Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis

Identification and antimicrobial susceptibility profiles of Campylobacter isolated from camel at municipal abattoirs in eastern Ethiopia

Campylobacteriosis is an infectious zoonotic disease caused by the genus Campylobacter. The disease is transmitted from animals to humans predominantly through the consumption of contaminated food and water. However, the lack of information on the status of Campylobacter makes it difficult to quantify the role of camel meat in the dissemination of the pathogen. A cross-sectional study was conducted from June 2022 to August 2023 to investigate the occurrence of Campylobacter and associated risk factors and to determine the antimicrobial susceptibility profiles of Campylobacter species from camels slaughtered at municipal abattoirs in the towns of Harar, Babile, Jigjiga and Dire Dawa in eastern Ethiopia. A total of 324 (146 carcass swabs, 146 camel feces and 32 abattoir environmental swab samples) were collected and analyzed using TaqMan real-time PCR and culture techniques following standard procedures. In addition, antimicrobial susceptibility tests were performed using the disk diffusion method for eight antimicrobial agents according to the Clinical Laboratory Standards Institute. The overall prevalence of Campylobacter was 7.7%. Campylobacter was more frequently detected from carcasses and surface contact environmental swabs. We isolated Campylobacter at the genus level from approximately half of the PCR-positive samples, representing 54.2% (13 out of 24) of the total. The isolation levels of C. jejuni and C. coli were also 5.56% and 2.2%, respectively, which varied significantly (p = 0.037) based on sample type and site. The odds of occurrence of C. jejuni in samples collected from abattoir environments was 7.52 times greater than those in carcass and fecal samples. We detected resistance to chloramphenicol (78.6%), followed by amoxicillin (71.4%). However, 93%, 78.6%, and 71.4% of the isolates were susceptible to ceftriaxone, ciprofloxacin, and nalidixic acid, respectively. Multidrug resistance (MDR) was detected in 60% of the isolates. Of these MDR isolates, 9 (75%) were C. jejuni and 3 (25%) were C. coli. This study revealed that a considerable proportion of multidrug-resistant Campylobacter species circulate in both camel meat and abattoir environments. This indicates possible carcass cross-contamination by Campylobacter during slaughtering that can pose a threat to humans and limit therapeutic options, which could be prevented by applying good hygienic practices at abattoirs. Therefore, abattoir workers need to be aware of abattoir hygienic standard operating procedures. Regular coordinated actions should be implemented for the rational use of veterinary and medical drugs at the national level, together with training and awareness of hygienic practices.

Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study

BACKGROUND

Foodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter.

RESULTS

Analysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species.

CONCLUSIONS

These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.

Campylobacter californiensis sp. nov., isolated from cattle and feral swine

Nine Campylobacter strains were isolated from cattle and feral swine faeces: three were recovered during a 2007 Campylobacter-associated outbreak linked to a dairy, and the other six were isolated during a 2009-2010 survey of farms and ranches in Central California. The species identification of these strains could not be determined by 16S rRNA gene sequencing but were most similar to Campylobacter concisus and Campylobacter mucosalis. Additional atpA typing indicated that the nine strains composed a discrete novel clade related to C. concisus and C. mucosalis. A polyphasic study was undertaken here to clarify their taxonomic position. Phylogenetic analyses were performed based on 16S rRNA gene sequences and the concatenated sequences of 330 core genes. The core gene analysis placed the nine strains into a clade well separated from the other Campylobacter taxa, indicating that these strains represent a novel Campylobacter species. Pairwise digital DNA-DNA hybridization and average nucleotide identity values between these strains and other campylobacters are lower than 16 and 73%, respectively, further supporting their placement into a novel taxon. Standard phenotypic testing was performed. All strains are microaerobic or anaerobic, motile, Gram-negative, slightly-curved rods that are oxidase positive but catalase negative. Strains can be distinguished from the other catalase-negative Campylobacter species using phenotypic markers such as motility, oxidase activity, cephalothin resistance, hippuricase activity, growth at 30 °C, and α-haemolysis. The data presented here show that these strains represent a novel species within Campylobacter, for which the name Campylobacter californiensis sp. nov. (type strain RM6914T=LMG 32304T=CCUG 75329T) is proposed.

Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids

In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.

Subtractive sequence-mediated therapeutic targets from the conserved gene clusters of Campylobacter hyointestinalis and computational inhibition assessment

Campylobacter hyointestinalis is a causative agent of enteritis, proctitis, human gastroenteritis, and diarrhea. Reported transmission is from pigs to humans. Link with gastrointestinal carcinoma has also been established in non-Helicobacter pylori patients carrying this strain. The genome size of the strain LMG9260 is 1.8 MB with 1785 chromosomal and seven plasmid proteins. No therapeutic targets have been identified and reported in this bacterium. Therefore, subtractive computational screening of its genome was carried out for the purpose. In total, 31 such targets were mined and riboflavin synthase was utilized for screening natural product inhibitors against it. Among more than 30,000 screened natural compounds from the NPASS library, three (NPC472060, NPC33653, and NPC313886) were prioritized to have the potential to be developed into new antimicrobial drugs. Dynamics simulation assay along with other relevant parameters like absorption, toxicity, and distribution of the inhibiting compounds were also predicted and NPC33653 was identified as having the best drug-like properties among the prioritized compounds. Thus, it has potential to be pursued further for the inhibition of riboflavin synthesis in C. hyointestinalis for subsequent obstruction of its growth and survival.Communicated by Ramaswamy H. Sarma.

CAMPYLOBACTER HYOINTESTINALIS ISOLATION FROM HOWLER (ALOUATTA CARAYA) AND SPIDER MONKEYS (ATELES FUSCICEPS ROBUSTUS) AT A ZOOLOGIC FACILITY IN CENTRAL ILLINOIS

Campylobacter hyointestinalis was initially isolated from an asymptomatic black howler monkey (Alouatta caraya) in a routine fecal culture examination. Fecal cultures from other individuals in this group and an adjacently housed black-headed spider monkey (Ateles fusciceps robustus) group recovered C. hyointestinalis from all but one of the individuals sampled (1.1 spider monkeys and 2.1 howler monkeys). Concurrently, one spider monkey presented with acute onset severe rectal prolapse and diarrhea. Whole-genome sequencing results of C. hyointestinalis isolates from all individuals were homologous and closely related to Campylobacter hyointestinalis subsp. hyointestinalis TTU_618, a strain typically associated with environmental samples. In addition, two cytolethal distending toxin (CDT) expressing gene clusters, cdt-I and cdt-II, were identified in all isolates. These results suggest C. hyointestinalis is transmissible to both howler monkeys and spider monkeys, though the origin of infection and whether it is transmissible between these species is undetermined.

Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization

Human-wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of Escherichia coli (Shiga toxin-producing E. coli (STEC) and non-STEC), Salmonella spp. and Campylobacter spp. A genotypic search for genes having virulence and antimicrobial resistance (AMR) was performed by means of PCR and Whole-Genome Sequencing (WGS) and phenotypic (serotyping and AMR profiles) characterization. Overall, 62 samples tested positive for at least one of these species: 27.3% for STEC, 11.4% for non-STEC, 3.0% for Salmonella spp. and 6.8% for Campylobacter spp. AMR was detected in four E. coli isolates and the only Campylobacter coli isolated in this study. WGS analysis revealed that 57.7% (30/52) of pathogenic E. coli integrated genetic clusters of highly closely related isolates (often involving different animal species), supporting the circulation and transmission of different pathogenic E. coli strains in the studied areas. These results support the idea that the health of humans, animals and ecosystems are interconnected, reinforcing the importance of a One Health approach to better monitor and control public health threats.

