Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli isolates from poultry, cattle and humans in Nigeria

Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni

Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.

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.

Zoonotic Transmission of Campylobacter jejuni to Caretakers From Sick Pen Calves Carrying a Mixed Population of Strains With and Without Guillain Barré Syndrome-Associated Lipooligosaccharide Loci

Campylobacter jejuni causes foodborne gastroenteritis and may trigger acute autoimmune sequelae including Guillain Barré Syndrome. Onset of neuromuscular paralysis is associated with exposure to C. jejuni lipooligosaccharide (LOS) classes A, B, C, D, and E that mimic and evoke antibodies against gangliosides on myelin and axons of peripheral nerves. Family members managing a Michigan dairy operation reported recurring C. jejuni gastroenteritis. Because dairy cattle are known to shed C. jejuni, we hypothesized that calves in the sick pen were the source of human infections. Fecal samples obtained from twenty-five calves, one dog, and one asymptomatic family member were cultured for Campylobacter. C. jejuni isolates were obtained from thirteen calves and the family member: C. coli from two calves, and C. hyointestinalis from two calves. Some calves had diarrhea; most were clinically normal. Typing of lipooligosaccharide biosynthetic loci showed that eight calf C. jejuni isolates fell into classes A, B, and C. Two calf isolates and the human isolate possessed LOS class E, associated mainly with enteric disease and rarely with Guillain Barré Syndrome. Multi-locus sequence typing, porA and flaA typing, and whole genome comparisons of the thirteen C. jejuni isolates indicated that the three LOS class E strains that included the human isolate were closely related, indicating zoonotic transmission. Whole-genome comparisons revealed that isolates differed in virulence gene content, particularly in loci encoding biosynthesis of surface structures. Family members experienced diarrheal illness repeatedly over 2 years, yet none experienced GBS despite exposure to calves carrying invasive C. jejuni with LOS known to elicit antiganglioside autoantibodies.

Genomic diversity and antimicrobial resistance of Campylobacter spp. from humans and livestock in Nigeria

Background

Campylobacter spp. are zoonotic pathogens, ubiquitous and are found naturally as commensals in livestock from where they can be transmitted to humans directly or through animal products. The genomic diversity and antimicrobial resistance profile of Campylobacter was investigated with a focus on C. jejuni and C. coli in humans and livestock (poultry and cattle) from Nigeria.

Methods

586 human stool samples and 472 faecal samples from livestock were cultured for thermophilic Campylobacter species on modified charcoal cefoperazone deoxycholate agar (mCCDA). Culture in combination with whole genome sequencing identified and confirmed the presence of Campylobacter in humans and animals from the study area. Further analysis of the sequences was performed to determine multilocus sequence types and genetic determinants of antimicrobial resistance to fluoroquinolone, betalactam, tetracycline and macrolide classes of antimicrobials.

Results

From the human stool samples tested, 50 (9%) were positive of which 33 (66%) were C. jejuni, 14 (28%) were C. coli while 3 (6%) were C. hyointestinalis. In livestock, 132 (28%) were positive. Thirty one (7%) were C. jejuni while 101 (21%) were C. coli. Whole genome sequencing and MLST of the isolates revealed a total of 32 sequence types (STs) identified from 47 human isolates while 48 STs were identified in 124 isolates from livestock indicating a population which was overall, genetically diverse with a few more dominant strains. The antimicrobial resistance profiles of the isolates indicated a higher prevalence of resistance in Campylobacter isolated from livestock than in humans. Generally, resistance was greatest for betalactams (42%) closely followed by fluoroquinolones (41%), tetracyclines (15%) and lastly macrolides (2%). Multidrug resistance to three or more antimicrobials was observed in 24 (13%) isolates from humans (n = 1, 4%) and chicken (n = 23, 96%).

Conclusions

This study has further contributed information about the epidemiology, genetic diversity and antimicrobial resistance profile of thermophilic Campylobacter in Nigeria.

