Genomics, Epidemiology and Evolution of Campylobacter, Helicobacter and Related Organisms

Consumption of raw, undercooked or contaminated animal food products is a frequent cause of Campylobacter jejuni infection. Brazil is the world’s third largest producer and a major exporter of chicken meat, yet population-level genomic investigations of C. jejuni in the country remain scarce. Analysis of 221 C. jejuni genomes from Brazil shows that the overall core and accessory genomic features of C. jejuni are influenced by the identity of the human or animal source. Of the 60 sequence types detected, ST353 is the most prevalent and consists of samples from chicken and human sources. Notably, we identified the presence of diverse bla genes from the OXA-61 and OXA-184 families that confer beta-lactam resistance as well as the operon cmeABCR related to multidrug efflux pump, which contributes to resistance against tetracyclines, macrolides and quinolones. Based on limited data, we estimated the most recent common ancestor of ST353 to the late 1500s, coinciding with the time the Portuguese first arrived in Brazil and introduced domesticated chickens into the country. We identified at least two instances of ancestral chicken-to-human infections in ST353. The evolution of C. jejuni in Brazil was driven by the confluence of clinically relevant genetic elements, multi-host adaptation and clonal population growth that coincided with major socio-economic changes in poultry farming.

Campylobacter jejuni is the leading cause of bacterial gastroenteritis worldwide, but, unlike other foodborne pathogens, is not commonly reported as causing outbreaks. The population structure of the species is characterized by a high degree of genetic diversity, but the presence of stable clonally derived genotypes persisting in space and time, and potentially leading to diffuse outbreaks, has recently been identified. The spread of these recurring genotypes could be enhanced by wild birds, suspected to act as vectors for a wide range of microorganisms that can be transmissible to other animals or humans. This study assessed the genetic diversity of C. jejuni carriage in wild birds and surface waters to explore a potential link between these environments and the persistence over years of recurring lineages infecting humans in Luxembourg. These lineages corresponded to over 40 % of clinical isolates over a 4 year period from 2018 to 2021. While mainly exotic genotypes were recovered from environmental samples, 4 % of C. jejuni from wild birds corresponded to human recurring genotypes. Among them, a human clinical endemic lineage, occurring for over a decade in Luxembourg, was detected in one bird species, suggesting a possible contribution to the persistence of this clone and its multi-host feature. Whereas 27 % of wild birds were carriers of C. jejuni, confirming their role as spreader or reservoir, only three out of 59 genotypes overlapped with recurring human strains. While direct transmission of C. jejuni infection through wild birds remains questionable, they may play a key role in the environmental spreading of stable clones to livestock, and this issue merits further investigation.

Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the ‘generalist’ category (n=188), 25  % as ‘poultry specialist’ (n=83), and only a few to ‘ruminant specialist’ (n=11) or ‘wild bird’ origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %). Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.

Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between Campylobacter (C.) jejuni and the intestinal microbiota might influence Campylobacter colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with C. jejuni in Campylobacter -specific phage-free chickens under standardized conditions and special biosafety precautions.

Therefore, 12 artificially infected ( C. jejuni inoculum with a challenge dose of 7.64 log10 c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No Campylobacter -specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between C. jejuni -negative and C. jejuni -positive chickens. The factor chickens’ infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (P=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (P=0.015). The strongest difference between C. jejuni -non-infected and C. jejuni -infected birds was observed for the family Peptococcaceae whose presence in C. jejuni -infected birds could not be demonstrated. Further, several genera of the family Ruminococcaceae appeared to be depressed in its abundance due to Campylobacter infection. A negative correlation was found between Christensenellaceae R-7 group and Campylobacter in C. jejuni -colonised chickens, both genera potentially competing for substrate. This makes Christensenellaceae R-7 group highly interesting for further studies that aim to find control options for Campylobacter infections and assess the relevance of this finding for chicken health and Campylobacter colonization.

  Campylobacter   is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of   Campylobacter   isolates from the Cairo metropolitan area, Egypt. In total, 112   Campylobacter   isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of   Campylobacter coli   isolates were multidrug resistant compared to   Campylobacter jejuni  . Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen.

