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PubMed2025

Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.

BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

Animals↗

PubMed2026

Longitudinal study of prevalence and antimicrobial resistance of thermotolerant Campylobacter spp. in German organic meat chicken farms.

Widespread prevalence of fluoroquinolone-resistant Campylobacter spp. in meat chicken is a major concern for public health. We examined the prevalence and antimicrobial resistance of thermotolerant Campylobacter spp. in 14 German organic meat chicken farms rearing slow-growing broilers, male layer hybrids, or dual-purpose cockerels in a longitudinal study. Most farms participated with four subsequent flocks. Each flock was sampled three times: approximately 1 month after hatching (before outdoor access), 2 weeks after first outdoor access, and at the end of the fattening period. Strikingly, most flocks were already Campylobacter-positive before first outdoor access. At the end of the fattening period, 98% of all flocks were positive, with C. jejuni being the predominant species. Antimicrobial resistance of 405 C. jejuni and 79 C. coli revealed overall high levels of ciprofloxacin and tetracycline resistance but absence of macrolide resistance. Ertapenem resistance was observed in individual farms. Generalized linear mixed models with random factors for farm and flocks within farm were used to assess predictors for the occurrence of ciprofloxacin- and tetracycline-resistant C. jejuni. Season, fattening type, and the interaction of sampling time point and fattening type were significant fixed effects. Results for flocks within farms showed clustering effects (ICCCIP = 0.447; ICCTET = 0.412). Whole-genome sequencing of representative isolates confirmed great overall genetic variety, with farm- or fattening type-dependent dissemination of certain multi-locus sequence types. ST21 clonal complex for sequenced C. jejuni and ST828 clonal complex for sequenced C. coli were most commonly detected.IMPORTANCECampylobacter spp. are major foodborne pathogens associated with the consumption and handling of chicken meat. This longitudinal study provides further insight into the prevalence and antimicrobial resistance of thermotolerant C. jejuni and C. coli in German organic meat chicken farms, a growing sector with strict limitations on antibiotic treatment. We included multiple flocks of farms fattening either slow-growing broilers, male layer hybrids, or dual-purpose cockerels to account for a variety of fattening types. Consequently, we were able to demonstrate significant differences in the occurrence of ciprofloxacin- and tetracycline-resistant C. jejuni based on fattening type, sampling time point, and season. Our findings highlight the successful spread and persistence of ciprofloxacin-, tetracycline-, and ertapenem-resistant C. jejuni and C. coli among all three types of organic meat chicken regardless of the lack of antibiotic treatment.

C. coli↗

PubMed2024

Genomic diversity of Campylobacter jejuni and Campylobacter coli isolated from the Ethiopian dairy supply chain.

Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission.

Campylobacter coli↗

PubMed2026

Dual-species interactions with intestinal bacteria drive multi-drug resistance in Campylobacter.

OBJECTIVES: Multidrug-resistant (MDR) Campylobacter infections are an increasing clinical concern, as rising fluoroquinolone (FQ) resistance leaves macrolides as the primary treatment option. We investigated multidrug resistance in clinical Campylobacter samples from Germany. METHODS: We analyzed 6980 clinical isolates (2010-2022), performing phenotypic susceptibility testing and sequencing on 2912 genomes. Cultures showing multidrug resistance were studied using scanning electron microscopy (SEM). RESULTS: We found that 453 (6%) Campylobacter samples were resistant to both FQ and macrolides. Two of the C. jejuni samples were resistant to antibiotics from ten different classes. Genome analysis revealed that these samples, despite being derived from single colonies, contained >10% Enterococcus DNA reads. SEM confirmed the presence of coccoid bacteria interspersed with spiral-shaped Campylobacter. Additional culture-based purification resulted in pure C. jejuni isolates that retained FQR but lost macrolide resistance. The presence of MDR Enterococcus spp. in the mixed samples protected C. jejuni from above-MIC (minimum inhibitory concentration) concentrations of several ribosome-targeting antimicrobials whereas pure Campylobacter were susceptible. CONCLUSIONS: The impact of microbial interactions on resistance phenotypes is poorly understood. We show that close interactions with highly resistant intestinal bacteria can induce multidrug resistance phenotypes in Campylobacter. These findings highlight that microbial context shapes antibiotic resistance and may influence treatment outcomes.

Campylobacter jejuni↗

PubMed2026

Prevalence, species diversity, and antimicrobial resistance profiles of Campylobacter spp. among children under five years of age with acute diarrhea in Ouagadougou, Burkina Faso.

Campylobacter species are major causes of pediatric gastroenteritis worldwide, yet their burden remains underestimated in West Africa due to diagnostic challenges. This study aimed to determine the prevalence, species diversity, and antimicrobial resistance (AMR) profiles of Campylobacter spp. among children under 5 years of age with acute diarrhea in Ouagadougou, Burkina Faso. From 1 May 2023 to 30 April 2024, 383 stool samples were collected at the Centre Hospitalier Universitaire Pédiatrique Charles de Gaulle. Samples were analyzed using standard culture on Karmali selective agar and biochemical identification via the API Campy system. AMR testing was performed using the disk diffusion method. Campylobacter spp. were detected in 33 samples (8.6% prevalence). Infection was significantly associated with the 12-23 months age group (48.5%; P < 0.05). Campylobacter jejuni was the most common species (42.4%), followed by C. coli (21.2%) and C. fetus subsp. fetus (21.2%). Other species included C. hyointestinalis (6.1%), C. sputorum (6.1%), and C. lari (3.0%). Alarmingly, 100% of isolates were resistant to ampicillin, erythromycin, and tetracycline. High resistance rates were also observed for amoxicillin-clavulanic acid (93.9%) and ciprofloxacin (75.8%). Gentamicin showed the highest susceptibility (57.6%). All isolates (100%) were classified as multidrug-resistant (MDR). These results highlight a high prevalence of MDR Campylobacter in Ouagadougou, with total resistance to erythromycin, the first-line treatment. The identification of C. fetus at 42°C suggests a high environmental and zoonotic pressure. These findings underscore the urgent need for enhanced genomic surveillance and updated clinical management guidelines for pediatric diarrhea in the region.IMPORTANCEThis study highlights the burden and antimicrobial resistance of Campylobacter spp. among children under five with acute diarrhea in Burkina Faso. Culture-based detection identified Campylobacter in 8.6% of children, confirming its role as an important but under-recognized cause of pediatric diarrheal disease. High levels of antimicrobial resistance, including complete resistance to erythromycin, raise concerns about the effectiveness of commonly used treatment options. The identification of multiple Campylobacter species, including C. fetus, suggests a broader diversity of circulating strains and possible zoonotic transmission pathways. These findings provide valuable baseline data to strengthen antimicrobial resistance surveillance, improve diagnostic practices, and support evidence-based treatment strategies in West African settings.

Humans↗