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.

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- and middle-income countries (LMICs), where infection can be fatal, culture based isolation is rare and the genotypes responsible for disease have not broadly been identified. The epidemiology of disease is different to that in high income countries, where sporadic infection associated with contaminated food consumption typically leads to acute gastroenteritis. In some LMICs infection is endemic among children and common asymptomatic carriage is associated with malnutrition, attenuated growth in early childhood, and poor cognitive and physical development. Here, we sequenced the genomes of isolates sampled from children in the Peruvian Amazon to investigate genotypes associated with varying disease severity and the source of infection. Among the common globally circulating genotypes and local genotypes rarely seen before, no single lineage was responsible for symptomatic or asymptomatic infection–suggesting an important role for host factors. However, consistent with other countries, poultry-associated strains were a likely major source of infection. This genomic surveillance approach, that integrates microbial ecology with population based studies in humans and animals, has considerable potential for describing cryptic epidemiology in LMICs and will inform work to improve infant health worldwide.

Molecular Characterization and Antibiotic Resistant Profiles of Campylobacter Species Isolated From Poultry and Diarrheal Patients in Southeastern China 2017-2019

Campylobacter is a zoonotic pathogen that causes foodborne diarrheal illness globally. To better understand health risks in Southeastern China, Campylobacter spp. were surveyed in humans and representative poultry products over 3 years. One hundred and ninety-five representative isolates (n = 148, Campylobacter jejuni; n = 45, Campylobacter coli; n = 2 Campylobacter hyointestinalis) were examined for genetic relatedness and antimicrobial susceptibility. Nearly all Campylobacter isolates (99.0%, 193/195) were resistant to at least one class of antimicrobials, and 45.6% (89/195) of the isolates exhibited multidrug resistance. Genotypic analysis revealed high diversity among tested strains. Multilocus sequence typing (MLST) displayed 120 sequence types (STs) including 42 novel STs being added to the PubMLST international database. Sixty-two STs belonged to 16 previously characterized clonal complexes (CCs), of which CC-21, CC-45, CC-464, CC-574, CC-353, and CC-828 were most frequently identified. In addition, pulsed-field gel electrophoresis (PFGE) fingerprinting resulted in 66 PFGE SmaI patterns among the 125 isolates, with eight patterns shared between human and poultry sources. Subtyping data did not correlate with antimicrobial resistance phenotypes. Taken together, this large-scale surveillance study highlights high antimicrobial resistance and molecular features of Campylobacter isolates in Southeastern China.

Epidemiology of thermotolerant Campylobacter infection in poultry in Nsukka agricultural zone, Nigeria

Backgrond and Aim: Thermotolerant Campylobacter organisms (TCOs) are primary causes of bacterial foodborne gastroenteritis worldwide. Although all warm-blooded animals are susceptible to colonization by TCOs, food-producing animals, especially poultry, are major reservoirs of the infection for transmission to humans. This epidemiological study for thermotolerant Campylobacter infection (TCI) in poultry was, therefore, conducted to determine the prevalence and to identify the risk factors of TCI in 60 randomly selected poultry farms in Nsukka agricultural zone. Materials and Methods: A structured questionnaire was used to elicit information on the farmers' involvement in practices that may aggravate TCI in poultry farms. Isolation of TCOs for the determination of prevalence of the infection was done following standard microbiological protocol. Results: The majority (93.3%) of the farms practiced intensive management system. Farm and individual prevalence of TCI were 78.3% and 19.4%, respectively. The prevalence of 15.7% and 23.6% was recorded for birds reared in urban and rural areas, respectively. Similarly, prevalence rates of 17.2%, 25%, 14.7%, and 24.5% were documented for broiler, layer, male, and female birds, respectively. Major risk factors of TCI found were non-sanitization of drinking water, rearing birds of different ages together, thinning, raising other animals alongside poultry, and overstocking. Conclusion: Overall prevalence of 19.4% is high from public health and food safety points of view. Farmers' participation in the risk factors for TCI is massive. Significant improvement in biosecurity practices in poultry farms in the study area is therefore imperative; to limit TCI in poultry and hence the risk of human infection through the food chain or at the poultry-human interface.

