Genetic diversity, antimicrobial resistance, and virulence genes of thermophilic Campylobacter isolated from broiler production chain

The Transmission of Campylobacter Strains in Dairy Herds in Different Housing Systems

Cattle are frequent carriers of Campylobacter spp.; therefore, these bacteria may be transmitted to humans through meat or milk. Campylobacter spp. in raw milk derives most commonly from secondary fecal contamination during the milking process; however, the udder excretion of Campylobacter may be a cause of milk-borne infection. Studies were carried out on a Campylobacter-positive farm with two different housing systems (with free-stall and tie-stall systems). The sampling process comprised several stages, including samples being taken from animals, such as from raw milk and feces, and from the environment, such as the from floor in the milking parlor and from teat cups. None of the individual raw milk samples or swabs from the floor in the parlor before the milking process were positive for Campylobacter spp. Simultaneously, Campylobacter spp. was isolated from all swabs from the floor after the milking process and in the bulk tank milk samples from the two farms. The incidence of Campylobacter isolated from fecal and teat swab samples ranged from 15.4% to 26.7% and from 8.9% to 25%, respectively. Altogether, 59 recovered Campylobacter isolates were classified, based on sequencing of the flaA short variable region, showing 15 different allele types, and the majority of them were distributed among one farm. Analysis of the virulence and antimicrobial properties showed that genes related to adherence, invasion and cytotoxicity were widely distributed among the Campylobacter recovered strains. In relation to AMR, multidrug resistance was noted in 16.1% of strains.

Genomic and clinical characteristics of campylobacteriosis in Australia

Campylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.We recruited 571 campylobacteriosis cases from three Australian states and territories (2018-2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422 C. jejuni and 84 C. coli case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65 C. jejuni and 21 C. coli sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (C. jejuni) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human C. jejuni cases from food source isolates.Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human C. jejuni cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.

Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni Isolated from Diarrheal Patients - Beijing Municipality, China, 2019-2021

Introduction

Campylobacter jejuni (C. jejuni) is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. The objective of the present study was to conduct whole genome sequencing (WGS) to determine the genetic diversity, virulence factors, and determinants of antimicrobial resistance of C. jejuni during a 3-year surveillance period in Beijing, China.

Methods

A total of 184 clinical isolates were obtained from sentinel hospital surveillance between 2019 and 2021. Antimicrobial susceptibility testing was conducted using the agar dilution method. WGS was employed to characterize the 184 C. jejuni strains.

Results

Multilocus sequence typing analysis revealed high genetic diversity among the 184 C. jejuni strains, identifying 71 sequence types (STs) and 19 clonal complexes (CCs). The most prevalent ST was ST760 (6.5%), and the most common CC was CC21 (24.5%), consisting of 11 STs. High resistance rates were observed for ciprofloxacin (76.6%), nalidixic acid (76.1%), and tetracycline (71.2%). A total of 77 C. jejuni isolates (41.8%) exhibited multidrug resistance with 43 resistance patterns. Virulome analysis disclosed the differential distribution of virulence factors related to adherence, colonization, chemotaxis, as well as lipo-oligosaccharide and capsular polysaccharide biosynthesis. Resistome analysis demonstrated widespread resistance to quinolones and tetracycline, but low rates of macrolides resistance. The phylogeny, based on whole genome single nucleotide polymorphisms, indicated a high degree of clonality and grouped the C. jejuni strains into six clades. Closely related isolates that were part of a genetic cluster mostly shared a homogenous clonal complex.

Conclusions

The present study emphasizes the rising resistance to quinolones and tetracycline, as well as the virulence potential and diverse genotypes identified among C. jejuni strains isolated from diarrheal patients in Beijing.

Persistence of Campylobacter spp. in Poultry Flocks after Disinfection, Virulence, and Antimicrobial Resistance Traits of Recovered Isolates