The East Asian region, including China, Japan and Korea, accounts for half of gastric cancer deaths. However, different areas have contrasting gastric cancer incidences and the population structure of Helicobacter pylori in this ethnically diverse region is yet unknown. We aimed to investigate genomic differences in H. pylori between these areas to identify sequence polymorphisms associated with increased cancer risk. We analysed 381  H . pylori genomes collected from different areas of the three countries using phylogenetic and population genetic tools to characterize population differentiation. The functional consequences of SNPs with a highest fixation index (Fst) between subpopulations were examined by mapping amino acid changes on 3D protein structure, solved or modelled. Overall, 329/381 genomes belonged to the previously identified hspEAsia population indicating that import of bacteria from other regions of the world has been uncommon. Seven subregional clusters were found within hspEAsia, related to subpopulations with various ethnicities, geographies and gastric cancer risks. Subpopulation-specific amino acid changes were found in multidrug exporters (hefC), transporters (frpB-4), outer membrane proteins (hopI) and several genes involved in host interaction, such as a catalase site, involved in H2O2 entrance, and a flagellin site mimicking host glycosylation. Several of the top hits, including frpB-4, hefC, alpB/hopB and hofC, have been found to be differentiated within the Americas in previous studies, indicating that a handful of genes may be key to local geographic adaptation. H. pylori within East Asia are not homogeneous but have become differentiated geographically at multiple loci that might have facilitated adaptation to local conditions and hosts. This has important implications for further evaluation of these changes in relation to the varying gastric cancer incidence between geographical areas in this region.

  Campylobacter jejuni   strains that produce sialylated lipooligosaccharides (LOS) can cause the immune-mediated disease Guillain-Barré syndrome (GBS). The risk of GBS after infection with   C. jejuni   Penner serotype HS:19 is estimated to be at least six times higher than the average risk. Aside from LOS biosynthesis genes, genomic characteristics that promote an increased risk for GBS following   C. jejuni   HS:19 infection, remain uncharacterized. We hypothesized that strains with the HS:19 serotype have unique genomic features that explain the increased risk for GBS. We performed genome sequencing, alignments, single nucleotide polymorphisms' analysis and methylome characterization on a subset, and pan-genome analysis on a large number of genomes to compare HS:19 with non-HS:19   C. jejuni   genome sequences. Comparison of 36   C. jejuni   HS:19 with 874   C. jejuni   non-HS:19 genome sequences led to the identification of three single genes and ten clusters containing contiguous genes that were significantly associated with   C. jejuni   HS:19. One gene cluster of seven genes, localized downstream of the capsular biosynthesis locus, was related to sulphation of biomolecules. This cluster also encoded the campylobacter sialyl transferase Cst-I. Interestingly, sulphated bacterial biomolecules such as polysaccharides can promote immune responses and, therefore, (in the presence of sialic acid) may play a role in the development of GBS. Additional gene clusters included those involved in persistence-mediated pathogenicity and gene clusters involved in restriction-modification systems. Furthermore, characterization of methylomes of two HS:19 strains exhibited novel methylation patterns (5′-CATG-3 and 5′-m6AGTNNNNNNRTTG-3) that could differentially effect gene-expression patterns of   C. jejuni   HS:19 strains. Our study provides novel insight into specific genetic features and possible virulence factors of   C. jejuni   associated with the HS:19 serotype that may explain the increased risk of GBS.

The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli / C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined ‘despeciation’. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli / C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C . coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni . The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1–9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli . Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.

The gut contains an enormous diversity of simple as well as complex molecules from highly diverse food sources, together with host-secreted molecules. This presents a large metabolic opportunity for the gut microbiota, but little is known about how gut microbes are able to catabolize this large chemical diversity. Recently, Fe-S flavoenzymes were found to be key in the transformation of bile acids, catalysing the key step in the 7α-dehydroxylation pathway that allows gut bacteria to transform cholic acid into deoxycholic acid, an exclusively microbe-derived molecule with major implications for human health. While this enzyme family has also been implicated in a limited number of other catalytic transformations, little is known about the extent to which it is of more global importance in gut microbial metabolism. Here, we perform a large-scale computational genomic analysis to show that this enzyme superfamily has undergone a remarkable expansion in Clostridiales, and occurs throughout a diverse array of >1000 different families of putative metabolic gene clusters. Analysis of the enzyme content of these gene clusters suggests that they encode pathways with a wide range of predicted substrate classes, including saccharides, amino acids/peptides and lipids. Altogether, these results indicate a potentially important role of this protein superfamily in the human gut, and our dataset provides significant opportunities for the discovery of novel pathways that may have significant effects on human health.