Campylobacter in Wild Birds: Is It an Animal and Public Health Concern?

Emergence of Plasmid-Mediated Quinolone Resistance (PMQR) Genes in Campylobacter coli in Tunisia and Detection of New Sequence Type ST13450

The aim of this study is to investigate the occurrence of plasmid mediated quinolone resistance (PMQR) determinants in Campylobacter coli isolates collected from broilers, laying hens and poultry farm environments. One hundred and thirty-nine C. coli isolates were isolated from broilers (n = 41), laying hens (n = 53), eggs (n = 4) and the environment (n = 41) of 23 poultry farms located in northeastern of Tunisia. Antimicrobial susceptibility testing was performed on all isolates according to the recommendation of the European Committee on Antimicrobial Susceptibility Testing guidelines. The detection of PMQR genes: qnrA, qnrB, qnrC, qnrD, qnrS, qepA, and aac(6)-Ib gene was performed using polymerase chain reaction (PCR) and specific primers. aac(6')-Ib amplicons were further analyzed by digestion with BtsCI to identify the aac(6')-Ib-cr variant. Mutations in GyrA and the occurrence of RE-CmeABC efflux pump were determined by mismatch amplification mutation assay (MAMA) PCR and PCR, respectively. In addition, eleven isolates were selected to determine their clonal lineage by MLST. The 139 C. coli isolates were resistant to ciprofloxacin, and 86 (61.8%) were resistant to nalidixic acid. High rates of resistance were also observed toward erythromycin (100%), azithromycin (96.4%), tetracycline (100%), chloramphenicol (98.56%), ampicillin (66.1%), amoxicillin-clavulanic acid (55.39%), and kanamycin (57.55%). However, moderate resistance rates were observed for gentamicin (9.35%) and streptomycin (22.3%). All quinolone-resistant isolates harbored the Thr-86-Ile amino acid substitution in GyrA, and the RE-CmeABC efflux pump was detected in 40.28% of isolates. Interestingly, the qnrB, qnrS, qepA, and aac(6')-Ib-cr were detected in 57.7%, 61.15%, 21.58%, and 10% of isolates, respectively. The eleven isolates studied by MLST belonged to a new sequence type ST13450. This study described for the first time the occurrence of PMQR genes in C. coli isolates in Tunisia and globally.

Exploring the Prevalence and Resistance of Campylobacter in Urban Bird Populations

The increasing urbanization of ecosystems has had a significant impact on wildlife over the last few years. Species that find an unlimited supply of food and shelter in urban areas have thrived under human presence. Wild birds have been identified as amplifying hosts and reservoirs of Campylobacter worldwide, but the information about its transmission and epidemiology is still limited. This study assessed the prevalence of Campylobacter in 137 urban birds admitted at a wildlife rescue center, with 18.8% of individuals showing positive. C. jejuni was the most frequent species (82.6%), followed by C. coli and C. lari (4.3% each). The order Passeriformes (33.3%) showed significant higher presence of Campylobacter when compared to orders Columbiformes (0%) and Ciconiiformes (17.6%), as well as in samples collected during the summer season (31.9%), from omnivorous species (36.8%) and young individuals (26.8%). Globally, Campylobacter displayed a remarkable resistance to ciprofloxacin (70.6%), tetracycline (64.7%), and nalidixic acid (52.9%). In contrast, resistance to streptomycin was low (5.8%), and all the isolates showed susceptibility to erythromycin and gentamycin. The results underline the importance of urban birds as reservoirs of thermophilic antimicrobial-resistant Campylobacter and contribute to enhancing the knowledge of its distribution in urban and peri-urban ecosystems.

Prediction of edapho-climatic parameters in the incidence of Campylobacter spp. in northwestern Mexico

Campylobacter spp. is one of the main causes of enteric zoonotic infections worldwide. In Mexico, although a commonly detected pathogen in both children and adults, there is limited surveillance and few studies. The northern part of Mexico stands out for an unnoticed outbreak of Campylobacter jejuni due to contaminated drinking water, which caused an abrupt increase in Guillain-Barré syndrome in the local population. Although it is suggested that its distribution in nature is related to edaphic and climatic factors, this relationship is scarcely known. To understand abiotic factors driving the occurrence and prevalence of Campylobacter spp. in three municipalities from three states in northwestern Mexico (Chihuahua, Sonora, and Baja California), we used the kriging interpolation method of unsampled areas and the correspondence analysis of 23 environmental variables. Of the three municipalities evaluated, Janos in Chihuahua (CHIH), has the highest number of geographic areas classified as high and medium incidence, followed by Santa Cruz, Sonora (SON) and Mexicali, Baja California (BC). Mexicali (BC) edaphic variables limit the potential incidence of the bacterium, mainly due to the lack of soil moisture and its difficulty of surviving on dry surfaces, related to electrical conductivity and salinity. Janos (CHIH) presents limitations in terms of soil water availability, although its presence is more heterogeneous (2 to 8 months). Santa Cruz (SON) has the highest soil water availability (4 to 5 months), and presents pH, texture and low percentage of salinity conditions for the potential incidence of Campylobacter spp. Mexicali (BC) reports a temperature in the warmest month of up to 43°C, which could influence the presence of thermophilic species. The annual precipitation is another limiting factor for the potential incidence of Campylobacter spp. since it does not exceed 509.5 mm, contributing to Janos (CHIH) as the municipality with the highest potential incidence of this bacterium.