To investigate the persistence risk of Campylobacter spp. in poultry farms, and to study the virulence and antimicrobial resistance characteristics in the recovered strains, we collected 362 samples from breeding hen flocks, before and after disinfection. The virulence factors were investigated by targeting the genes; flaA, cadF, racR, virB11, pldA, dnaJ, cdtA, cdtB, cdtC, ciaB, wlaN, cgtB, and ceuE by PCR. Antimicrobial susceptibility was tested and genes encoding antibiotic resistance were investigated by PCR and MAMA-PCR. Among the analyzed samples, 167 (46.13%) were positive for Campylobacter. They were detected in 38.7% (38/98) and 3% (3/98) of environment samples before and after disinfection, respectively, and in 126 (75.9%) out of 166 feces samples. In total, 78 C. jejuni and 89 C. coli isolates were identified and further studied. All isolates were resistant to macrolids, tetracycline, quinolones, and chloramphenicol. However, lower rates were observed for beta-lactams [ampicillin (62.87%), amoxicillin-clavulanic acid (47.3%)] and gentamicin (0.6%). The tet(O) and the cmeB genes were detected in 90% of resistant isolates. The bla_OXA-61 gene and the specific mutations in the 23S rRNA were detected in 87% and 73.5% of isolates, respectively. The A2075G and the Thr-86-Ile mutations were detected in 85% and 73.5% of macrolide and quinolone-resistant isolates, respectively. All isolates carried the flaA, cadF, CiaB, cdtA, cdtB, and cdtC genes. The virB11, pldA, and racR genes were frequent in both C. jejuni (89%, 89%, and 90%, respectively) and C. coli (89%, 84%, and 90%). Our findings highlight the high occurrence of Campylobacter strains exhibiting antimicrobial resistance with potential virulence traits in the avian environment. Thus, the improvement of biosecurity measures in poultry farms is essential to control bacterial infection persistence and to prevent the spread of virulent and resistant strains.

Antibiotic Resistance in Campylobacter: A Systematic Review of South American Isolates

In recent years, Campylobacter has become increasingly resistant to antibiotics, especially those first-choice drugs used to treat campylobacteriosis. Studies in South America have reported cases of antibiotic-resistant Campylobacter in several countries, mainly in Brazil. To understand the current frequency of antibiotic-resistant Campylobacter in humans, farm animals, and food of animal origin in South America, we systematically searched for different studies that have reported Campylobacter resistance. The most commonly reported species were C. jejuni and C. coli. Resistance to ciprofloxacin was found to be ubiquitous in the isolates. Nalidixic acid and tetracycline showed a significantly expressed resistance. Erythromycin, the antibiotic of first choice for the treatment of campylobacteriosis, showed a low rate of resistance in isolates but was detected in almost all countries. The main sources of antibiotic-resistant Campylobacter isolates were food of animal origin and farm animals. The results demonstrate that resistant Campylobacter isolates are disseminated from multiple sources linked to animal production in South America. The level of resistance that was identified may compromise the treatment of campylobacteriosis in human and animal populations. In this way, we are here showing all South American communities the need for the constant surveillance of Campylobacter resistance and the need for the strategic use of antibiotics in animal production. These actions are likely to decrease future difficulties in the treatment of human campylobacteriosis.

Campylobacter spp. isolated from poultry in Iran: Antibiotic resistance profiles, virulence genes, and molecular mechanisms

Campylobacter spp. genera is one of the most common causes of microbial enteritis worldwide. The objective of this work was to investigate the antimicrobial resistance (AMR) patterns, virulence genes, and genetic variation of thermophilic Campylobacter species collected from chicken meat samples in Iran. A total of 255 meat specimens were taken and transferred to the laboratory. Culture methods were utilized to identify the Campylobacter genus, and PCR and sequencing were performed to confirm the organisms. Antimicrobial susceptibility evaluation was performed using broth microdilution for six antimicrobials [ciprofloxacin (CIP), nalidixic acid (NAL), sitafloxacin (SIT), erythromycin (ERY), tetracycline (TET), and gentamicin (GEN)]. By using PCR, AMR and virulence genes were detected. The detection rate of Campylobacter spp. was 64 (25.09%) out of 255 meat samples, with C. jejuni and C. coli accounting for 41 (64.06%) and 14 (21.87%), respectively. Other Campylobacter isolates accounted for 14.06% of the total (nine samples). The antibiotic susceptibility of all Campylobacter isolates was tested using six antibiotics, and all (100%) were resistant to CIP and NAL. However, TET resistance was observed in 93.9% and 83.3% of C. jejuni and C. coli isolates, respectively. Four (8.2%) C. jejuni isolates were multidrug-resistant (MDR), while none of the C. coli isolates were MDR. Two of the four MDR isolates were resistant to CIP, NAL, TET, and ERY, whereas the other two isolates were resistant to CIP, NAL, TET, and GEN. The values of the Minimum Inhibitory Concentration (MIC) were as follows: CIP, 64-256 μg/ml; NAL, 128-512 μg/ml; TET, 2-1024 μg/ml; SIT, 0.25-1 μg/ml; ERY, 1-32 μg/ml; and GEN, 1-256 μg/ml. recR, dnaJ, cdtC, cdtB, cdtA, flaA, ciaB, cadF, and pidA were discovered in more than 50% of C. jejuni isolates, although wlaN, virbll, cgtB, and ceuE were found in <50%. flaA, cadF, pidA, and ciaB were discovered in more than 50% of the C. coli samples, whereas recR, cdtC, cdtB, cdtA, and cgtB were found in less than half. For C. coli, the percentages for wlaN, dnaJ, virbll, and ceuE were all zero. The results of this study show Campylobacter isolates obtained from poultry have higher resistance to quinolones and TET, pathogenicity potential, and varied genotypes.

