gradient strip diffusion method (E-test, bio Mérieux, Nürtingen, Germany) following the manufacturer’s instruction as previously reported ( Li et al, 2020 ; Zhou et al, 2020 ). The MIC was read as the lowest concentration without visible growth.…”