A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains

Genome-Wide association study to identify genetic markers associated with Campylobacter jejuni motility

The ability of Campylobacter jejuni to survive and persist under harsh conditions is linked to the presence of flagella. This structure promotes the motility of the bacteria towards their optimum environment. The aim of this study was to examine the genetic basis for motility within 136 C. jejuni isolates through two different Genome-Wide Association Studies, gene presence/absence and Single Nucleotide Polymorphisms (SNPs). The motility phenotype was widely distributed across the phylogeny with large intra-lineage swarming performance variabilities. Accessory genes significantly associated with motility were found in four key genomic regions. One of these regions affected the Cj0727-Cj0733 operon, that encodes a putative ABC transporter system for phosphate uptake, while other influenced the capsule biosynthesis locus. Multiple SNPs mostly linked to increased motility were also discovered in clusters of genes, with special relevance to transport and membrane proteins. Therefore, the capsule and membrane composition might influence nutrient transfer, further impacting the protonmotive force that drives flagellar motor rotation in C. jejuni. The study provides novel genetic markers with a potential role in the motility phenotype of the pathogen.

Source attribution of Listeria monocytogenes in the Netherlands

The aim of this study was to determine the relative contributions of various potential food sources of human listeriosis and to identify source-specific risk factors, at exposure level, for human Listeria monocytogenes (Lm) infection. To achieve this, available Lm isolates from human cases (n = 756) and food/animal sources (n = 950) from national surveillance systems in the Netherlands (2010-2020) were whole genome sequenced. Additionally, questionnaire-based exposure data for human cases was collected. Source attribution analysis was performed using a Random Forest model based on core-genome multilocus sequence typing (cgMLST). Risk factors for human Lm infection of cattle, chicken and seafood origin were determined using beta regression analysis on the cgMLST-based attribution estimates. Results indicated that the 756 human Lm isolates were mainly attributed to cattle (62.3 %), chicken (19.4 %), and seafood (16.9 %). Specifically, fresh meat (86.2 %), including fresh bovine meat (43.7 %) and fresh chicken meat (39.3 %), accounted for most cases. These attributions stemmed from Lm contamination of either the food products or their production environments. Consumption of steak tartare and smoked salmon was associated with an increased risk of human Lm infections attributed to cattle and seafood, respectively, while no specific risk factors for chicken-borne listeriosis were identified. This study indicated that Lm isolates of cattle origin, particularly those from fresh bovine meat and associated production environments, are estimated to be the primary cause of human listeriosis in the Netherlands. This aligns with several other European source attribution studies on Lm. Moreover, the identified risk factors for human Lm infection from cattle (i.e. steak tartare) and seafood (i.e. smoked salmon) clearly indicated their attributable sources. This joint analysis of core genome and epidemiological data provided novel insights into the origins and transmission pathways of human listeriosis.

Employing genome-wide association studies to investigate acid adaptation mechanisms in Listeria monocytogenes

Listeria monocytogenes is a critical foodborne pathogen known to develop adaptation traits in mildly acidic food processing environments. This study analyzed the genomic data of 49 strains derived from clinical and food sources, utilizing genome-wide association studies (GWAS) to explore the correlation between the genotypic and phenotypic traits of L. monocytogenes, thereby identifying the genetic determinants of its acid adaptation capability. The findings revealed no significant association between the collected acid adaptation genes and the bacterial growth parameters. The GWAS results indicated that numerous single nucleotide polymorphism (SNP) sites were significantly correlated with the growth parameters of L. monocytogenes in a pH = 5.0 acidic environment, whereas the associations diminished as the pH approached neutrality at pH = 6.7. Analysis and annotation of synonymous mutation loci revealed that non-synonymous mutations primarily impact function. The phenotypes pH = 5.0, ΔpH (5.0-5.5), SNPλ, and SNPμmax show the strongest associations with non-synonymous mutation loci. The genes lmo0017, lmo1173, lmo0794, and lmo2783 are significant non-synonymous mutation loci influencing acid adaptation. These genes play critical roles in intracellular pH regulation, cell wall synthesis and environmental response control, directly or indirectly affecting bacterial acid tolerance. Future research could leverage existing data combined with machine learning and causal inference methods to further dissect the genotype-phenotype causal relationships, identifying causative genetic factors that govern the acid adaptation in L. monocytogenes, providing insights for risk assessment and management strategies in food safety.