Evaluation of Two Multiplex PCR-High-Resolution Melt Curve Analysis Methods for Differentiation of Campylobacter jejuni and Campylobacter coli Intraspecies

Campylobacter infection is a common cause of bacterial gastroenteritis in humans and remains a significant global public health issue. The capability of two multiplex PCR (mPCR)-high-resolution melt (HRM) curve analysis methods (i.e., mPCR1-HRM and mPCR2-HRM) to detect and differentiate 24 poultry isolates and three reference strains of Campylobacter jejuni and Campylobacter coli was investigated. Campylobacter jejuni and C. coli were successfully differentiated in both assays, but the differentiation power of mPCR2-HRM targeting the cadF gene was found superior to that of mPCR1-HRM targeting the gpsA gene or a hypothetical protein gene. However, higher intraspecies variation within C. coli and C. jejuni isolates was detected in mPCR1-HRM when compared with mPCR2-HRM. Both assays were rapid and required minimum interpretation skills for discrimination between and within Campylobacter species when using HRM curve analysis software.

Aerotolerance and multilocus sequence typing among Campylobacter jejuni strains isolated from humans, broiler chickens, and cattle in Miyazaki Prefecture, Japan

Campylobacter jejuni is one of the leading causes of human gastroenteritis in Japan. As chickens and cattle are common reservoirs for C. jejuni, this microaerophilic, stress-sensitive bacterium can overcome and survive various stress conditions during zoonotic transmission, particularly foodborne, to humans. How C. jejuni overcomes stress conditions is, however, unclear. In the present study, 70 C. jejuni strains isolated from various sources (26 human, 20 broilers, and 24 cattle isolates) in Miyazaki, Japan, from 2010 to 2012, were subjected to multilocus sequence typing (MLST) and aerotolerance testing (aerobic shaking at 200 rpm). The results demonstrated that C. jejuni strains from Miyazaki belonged to 12 clonal complexes (CCs) and 43 sequence types (STs). CC-21 and CC-460 were mainly detected in human clinical strains. Most tested strains were aerotolerant, and only one (1.4%) was deemed sensitive to aerobic stress. Approximately 40% strains survived the 24-hr vigorous aerobic shaking at 200 rpm, and these hyper-aerotolerant strains were more prevalent in broiler and cattle isolates than in human isolates. Phylogenetic analysis divided the strains into five clusters, each showing a different pattern of host association. Thus, we have demonstrated for the first time that C. jejuni strains with increased tolerance to aerobic stress are highly prevalent in broilers and cattle in Miyazaki, Japan, and that certain clonal populations are frequently implicated in human infection in this area.

Antibiotic Susceptibility Profiles of Campylobacter coli Isolated from Poultry Farms in Lagos Nigeria - A Pilot Study

Campylobacter jejuni and Campylobacter coli are among the leading causes of gastroenteritis in humans worldwide, particularly in Africa. Poultry remains a major source of Campylobacter species and a vector of transmission to humans.

This pilot study was aimed at isolating and determining the antibiotic susceptibility profiles of Campylobacter spp. from fresh poultry droppings collected from poultry farms in Lagos State, Nigeria. Susceptibility was assessed using the CLSI standards.

Standard microbiological methods were used in isolation, identification, and characterization of Campylobacter spp. Isolates were subjected to antibiotic susceptibility testing by the disk diffusion method.

Of the 150 poultry droppings analyzed, 8 (5.3%) harbored Campylobacterspp. All isolates proved to be C. coli since they were all negative for the hip gene. A percentage of 100% showed resistance to nalidixic acid, chloramphenicol, cloxacillin, and streptomycin. While 87.5% were susceptible to amoxicillin and amoxicillin/clavulanic acid, 62.5% were susceptible to tetracycline. Surprisingly, 62.5% of C. coli had decreased (intermediate) susceptibility to erythromycin.