The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China

Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to Astroviridae, Caliciviridae, Dicistroviridae, Picornaviridae, and Tombusviridae were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.

Overview of Ecology and Aspects of Antibiotic Resistance in Campylobacter spp. Isolated from Free-Grazing Chicken Tissues in Rural Households

Rural households all over the world rear backyard chicken mainly for their own consumption and, to a lesser extent, for barter trade. These chickens represent a staple dish with numerous culinary variations and a cheap source of protein. Although some Campylobacter species, and particularly Campylobacter jejuni and Campylobacter coli, have been associated with industrial poultry carcasses, studies concerning the ecology of this genus in rural households do not exist. To assess the prevalence of Campylobacter species in the tissues of backyard chickens, samples were collected from birds Gallus domesticus bred in households in the rural area of Epirus (Greece), and Campylobacter strains were isolated by quantitative methods at 37 °C and 42 °C. In total, 256 strains were identified, belonging to 17 Campylobacter species, with C. jejuni and C. coli being the most prevalent. From the four ecological parameters studied (size of the flock, presence of small ruminants in the same household, presence of other poultry species in the same household, and feeding leftovers of the household), the size of the flock and the presence of small ruminants and/or pigs in the same household mostly affected the distribution of these strains. To study the phenotypical resistance against 14 antibiotics, 215 strains were selected. The results showed a high prevalence of multidrug-resistance (MDR) strains extending to all classes of antibiotics. Further genome analysis revealed the presence of genes coding resistance (blaOxA-61, tet(O), tet(A) cmeA, cmeB, cmeC, and gyrA (Thr-86-Ile mutation)), with the efflux pump CmeABC being the most prevalent. All antimicrobial resistance-encoded genes co-circulated, except for blaOXA-61, which moved independently. The minimum inhibitory concentration (MIC) values of two out of three antibiotics (representing different classes) were reduced when the strains tested were exposed to carbonyl cyanide 3-chlorophenylhydrazone (CCCP), a known efflux pump inhibitor. The same result was obtained with the addition of CCCP to the MIC values of bile salts. These results lead to the conclusion that Campylobacter species are present in an impressive diversity in backyard chicken tissues and that they exert a significant resistance to antibiotics, raising a potential danger for public health.

Campylobacter jejuni Surface-Bound Protease HtrA, but Not the Secreted Protease nor Protease in Shed Membrane Vesicles, Disrupts Epithelial Cell-to-Cell Junctions

Fundamental functions of the intestinal epithelium include the digestion of food, absorption of nutrients, and its ability to act as the first barrier against intruding microbes. Campylobacter jejuni is a major zoonotic pathogen accounting for a substantial portion of bacterial foodborne illnesses. The germ colonizes the intestines of birds and is mainly transmitted to humans through the consumption of contaminated poultry meat. In the human gastrointestinal tract, the bacterium triggers campylobacteriosis that can progress to serious secondary disorders, including reactive arthritis, inflammatory bowel disease and Guillain-Barré syndrome. We recently discovered that C. jejuni serine protease HtrA disrupts intestinal epithelial barrier functions via cleavage of the tight and adherens junction components occludin, claudin-8 and E-cadherin. However, it is unknown whether epithelial damage is mediated by the secreted soluble enzyme, by HtrA contained in shed outer-membrane vesicles (OMVs) or by another mechanism that has yet to be identified. In the present study, we investigated whether soluble recombinant HtrA and/or purified OMVs induce junctional damage to polarized intestinal epithelial cells compared to live C. jejuni bacteria. By using electron and confocal immunofluorescence microscopy, we show that HtrA-expressing C. jejuni bacteria trigger efficient junctional cell damage, but not soluble purified HtrA or HtrA-containing OMVs, not even at high concentrations far exceeding physiological levels. Instead, we found that only bacteria with active protein biosynthesis effectively cleave junctional proteins, which is followed by paracellular transmigration of C. jejuni through the epithelial cell layer. These findings shed new light on the pathogenic activities of HtrA and virulence strategies of C. jejuni.

Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species

Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.