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Improvements in sequencing quality, availability, speed and costs results in an increased presence of genomics in infectious disease applications. Nevertheless, there are still hurdles in regard to the optimal use of WGS for public health purposes. Here, we discuss the current state ("status quo") and future directions ("quo vadis") based on literature regarding the use of genomics in surveillance, hazard characterization and source attribution of foodborne pathogens. The future directions include the application of new techniques, such as machine learning and network approaches that may overcome the current shortcomings. These include the use of fixed genomic distances in cluster delineation, disentangling similarity or lack thereof in source attribution, and difficulties ascertaining function in hazard characterization. Although, the aforementioned methods can relatively easily be applied technically, an overarching challenge is the inference and biological/epidemiological interpretation of these large amounts of high-resolution data. Understanding the context in terms of bacterial isolate and host diversity allows to assess the level of representativeness in regard to sources and isolates in the dataset, which in turn defines the level of certainty associated with defining clusters, sources and risks. This also marks the importance of metadata (clinical, epidemiological, and biological) when using genomics for public health purposes.

Comparative pangenomic analysis of Campylobacter fetus isolated from Spanish bulls and other mammalian species

Campylobacter fetus comprises two closely related mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv). The latter causes bovine genital campylobacteriosis, a sexually-transmitted disease endemic in Spain that results in significant economic losses in the cattle industry. Here, 33 C. fetus Spanish isolates were whole-genome sequenced and compared with 62 publicly available C. fetus genomes from other countries. Genome-based taxonomic identification revealed high concordance with in silico PCR, confirming Spanish isolates as Cff (n = 4), Cfv (n = 9) and Cfv biovar intermedius (Cfvi, n = 20). MLST analysis assigned the Spanish isolates to 6 STs, including three novel: ST-76 and ST-77 for Cfv and ST-78 for Cff. Core genome SNP phylogenetic analysis of the 95 genomes identified multiple clusters, revealing associations at subspecies and biovar level between genomes with the same ST and separating the Cfvi genomes from Spain and other countries. A genome-wide association study identified pqqL as a Cfv-specific gene and a potential candidate for more accurate identification methods. Functionality analysis revealed variations in the accessory genome of C. fetus subspecies and biovars that deserve further studies. These results provide valuable information about the regional variants of C. fetus present in Spain and the genetic diversity and predicted functionality of the different subspecies.

Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio

Introduction

With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States.

Methods

The goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020.

Results

A total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3'-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%).

Discussion/Conclusion

Our study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.

Phylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni

Campylobacter jejuni is a major foodborne pathogen transmitted to humans primarily via contaminated poultry meat. Since poultry meat is generally processed, distributed, and stored in the cold chain, the survival of C. jejuni at refrigeration temperatures crucially affects human exposure to C. jejuni. Here, we investigated genetic factors associated with cold stress tolerance in C. jejuni. Seventy-nine C. jejuni strains isolated from retail raw chicken exhibited different survival levels at 4°C for 21 days. Multilocus sequence typing (MLST) clonal complex 21 (CC-21) and CC-443 were dominant among cold stress-tolerant strains, whereas CC-45 was common among cold stress-sensitive strains. Genome-wide average nucleotide identity (ANI) analysis identified a phylogenetic cluster associated with cold stress tolerance. Moreover, a pangenome analysis revealed 58 genes distinctively present in the cold stress-tolerant phylogenetic cluster. Among these 58 genes, cfrA, encoding the ferric enterobactin receptor involved in ion transport and metabolism, was selected for further analysis. Remarkably, the viability of a ΔcfrA mutant at 4°C was significantly decreased, while the levels of total reactive oxygen species and intracellular iron exceeded those of the wild type. Additionally, a knockout mutation of cfrA also significantly decreased the viability of three cold stress-tolerant isolates at 4°C, confirming the role of cfrA in cold stress tolerance. The results of this study demonstrate that unique phylogenetic clusters of C. jejuni associated with cold stress tolerance exist and that cfrA is a genetic factor contributing to cold stress tolerance in C. jejuni. IMPORTANCE The tolerance of foodborne pathogens to environmental stresses significantly affects food safety. Several studies have demonstrated that C. jejuni survives extended exposures to low temperatures, but the mechanisms of cold stress tolerance are not fully understood. Here, we demonstrate that C. jejuni strains in certain phylogenetic groups exhibit increased tolerance to cold stress. Notably, cfrA is present in the phylogenetic cluster associated with cold stress tolerance and plays a role in the survival of C. jejuni at low temperatures by alleviating oxidative stress. This is the first study to discover phylogenetic associations involving cold stress tolerance and to identify genetic elements conferring cold stress tolerance to C. jejuni.

Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective

BACKGROUND

Campylobacteriosis represents a global public health threat with various socio-economic impacts. Among different Campylobacter species, Campylobacter jejuni (C. jejuni) is considered to be the foremost Campylobacter species responsible for most of gastrointestinal-related infections. Although these species are reported to primarily inhabit birds, its high genetic and phenotypic diversity allowed their adaptation to other animal reservoirs and to the environment that may impact on human infection.

MAIN BODY

A stringent and consistent surveillance program based on high resolution subtyping is crucial. Recently, different epidemiological investigations have implemented high-throughput sequencing technologies and analytical pipelines for higher resolution subtyping, accurate source attribution, and detection of antimicrobial resistance determinants among these species. In this review, we aim to present a comprehensive overview on the epidemiology, clinical presentation, antibiotic resistance, and transmission dynamics of Campylobacter, with specific focus on C. jejuni. This review also summarizes recent attempts of applying whole-genome sequencing (WGS) coupled with bioinformatic algorithms to identify and provide deeper insights into evolutionary and epidemiological dynamics of C. jejuni precisely along the farm-to-fork continuum.

CONCLUSION

WGS is a valuable addition to traditional surveillance methods for Campylobacter. It enables accurate typing of this pathogen and allows tracking of its transmission sources. It is also advantageous for in silico characterization of antibiotic resistance and virulence determinants, and hence implementation of control measures for containment of infection.

Critical assessment of pan-genomic analysis of metagenome-assembled genomes

Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.

Genomic Relatedness, Antibiotic Resistance and Virulence Traits of Campylobacter jejuni HS19 Isolates From Cattle in China Indicate Pathogenic Potential

Although campylobacteriosis is a zoonotic foodborne illness, high-risk isolates from animal sources are rarely characterized, and the pathogenic potential of zoonotic strains remains an obstacle to effective intervention against human infection. HS19 has been acknowledged as a maker serotype represented by Campylobacter jejuni (C. jejuni) isolates from patients with post-infection Guillain-Barré syndrome (GBS), which is circulation in developed countries. However, a previous serotype epidemiological study of C. jejuni isolates in an animal population revealed that HS19 was also prevalent in isolates from cattle in China. In this study, to investigate the hazardous potential of zoonotic strains, 14 HS19 isolates from cattle were systematically characterized both by genotype and phenotype. The results showed that all of these cattle isolates belonged to the ST-22 complex, a high-risk lineage represented by 77.2% HS19 clinical isolates from patients worldwide in the PubMLST database, indicating that the ST-22 complex is the prominent clonal complex of HS19 isolates, as well as the possibility of clonal spread of HS19 isolates across different regions and hosts. Nevertheless, these cattle strains clustered closely with the HS19 isolates from patients, suggesting a remarkable phylogenetic relatedness and genomic similarity. Importantly, both tetracycline genes tet(O) and gyrA (T86I) reached a higher proportional representation among the cattle isolates than among the human clinical isolates. A worrying level of multidrug resistance (MDR) was observed in all the cattle isolates, and two MDR profiles of the cattle isolates also existed in human clinical isolates. Notably, although shared with the same serotype HS19 and sequence type ST-22, 35.7% of cattle isolates induced severe gastrointestinal pathology in the IL-10^–/– C57BL/6 mice model, indicating that some bacteria could change due to host adaptation to induce a disease epidemic, thus the associated genetic elements deserve further investigation. In this study, HS19 isolates from cattle were first characterized by a systematic evaluation of bacterial genomics and in vitro virulence, which improved our understanding of the potential zoonotic hazard from food animal isolates with high-risk serotypes, and provided critical information for the development of targeted C. jejuni mitigation strategies.

Functional Mapping of Phenotypic Plasticity of Staphylococcus aureus Under Vancomycin Pressure

Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 (walR), SAOUHSC_00176, SAOUHSC_00544 (sdrC), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.