Although there was a low prevalence of C. coli from poultry in this study, the presence of antibiotic resistant strains circulating the food chain could result in treatment failures and difficulty in case management if involved in infections of humans.

Long-term observation of antimicrobial susceptibility and molecular characterisation of Campylobacter jejuni isolated in a Japanese general hospital 2000-2017

OBJECTIVES

Campylobacter jejuni (C. jejuni) is one of the most common pathogens that causes gastroenteritis. Because there is currently insufficient epidemiological information about the antimicrobial susceptibility and molecular characterisation of clinical isolates of C. jejuni in Japan, this study carried out antimicrobial susceptibility testing and multilocus sequence typing (MLST) of clinical C. jejuni isolates in Tokyo between 2000-2017.

METHODS

Antimicrobial susceptibility to erythromycin and ciprofloxacin was tested using the broth microdilution method in 430 C. jejuni clinical isolates collected over 18 years, between 2000-2017, at a Tokyo general hospital. To observe the sequence type (ST) evolution, 82 isolates were chosen from three non-consecutive years (16 isolates from 2000, 25 isolates from 2008, and 41 isolates from 2017) and analysed by MLST as a molecular characterisation test. Mutations in the quinolone resistance-determining region of the gyrA and gyrB genes were identified.

RESULTS

The rate of resistance to erythromycin was low, but that of ciprofloxacin resistance was 34.9% in 2000-2008 and 41.9% in 2009-2017. The most common clonal complex (CC) identified during the entire period was CC21; ST4526 with ciprofloxacin resistance was highly prevalent in 2017 (6 of 11; 54.5%).

CONCLUSION

The results indicate that the rate of resistance to quinolone has gradually increased. Since ST4526 was not isolated in 2000 and 2008, it is likely that ST4526 is rapidly increasing in Japan.

Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for bla_OXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.

Prevalence, antimicrobial resistance and genetic diversity of Campylobacter coli and Campylobacter jejuni in Ecuadorian broilers at slaughter age

Thermotolerant Campylobacter spp. are a major cause of foodborne gastrointestinal infections worldwide. The linkage of human campylobacteriosis and poultry has been widely described. In this study we aimed to investigate the prevalence, antimicrobial resistance and genetic diversity of C. coli and C. jejuni in broilers from Ecuador. Caecal content from 379 randomly selected broiler batches originating from 115 farms were collected from 6 slaughterhouses located in the province of Pichincha during 1 year. Microbiological isolation was performed by direct plating on mCCDA agar. Identification of Campylobacter species was done by PCR. Minimum inhibitory concentration (MIC) values for gentamicin, ciprofloxacin, nalidixic acid, tetracycline, streptomycin, and erythromycin were obtained. Genetic variation was assessed by RFLP-flaA typing and Multilocus Sequence Typing (MLST) of selected isolates. Prevalence at batch level was 64.1%. Of the positive batches 68.7% were positive for C. coli, 18.9% for C. jejuni, and 12.4% for C. coli and C. jejuni. Resistance rates above 67% were shown for tetracycline, ciprofloxacin, and nalidixic acid. The resistance pattern tetracycline, ciprofloxin, and nalidixic acid was the dominant one in both Campylobacter species. RFLP-flaA typing analysis showed that C. coli and C. jejuni strains belonged to 38 and 26 profiles respectively. On the other hand MLST typing revealed that C. coli except one strain belonged to CC-828, while C. jejuni except 2 strains belonged to 12 assigned clonal complexes (CCs). Furthermore 4 new sequence types (STs) for both species were described, whereby 2 new STs for C. coli were based on new allele sequences. Further research is necessary to estimate the impact of the slaughter of Campylobacter positive broiler batches on the contamination level of carcasses in slaughterhouses and at retail in Ecuador.