Zoonotic Campylobacter spp. and Salmonella spp. carried by wild boars in a metropolitan area: occurrence, antimicrobial susceptibility and public health relevance

Campylobacter spp. and Salmonella spp. are the most reported zoonotic agents in Europe. They can be transmitted from wildlife to humans, and wild boars (Sus scrofa) can harbour them. In the Metropolitan Area of Barcelona (MAB, NE Spain) wild boars are found in urbanized areas. To assess the potential public health risk of this increasing wild boar population, we collected stool samples from 130 wild boars from the MAB (June 2015 - February 2016), to determine the Campylobacter and Salmonella occurrence and the antimicrobial susceptibility of the isolates. We also investigated the genetic diversity and virulence potential of Campylobacter. Campylobacter prevalence in wild boars was 61%. Forty six percent of wild boars carried Campylobacter lanienae, 16% carried Campylobacter coli, and 1% carried Campylobacter hyointestinalis; 4% carried both C. lanienae and C. coli, and 1% carried both C. lanienae and C. hyointestinalis. This is the first report of C. hyointestinalis in wildlife in Spain. Using pulse-field gel electrophoresis and multilocus sequence typing, we observed a high genetic diversity of Campylobacter and identified new sequence types. Thirty-three percent of C. coli and 14% of C. lanienae isolates showed a high virulence potential. All of the Campylobacter isolates analysed were resistant to at least one antimicrobial agent. Multidrug resistance was only detected in C. coli (67%). Salmonella enterica subsp. enterica was detected in four wild boars (3%) and included a S. Enteritidis serovar (1/4 wild boars) and a multidrug-resistant (ASSuT) monophasic S. Typhimurium serovar (1/4 wild boars) which is associated with human infections and pig meat in Europe. The characteristics of some of the Campylobacter and Salmonella isolates recovered suggest an anthropogenic origin. Wild boars are a reservoir of Campylobacter and have the potential to spread antimicrobial resistant Campylobacter and Salmonella in urbanized areas in the MAB.

Prevalence and whole-genome sequence analysis of Campylobacter spp. strains isolated from wild deer and boar in Japan

As a part of risk analysis for consumption of meat from wild animals, the prevalence of Campylobacter spp. in wild deer and boar in Japan was investigated. C. hyointestinalis subsp. hyointestinalis (C. hyointestinalis) was isolated from 2.8% (7/253) of the wild deer and 22.1% (71/321) of the wild boar examined. All 23 wild deer isolates and 141 (72.7%) wild boar isolates carried both chcdt-I and chcdt-II genes. The remaining 53 (27.3%) wild boar isolates had only the chcdt-II gene. By whole-genome sequence analysis, we detected 38-40 virulence- and survival-associated genes (motility, chemotactic, adhesion, invasion, toxin, glycosylation, iron uptake, drug resistance, and stress response), which had been identified in C. jejuni and C. coli. In conclusion, our study highlights C. hyointestinalis as a possible cause of food-borne disease in humans and emphasizes the importance of food hygiene in the processing of wild meats for human consumption.

Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator

A novel Gram-stain negative, aerobic, halotolerant, motile, rod-shaped, predatory bacterium ASxL5^T, was isolated from a bovine slurry tank in Nottinghamshire, UK using Campylobacter hyointestinalis as prey. Other Campylobacter species and members of the Enterobacteriaceae were subsequently found to serve as prey. Weak axenic growth on Brain Heart Infusion agar was achieved upon subculture without host cells. The optimal growth conditions were 37 °C, at pH 7. Transmission electron microscopy revealed some highly unusual morphological characteristics related to prey availability. Phylogenetic analyses using 16S rRNA gene sequences showed that the isolate was related to members of the Oceanospirillaceae family but could not be classified clearly as a member of any known genus. Whole genome sequencing of ASxL5^T confirmed the relationship to members the Oceanospirillaceae. Database searches revealed that several ASxL5^T share 16S rRNA gene sequences with several uncultured bacteria from marine, and terrestrial surface and subsurface water. We propose that strain ASxL5^T represents a novel species in a new genus. We propose the name Venatorbacter cucullus gen. nov., sp. nov. with ASxL5^T as the type strain.

Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts

Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. hyointestinalis subsp. lawsonii which is predominantly recovered from pigs, and C. hyointestinalis subsp. hyointestinalis which can be found in a much wider range of mammalian hosts. Despite C. hyointestinalis being reported as an emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For this reason, we generated whole-genome sequences of 13 C. hyointestinalis subsp. hyointestinalis strains and performed a comprehensive comparative analysis including publicly available C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii genomes, to gain insight into the genomic variation of these differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present an apparent barrier to homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian hosts unlike C. hyointestinalis subsp. lawsonii that is presumably host-restricted. This greater plasticity in the accessory genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-associated proteins and restriction-modification systems. Together, our results provide an overview of the genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the biology of Campylobacter species that are increasingly recognized as emerging pathogens.

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.

A systematic review and meta-analysis reveal that Campylobacter spp. and antibiotic resistance are widespread in humans in sub-Saharan Africa

INTRODUCTION

Campylobacter spp. are zoonotic bacteria that cause gastroenteritis in humans worldwide, whose main symptom is diarrhea. In certain cases, extra intestinal manifestations may occur, such as Guillain Barré syndrome. The bacteria cause severe diarrhea mostly in children and in immunocompromised individuals. This review aims to address the prevalence of Campylobacter spp. in humans in sub-Saharan Africa. It also aims to understand the impact of HIV in the prevalence, as well as to report data on antibiotic resistance and propose research priorities.

METHODS

We followed PRISMA guidelines to find studies on the occurrence of Campylobacter spp. in humans in all countries from sub-Saharan Africa. Studies published between 2000 and 2020 were searched in PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct. We have conducted a random-effect meta-analysis and calculated the proportion of resistant isolates to different antibiotics.

RESULTS AND DISCUSSION

We found 77 studies that described such occurrence in humans in 20 out of 53 sub-Saharan African countries. Campylobacter jejuni was the most prevalent species. Pooled prevalence was 9.9% (CI: 8.4%-11.6%). No major variations within the different sub-regions were found. Most studies reported Campylobacter spp. as the cause of diarrhea, mainly in children. Some studies reported the bacteria as a possible etiologic agent of acute flaccid paralysis and urinary tract infection. Campylobacter spp. presented a higher pooled prevalence in HIV infected patients, although not statistically significant. High proportions of resistant strains were reported for many antibiotics, including erythromycin and tetracycline.

CONCLUSION

Campylobacter spp. occur in sub-Saharan Africa, although information is scarce or inexistent for many countries. Research priorities should include investigation of the understudied species; extra intestinal manifestations; the impact of HIV infection and associated risk factors. Control strategies should be reinforced to contain the spread of this pathogen and drug resistance.

Campylobacter Colonization, Environmental Enteric Dysfunction, Stunting, and Associated Risk Factors Among Young Children in Rural Ethiopia: A Cross-Sectional Study From the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project

Livestock farming provides a possible mechanism by which smallholder farmers can meet their household need for animal source foods (ASF), which may reduce the risk of stunting. However, direct/indirect contacts with domestic animals may increase colonization by Campylobacter spp., which has been associated with Environmental Enteric Dysfunction (EED) and stunting. A cross-sectional study involving 102 randomly selected children between 12 and 16 months of age was conducted in rural eastern Ethiopia to establish prevalence rates of Campylobacter colonization, EED, and stunting, and evaluate potential risk factors. Data were collected between September and December 2018. The prevalence of EED and stunting was 50% (95% CI: 40-60%) and 41% (95% CI: 32-51%), respectively. Among enrolled children, 56% had consumed some ASF in the previous 24 h; 47% had diarrhea and 50% had fever in the past 15 days. 54, 63, 71 or 43% of households owned at least one chicken, cow/bull, goat, or sheep; 54 (53%) households kept chickens indoors overnight and only half of these confined the animals. Sanitation was poor, with high levels of unimproved latrines and open defecation. Most households had access to an improved source of drinking water. The prevalence of Campylobacter colonization was 50% (95% CI: 41-60%) by PCR. In addition to the thermotolerant species Campylobacter jejuni, Campylobacter coli and Campylobacter upsaliensis, non-thermotolerant species related to Campylobacter hyointestinalis and Campylobacter fetus were frequently detected by Meta-total RNA sequencing (MeTRS). Current breastfeeding and ASF consumption increased the odds of Campylobacter detection by PCR, while improved drinking water supply decreased the odds of EED. No risk factors were significantly associated with stunting. Further studies are necessary to better understand reservoirs and transmission pathways of Campylobacter spp. and their potential impact on child health.