Campylobacter coli strains from Brazil can invade phagocytic and epithelial cells and induce IL-8 secretion

Campylobacter spp. have been a predominant cause of bacterial foodborne gastroenteritis worldwide, causing substantial costs to public healthcare systems. This study aimed to assess the invasion and pro-inflammatory cytokine production capacity of Campylobacter coli strains isolated in Brazil. A total of 50 C. coli isolated from different sources in Brazil were analyzed for their capacity of invasion in Caco-2 and U-937 cell lines. The production of pro-inflammatory cytokines was quantitatively measured in response to C. coli. All the strains studied showed invasion percentage ≥ 40% in polarized Caco-2 cells. In U-937 cells assay, 35 of 50 C. coli strains studied showed invasion percentage ≥ 50%. A significant increase in IL-8 production by infected U-937 cells was observed for 17.5% of the C. coli isolates. The high percentages of invasion in Caco-2 and U-937 cells observed for all studied strains, plus the increased production of IL-8 by U-937 cells against some strains, highlighted the pathogenic potential of the C. coli studied and bring extremely relevant data since it has never been reported for strains isolated in Brazil and there are a few data for C. coli in the literature.

Genome-wide insights into population structure and host specificity of Campylobacter jejuni

The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species' guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada. We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.

Genetic variation and function: revealing potential factors associated with microbial phenotypes

Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.

Identification of Novel Sensitive and Reliable Serovar-Specific Targets for PCR Detection of Salmonella Serovars Hadar and Albany by Pan-Genome Analysis

The accurate and rapid classification of Salmonella serovars is an essential focus for the identification of isolates involved in disease in humans and animals. The purpose of current research was to identify novel sensitive and reliable serovar-specific targets and to develop PCR method for Salmonella C2 serogroups (O:8 epitopes) in food samples to facilitate timely treatment. A total of 575 genomic sequences of 16 target serovars belonging to serogroup C2 and 150 genomic sequences of non-target serovars were analysed by pan-genome analysis. As a result, four and three specific genes were found for serovars Albany and Hadar, respectively. Primer sets for PCR targeting these serovar-specific genes were designed and evaluated based on their specificity; the results showed high specificity (100%). The sensitivity of the specific PCR was 2.8 × 10¹–10³ CFU/mL and 2.3 × 10³–10⁴ CFU/mL for serovars Albany and Hadar, respectively, and the detection limits were 1.04 × 10³–10⁴ CFU/g and 1.16 × 10⁴–10⁵ CFU/g in artificially contaminated raw pork samples. Furthermore, the potential functions of these serovar-specific genes were analysed; all of the genes were functionally unknown, except for one specific serovar Albany gene known to be a encoded secreted protein and one specific gene for serovars Hadar and Albany that is a encoded membrane protein. Thus, these findings demonstrate that pan-genome analysis is a precious method for mining new high-quality serovar-targets for PCR assays or other molecular methods that are highly sensitive and can be used for rapid detection of Salmonella serovars.

Revisiting Campylobacter jejuni Virulence and Fitness Factors: Role in Sensing, Adapting, and Competing

Campylobacter jejuni is the leading cause of bacterial foodborne gastroenteritis world wide and represents a major public health concern. Over the past two decades, significant progress in functional genomics, proteomics, enzymatic-based virulence profiling (EBVP), and the cellular biology of C. jejuni have improved our basic understanding of this important pathogen. We review key advances in our understanding of the multitude of emerging virulence factors that influence the outcome of C. jejuni–mediated infections. We highlight, the spatial and temporal dynamics of factors that promote C. jejuni to sense, adapt and survive in multiple hosts. Finally, we propose cohesive research directions to obtain a comprehensive understanding of C. jejuni virulence mechanisms.

Population Biology and Comparative Genomics of Campylobacter Species

The zoonotic pathogen Campylobacter is the leading cause for bacterial foodborne infections in humans. Campylobacters are most commonly transmitted via the consumption of undercooked poultry meat or raw milk products. The decreasing costs of whole genome sequencing enabled large genome-based analyses of the evolution and population structure of this pathogen, as well as the development of novel high-throughput molecular typing methods. Here, we review the evolutionary development and the population diversity of the two most clinically relevant Campylobacter species; C. jejuni and C. coli. The state-of-the-art phylogenetic studies showed clustering of C. jejuni lineages into host specialists and generalists with coexisting lifestyles in chicken and livestock-associated hosts, as well as the separation of C. coli isolates of riparian origin (waterfowl, water) from C. coli isolated from clinical and farm-related samples. We will give an overview of recombination between both species and the potential impact of horizontal gene transfer on host adaptation in Campylobacter. Additionally, this review briefly places the current knowledge of the population structure of other Campylobacter species such as C. lari, C. concisus and C. upsaliensis into perspective. We also provide an overview of how molecular typing methods such as multilocus sequence typing (MLST) and whole genome MLST have been used to detect and trace Campylobacter outbreaks along the food chain.

Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.

AB_SA: Accessory genes-Based Source Attribution - tracing the source of Salmonella enterica Typhimurium environmental strains

The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Salmonella enterica Typhimurium and its monophasic variant (S. enterica 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 S. enterica Typhimurium and S. enterica 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.

Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

MOTIVATION

Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers.

RESULTS

In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research.

AVAILABILITY AND IMPLEMENTATION

The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Campylobacter jejuni: collective components promoting a successful enteric lifestyle

Campylobacter jejuni is the leading cause of bacterial diarrhoeal disease in many areas of the world. The high incidence of sporadic cases of disease in humans is largely due to its prevalence as a zoonotic agent in animals, both in agriculture and in the wild. Compared with many other enteric bacterial pathogens, C. jejuni has strict growth and nutritional requirements and lacks many virulence and colonization determinants that are typically used by bacterial pathogens to infect hosts. Instead, C. jejuni has a different collection of factors and pathways not typically associated together in enteric pathogens to establish commensalism in many animal hosts and to promote diarrhoeal disease in the human population. In this Review, we discuss the cellular architecture and structure of C. jejuni, intraspecies genotypic variation, the multiple roles of the flagellum, specific nutritional and environmental growth requirements and how these factors contribute to in vivo growth in human and avian hosts, persistent colonization and pathogenesis of diarrhoeal disease.

Genomic Analysis of Chilean Strains of Campylobacter jejuni from Human Faeces

Campylobacter spp., especially C. jejuni, are recognized worldwide as the bacterial species that most commonly cause food-related diarrhea. C. jejuni possesses many different virulence factors, has the ability to survive in different reservoirs, and has shown among isolates the emergence of Antimicrobial Resistance (AMR). Genome association analyses of this bacterial pathogen have contributed to a better understanding of its pathogenic and AMR associated determinants. However, the epidemiological information of these bacteria in Latin American countries is scarce and no genomic information is available in public databases from isolates in these countries. Considering this, the present study is aimed to describe the genomic traits from representative Campylobacter spp. strains recovered from faecal samples of patients with acute diarrhoea from Valparaíso, Chile. Campylobacter spp. was detected from the faeces of 28 (8%) out of 350 patients with acute diarrhoea, mainly from young adults and children, and 26 (93%) of the isolates corresponded to C. jejuni. 63% of the isolates were resistant to ciprofloxacin, 25.9% to tetracycline, and 3.5% to erythromycin. Three isolates were selected for WGS on the basis of their flaA-RFLP genotype. They belonged to the multilocus sequence typing (MLST) clonal clomplex (CC) 21(PUCV-1), CC-48 (PUCV-3), and CC-353 (PUCV-2) and presented several putative virulence genes, including the Type IV and Type VI Secretion Systems, as well as AMR-associated genes in agreement with their susceptibility pattern. On the basis of the wgMLST, they were linked to strains from poultry and ruminants. These are the first genomes of Chilean C. jejuni isolates available in public databases and they provide relevant information about the C. jejuni isolates associated with human infection in this country.

Whole-genome comparative analysis of Campylobacter jejuni strains isolated from patients with diarrhea in northeastern Poland

BACKGROUND

Campylobacter jejuni is the leading cause of bacterial gastroenteritis (campylobacteriosis) in humans worldwide, and the most frequent pathogen associated with Guillain-Barré syndrome (GBS) and Miller-Fisher syndrome (MFS). The study was designed in order to assess similarities between genomes of Campylobacter jejuni strains, isolated from children suffering from acute diarrhea in northeastern Poland, in comparison to C. jejuni genomes stored in public databases. The analysis involved phylogeny, resistome and virulome. In addition, the Campylobacter PubMLST database was used to estimate the prevalence of the analyzed C. jejuni sequence type (STs) in other countries.

RESULTS

Campylobacter jejuni ST50, ST257 and ST51 represented 5.3%, 4.5% and 2.2% of the PubMLST records, respectively. Overall, strains representing the STs showed common resistance to tetracyclines (51.3%) and fluoroquinolones (31.8%), mediated through the tetO gene (98.2%) and point mutation (T86I) in the gyrA gene (100%). However, the latter was present in all our isolates. The major differences in virulence patterns concerned serotypes, lipooligosaccharide (LOS) classes and certain clinically relevant genes.