Helicobacter ibis sp. nov., isolated from faecal droppings of black-faced ibis (Theristicus melanopis)

As part of a larger study on Epsilonproteobacteria carried by wild birds in the city of Valdivia (southern Chile), two curved rod-shaped Gram-stain-negative strains (A82T and WB-40) were recovered from faecal samples and subjected to a taxonomic study. Results of a genus-specific PCR showed that these isolates belonged to the genus Helicobacter. Further identification by 16S rRNA and hsp60 (60 kDa heat-shock protein) gene sequence analysis revealed that they formed a separate phylogenetic clade, different from other known Helicobacter species with 'Helicobacter burdigaliensis' CNRCH 2005/566HT and Helicobacter valdiviensis WBE14T being the most closely related species. This was confirmed by core-genome phylogeny as well as digital DNA-DNA hybridization and average nucleotide identity analyses between the genomes of strains A82T and WB-40 and all other Helicobacter species. The draft genome sequences of A82T and WB-40, obtained by Illumina NextSeq 2000 sequencing, consisted of 1.6 Mb with a G+C content of 31.9-32.0 mol%. The results obtained from the phylogenetic and genomic characterization, together with their different morphological and biochemical features, revealed that these two strains represent a novel species, for which we propose the name Helicobacter ibis sp. nov. with A82T (=LMG 32718T=CCCT 22.04T) as the type strain.

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

Populations of resident, non-migratory Canada geese are rapidly increasing. Canada geese are known to transmit viral and bacterial diseases, posing a possible threat to human health. The most prevalent pathogens vectored by geese are Campylobacter species, yet the current understanding of the identity and virulence of these pathogens is limited. In our previous study, we observed a high prevalence of Campylobacter spp. in the Banklick Creek wetland—a constructed treatment wetland (CTW) located in northern KY (USA) used to understand sources of fecal contamination originating from humans and waterfowl frequenting the area. To identify the types of Campylobacter spp. found contaminating the CTW, we performed genetic analyses of Campylobacter 16s ribosomal RNA amplified from CTW water samples and collected fecal material from birds frequenting those areas. Our results showed a high occurrence of a Campylobacter canadensis-like clade from the sampling sites. Whole-genome sequence analyses of an isolate from Canada goose fecal material, called MG1, were used to confirm the identity of the CTW isolates. Further, we examined the phylogenomic position, virulence gene content, and antimicrobial resistance gene profile of MG1. Lastly, we developed an MG1-specific real-time PCR assay and confirmed the presence of MG1 in Canada goose fecal samples surrounding the CTW. Our findings reveal that the Canada goose-vectored Campylobacter sp. MG1 is a novel isolate compared to C. canadensis that possesses possible zoonotic potential, which may be of human health concern.

The Missing Pieces: The Role of Secretion Systems in Campylobacter jejuni Virulence

Campylobacter jejuni is likely the most common bacterial cause of gastroenteritis worldwide, responsible for millions of cases of inflammatory diarrhea characterized by severe abdominal cramps and blood in the stool. Further, C. jejuni infections are associated with post-infection sequelae in developed countries and malnutrition and growth-stunting in low- and middle-income countries. Despite the increasing prevalence of the disease, campylobacteriosis, and the recognition that this pathogen is a serious health threat, our understanding of C. jejuni pathogenesis remains incomplete. In this review, we focus on the Campylobacter secretion systems proposed to contribute to host-cell interactions and survival in the host. Moreover, we have applied a genomics approach to defining the structural and mechanistic features of C. jejuni type III, IV, and VI secretion systems. Special attention is focused on the flagellar type III secretion system and the prediction of putative effectors, given that the proteins exported via this system are essential for host cell invasion and the inflammatory response. We conclude that C. jejuni does not possess a type IV secretion system and relies on the type III and type VI secretion systems to establish a niche and potentiate disease.

Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds

As the world's leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.

The rise of antibiotic resistance in Campylobacter

PURPOSE OF REVIEW

Campylobacter is a major foodborne pathogen that infects the human intestinal tract. This review discusses the current status of antibiotic resistance, transmission of antibiotic resistance genes, and strategies to combat the global Campylobacter epidemic.

RECENT FINDINGS

Over the past 18 months, articles on Campylobacter antibiotic resistance have been published in ∼39 countries. Antibiotic-resistant Campylobacter have been detected in humans, livestock, poultry, wild animals, the environment, and food. Campylobacter spp. are resistant to a wide spectrum of antimicrobial agents, including the antibiotics quinolones, macrolides, tetracyclines, aminoglycosides, and chloramphenicols. Multidrug resistance is a globally emerging problem. Continuous antibiotic pressure promotes the spread of drug-resistant Campylobacter spp. Additionally, Campylobacter is well adapted to acquiring foreign drug resistance genes, including ermB, optrA, fexA, and cfrC, which are usually acquired from gram-positive bacteria.

SUMMARY

The widespread use of antibiotics has caused a global epidemic of drug-resistant Campylobacter infections. Many countries are actively reducing the use of antibiotics and adopting alternatives in the livestock and poultry industries to control the spread of drug-resistant Campylobacter spp.