Isolates, antimicrobial susceptibility profiles and multidrug resistance of bacteria cultured from samples collected from sheep in New Zealand (2003-2016)

Aim: To describe the common species, antimicrobial susceptibility and multidrug resistance (MDR) of bacteria cultured from samples submitted to veterinary diagnostic laboratories from sheep in New Zealand between 2003 and 2016. Methods: Bacterial culture and antimicrobial susceptibility test data from June 2003 to March 2016 for animals identified as sheep were obtained from two commercial veterinary diagnostic laboratories in New Zealand. Submission information included animal signalment, geographic origin, specimen description, the organisms cultured, and where available, antimicrobial susceptibilities of the isolates. MDR was defined as any isolate with resistance to ≥3 antimicrobial classes. Results: There were 1,971 unique laboratory submissions, yielding 2,188 isolates. Of the 1,971 submissions, the most commonly represented breeds were Romney (933; 47.3%), Romney cross (264; 13.4%), and Coopworth (197; 10.0%), and there were more submissions from females (1,006; 51.0%) than males (184; 9.3%). Most submissions were from Canterbury (549; 27.9%), Southland (471; 23.9%), and Manawatu-Wanganui (272; 13.8%) regions. Other signalment data were inconsistently described. Submitted samples most commonly originated from the gastrointestinal tract (852; 43.2%), faeces (378; 12.1%), or liver (146; 7.4%). Of the 2,188 isolates, 1,771 (80.9%) were identified by species and 247 (11.4%) by genus, with the most common isolates being Salmonella spp. (880; 40.2%), Campylobacter spp. (408; 18.6%), Listeria spp. (140; 6.4%) and Yersinia spp. (113; 5.2%). Susceptibility results were available for 117/2,188 (5.3%) isolates from 51/1,971 (2.6%) submissions. No antimicrobial susceptibility data were available for Salmonella spp., Campylobacter spp., Listeria spp. or Yersinia spp. Overall for the isolates tested, susceptibility to the fluoroquinolones and tetracyclines was greatest, and MDR was found in 24/117 (20.5%) isolates. MDR was a more frequent finding for Enterococcus spp., Bacillus spp., and Proteus mirabilis, but was infrequent in isolates of Staphylococcus aureus, alpha-haemolytic streptococci, Escherichia coli or Enterobacter spp. Conclusions and clinical relevance: This is the first report on antimicrobial susceptibility and MDR for isolates from laboratory submissions from sheep in New Zealand. The low numbers of isolates submitted for antimicrobial susceptibility testing during the period studied mean that these findings provide limited insights into antimicrobial resistance in this population, and highlight the need to address significant gaps in our understanding of why veterinarians do not more frequently submit samples from sheep for bacterial culture and susceptibility testing. Abbreviation: AMR: Antimicrobial resistance; MDR: Multidrug resistance.

Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam

Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis, is a fastidious organism when grown in the laboratory. Oxygen is required for growth, despite the presence of the metabolic mechanism for anaerobic respiration. Amino acid auxotrophies are variably reported and energy metabolism can occur through several electron donor/acceptor combinations. Overall, the picture is one of a flexible, but vulnerable metabolism. To understand Campylobacter metabolism, we have constructed a fully curated, metabolic model for the reference organism M1 (our variant is M1cam) and validated it through laboratory experiments. Our results show that M1cam is auxotrophic for methionine, niacinamide, and pantothenate. There are complete biosynthesis pathways for all amino acids except methionine and it can produce energy, but not biomass, in the absence of oxygen. M1cam will grow in DMEM/F-12 defined media but not in the previously published Campylobacter specific defined media tested. Using the model, we identified potential auxotrophies and substrates that may improve growth. With this information, we designed simple defined media containing inorganic salts, the auxotrophic substrates, L-methionine, niacinamide, and pantothenate, pyruvate and additional amino acids L-cysteine, L-serine, and L-glutamine for growth enhancement. Our defined media supports a 1.75-fold higher growth rate than Brucella broth after 48 h at 37°C and sustains the growth of other Campylobacter jejuni strains. This media can be used to design reproducible assays that can help in better understanding the adaptation, stress resistance, and the virulence mechanisms of this pathogen. We have shown that with a well-curated metabolic model it is possible to design a media to grow this fastidious organism. This has implications for the investigation of new Campylobacter species defined through metagenomics, such as C. infans.

Species distribution, genetic diversity and antimicrobial susceptibility of Campylobacter isolates recovered from the preputial cavity of healthy rams in Turkey

AIMS

Campylobacter sp. are important causes of reproductive disease in ruminants worldwide. Although healthy bulls are well-known carriers for infection of cows, the role of rams as a potential source for infecting ewes is unclear. This study aimed to determine prevalence, species distribution, genetic diversity and antimicrobial susceptibility profiles of Campylobacter sp. isolated from the preputial cavity of healthy rams.

METHODS AND RESULTS

The material of this prospective study comprised 191 swab samples taken from the preputial cavity of healthy rams. Enrichment and membrane filtration were employed for the isolation of Campylobacter. Presumptive isolates were confirmed as Campylobacter by phenotypic and molecular tests. 16S rRNA gene sequence analysis was used for the definitive identification of the isolates at species level, and genotyping was performed using pulsed-field gel electrophoresis (PFGE). The susceptibility of the Campylobacter sp. isolates to various antibiotics was determined by the disk diffusion test. In all, 27 of the 191 (14·13%) swab samples were found to be positive for Campylobacter sp. (28 isolates were recovered in total). Per phenotypic and genotypic analyses, one isolate was identified as Campylobacter mucosalis and the remaining 27 isolates were identified as Campylobacter sputorum bv. faecalis. The PFGE analysis of the C. sputorum biovar faecalis isolates produced 17 clusters and 24 different pulsotypes, indicating high genetic heterogeneity. All 28 isolates were found to be susceptible to all of the antibiotics tested.

CONCLUSIONS

Healthy rams may be an important reservoir of different Campylobacter species in the preputium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrated for the first time that healthy rams can carry different Campylobacter sp. including genetically diverse C. sputorum bv. faecalis and C. mucosalis in the preputial cavity. Further investigation on the potential implication of this finding on sheep reproductive health (e.g. infectious infertility, and abortion) and overall epidemiology of Campylobacter may be warranted.

Campylobacter novaezeelandiae sp. nov., isolated from birds and water in New Zealand

Six isolates of Campylobacter with similar non-standard colonial morphologies were identified during studies isolating Campylobacter from bird faeces and rivers in New Zealand. Genomic (16S rRNA gene sequencing and whole genome analysis) and phenotypic (MALDI-TOF analysis and conventional biochemical tests) showed that the isolates form a monophyletic clade with genetic relationships to Campylobacter coli/Campylobacter jejuni and Campylobacter peloridis/Campylobacter amoricus. They may be distinguished from other Campylobacter by their MALDI-TOF spectral pattern, their florid α-haemolysis, their ability to grow anaerobically at 37 °C, and on 2 % NaCl nutrient agar, and their lack of hippuricase. This study shows that these isolates represent a novel species within the genus Campylobacter for which the name Campylobacter novaezeelandiae sp. nov. is proposed. The presence of C. novaezeelandiae in water may be a confounder for freshwater microbial risk assessment as they may not be pathogenic for humans. The type strain is B423bT (=NZRM 4741T=ATCC TSD-167T).

Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome

High Campylobacter prevalence during early childhood has been associated with stunting and environmental enteric dysfunction (EED), especially in low resource settings. This study assessed the prevalence, diversity, abundance, and co-occurrence of Campylobacter spp. in stools from children in a rural area of eastern Ethiopia and their association with microbiome, diarrhea, and EED in children. Stool samples (n = 100) were collected from randomly selected children (age range: 360-498 days) in five kebeles in Haramaya District, Ethiopia. Diarrhea, compromised gut permeability, and gut inflammation were observed in 48, 45, and 57% of children, respectively. Campylobacter prevalence and species diversity were assessed using PCR and meta-total RNA sequencing (MeTRS). The prevalence of Campylobacter spp. in the children's stools was 50% (41-60%) by PCR and 88% (80-93.6%) by MeTRS (P < 0.01). Further, seven Campylobacter species (Campylobacter jejuni, Campylobacter upsaliensis, Campylobacter hyointestinalis, Campylobacter coli, Campylobacter sp. RM6137, uncultured Campylobacter sp., and Campylobacter sp. RM12175) were detected by MeTRS in at least 40% of children stools in high abundance (>1.76-log read per million per positive stool sample). Four clusters of Campylobacter species (5-12 species per cluster) co-occurred in the stool samples, suggesting that Campylobacter colonization of children may have occurred through multiple reservoirs or from a reservoir in which several Campylobacter species may co-inhabit. No associations between Campylobacter spp., EED, and diarrhea were detected in this cross-sectional study; however, characteristic microbiome profiles were identified based on the prevalence of Campylobacter spp., EED severity, and diarrhea. Forty-seven bacterial species were correlated with Campylobacter, and 13 of them also correlated with gut permeability, gut inflammation and/or EED severity. Forty-nine species not correlated with Campylobacter were correlated with gut permeability, gut inflammation, EED severity and/or diarrhea. This study demonstrated that (1) in addition to C. jejuni and C. coli, multiple non-thermophilic Campylobacter spp. (i.e., Campylobacter hyointestinalis, Campylobacter fetus, and Campylobacter concisus) were frequently detected in the children's stools and (2) the Campylobacter, gut permeability, gut inflammation, EED severity, and diarrhea were associated with characteristic microbiome composition. Additional spatial and longitudinal studies are needed to identify environmental reservoirs and sources of infection of children with disparate Campylobacter species and to better define their associations with EED in low-income countries.

Human campylobacteriosis: A public health concern of global importance

Campylobacter species are among the leading cause of bacterial foodborne and waterborne infections. In addition, Campylobacter is one of the major causative agent of bacterial gastrointestinal infections and the rise in the incidence of Campylobacter infections have been reported worldwide. Also, the emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents; position them as a serious threat to the public health. This paper reviews Campylobacter pathogenicity, infections, isolation and diagnosis, their reservoirs, transmission pathways, epidemiology of Campylobacter outbreaks, prevention and treatment option, antibiotics resistance and control of antibiotics use.

Pathogenomics of Emerging Campylobacter Species

Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.

Draft Genome Sequences of Nine Campylobacter hyointestinalis subsp. lawsonii Strains

With increasing reports of Campylobacter hyointestinalis species associated with human diseases, more genome sequences are required to understand the virulence mechanisms of this emerging pathogen. Here, we describe the genome sequences of nine C. hyointestinalis subsp. lawsonii strains.

With increasing reports of Campylobacter hyointestinalis species associated with human diseases, more genome sequences are required to understand the virulence mechanisms of this emerging pathogen. Here, we describe the genome sequences of nine C. hyointestinalis subsp. lawsonii strains.