CONCLUSIONS

Campylobacter jejuni ST50, ST51 and ST257 are among the top ten of STs isolated in Europe. WGS revealed diversity of serotypes and LOS classes in ST50 strains, that deserves further clinical and epidemiological investigations as it might be related to a risk of post-infectious neurological sequels such as Guillain-Barré syndrome. Additionally, the results implicate lower pathogenic potential and distinct transmission chains or reservoirs for C. jejuni ST51 isolates responsible for campylobacteriosis in northeastern Poland.

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures. This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR. We describe how WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling. Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. WGS results can be used to stratify hazards into strains with similar genetic profiles that are expected to behave similarly, e.g., in terms of growth, survival, virulence or response to antimicrobial treatment. The QMRA input distributions can be tailored to each strain accordingly, making it possible to capture the variability in the strains of interest while decreasing the uncertainty in the model. WGS also allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption. WGS therefore has the potential to substantially improve the utility of foodborne AMR QMRA models. However, some degree of uncertainty remains in relation to the thresholds of genetic similarity to be used, as well as the degree of correlation between genotypic and phenotypic profiles. The latter could be improved using a functional approach based on prediction of microbial behavior from a combination of 'omics' techniques (e.g., transcriptomics, proteomics and metabolomics). We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.

Frequent Implication of Multistress-Tolerant Campylobacter jejuni in Human Infections

Campylobacter jejuni, a major cause of bacterial foodborne illnesses, is considered highly susceptible to environmental stresses. In this study, we extensively investigated the stress tolerance of 121 clinical strains of C. jejuni against 5 stress conditions (aerobic stress, disinfectant exposure, freeze-thaw, heat treatment, and osmotic stress) that this pathogenic bacterium might encounter during foodborne transmission to humans. In contrast to our current perception about high stress sensitivity of C. jejuni, a number of clinical strains of C. jejuni were highly tolerant to multiple stresses. We performed population genetics analysis by using comparative genomic fingerprinting and showed that multistress-tolerant strains of C. jejuni constituted distinct clades. The comparative genomic fingerprinting subtypes belonging to multistress-tolerant clades were more frequently implicated in human infections than those in stress-sensitive clades. We identified unique stress-tolerant C. jejuni clones and showed the role of stress tolerance in human campylobacteriosis.

Developments in Rapid Detection Methods for the Detection of Foodborne Campylobacter in the United States

The accurate and rapid detection of Campylobacter spp. is critical for optimal surveillance throughout poultry processing in the United States. The further development of highly specific and sensitive assays to detect Campylobacter in poultry matrices has tremendous utility and potential for aiding the reduction of foodborne illness. The introduction and development of molecular methods such as polymerase chain reaction (PCR) have enhanced the diagnostic capabilities of the food industry to identify the presence of foodborne pathogens throughout poultry production. Further innovations in various methodologies, such as immune-based typing and detection as well as high throughput analyses, will provide important epidemiological data such as the identification of unique or region-specific Campylobacter. Comparable to traditional microbiology and enrichment techniques, molecular techniques/methods have the potential to have improved sensitivity and specificity, as well as speed of data acquisition. This review will focus on the development and application of rapid molecular methods for identifying and quantifying Campylobacter in U.S. poultry and the emergence of novel methods that are faster and more precise than traditional microbiological techniques.

Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions

Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with "slow" growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.

The role of meat in foodborne disease: Is there a coming revolution in risk assessment and management?

Meat has featured prominently as a source of foodborne disease and a public health concern. For about the past 20 years the risk management paradigm has dominated international thinking about food safety. Control through the supply chain is supported by risk management concepts, as the public health risk at the point of consumption becomes the accepted outcome based measure. Foodborne pathogens can be detected at several points in the supply chain and determining the source of where these pathogens arise and how they behave throughout meat production and processing are important parts of risk based approaches. Recent improvements in molecular and genetic based technologies and data analysis for investigating source attribution and pathogen behaviour have enabled greater insights into how foodborne outbreaks occur and where controls can be implemented. These new approaches will improve our understanding of the role of meat in foodborne disease and are expected to have a significant impact on our understanding in the coming years.

Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example

How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.