Relationships between Virulence Genes and Antibiotic Resistance Phenotypes/Genotypes in Campylobacter spp. Isolated from Layer Hens and Eggs in the North of Tunisia: Statistical and Computational Insights

Globally, Campylobacter is a significant contributor to gastroenteritis. Efficient pathogens are qualified by their virulence power, resistance to antibiotics and epidemic spread. However, the correlation between antimicrobial resistance (AR) and the pathogenicity power of pathogens is complex and poorly understood. In this study, we aimed to investigate genes encoding virulence and AR mechanisms in 177 Campylobacter isolates collected from layer hens and eggs in Tunisia and to assess associations between AR and virulence characteristics. Virulotyping was determined by searching 13 virulence genes and AR-encoding genes were investigated by PCR and MAMA-PCR. The following genes were detected in C. jejuni and C. coli isolates: tet(O) (100%/100%), bla_OXA-61 (18.82%/6.25%), and cmeB (100%/100%). All quinolone-resistant isolates harbored the Thr-86-Ile substitution in GyrA. Both the A2074C and A2075G mutations in 23S rRNA were found in all erythromycin-resistant isolates; however, the erm(B) gene was detected in 48.38% and 64.15% of the C. jejuni and C. coli isolates, respectively. The machine learning algorithm Random Forest was used to determine the association of virulence genes with AR phenotypes. This analysis showed that C. jejuni virulotypes with gene clusters encompassing the racR, ceuE, virB11, and pldA genes were strongly associated with the majority of phenotypic resistance. Our findings showed high rates of AR and virulence genes among poultry Campylobacter, which is a cause of concern to human health. In addition, the correlations of specific virulence genes with AR phenotypes were established by statistical analysis.

Agents of Campylobacteriosis in Different Meat Matrices in Brazil

We aimed to identify the prevalence of thermophilic species of Campylobacter in meats of different species available on the Brazilian commercial market and to determine the genetic diversity, antimicrobial resistance and virulence potential of the isolates. A total of 906 samples, including chicken, beef and pork carcasses and chicken and beef livers, were purchased in retail outlets, and prevalences of 18.7% (46/246), 3.62% (5/138), 10.14% (14/138), 3.62% (5/138) and 4.47% (11/132), respectively, were identified, evidencing the dissemination of genotypes in the main producing macro-regions. Of all isolates, 62.8% were classified as multidrug resistant (MDR), with resistance to amoxicillin-clavulanate (49.4%), tetracycline (51.8%) and ciprofloxacin (50.6%) and co-resistance to macrolides and fluoroquinolones (37.1%). Multivirulent profiles were identified mainly in isolates from chicken carcasses (84.8%), and the emergence of MDR/virulent strains was determined in pork isolates. All isolates except those from chicken carcasses showed a high potential for biofilm formation (71.4% luxS) and consequent persistence in industrial food processing. For chicken carcasses, the general virulence was higher in C. jejuni (54.3%), followed by C. coli (24%) and Campylobacter spp. (21.7%), and in the other meat matrices, Campylobacter spp. showed a higher prevalence of virulence (57.2%). The high rates of resistance and virulence reinforce the existence of strain selection pressure in the country, in addition to the potential risk of strains isolated not only from chicken carcasses, but also from other meat matrices.

Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru

Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (bla_oxa–61), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.

Genomic Characterization of Fluoroquinolone-Resistant Thermophilic Campylobacter Strains Isolated from Layer Chicken Feces in Gangneung, South Korea by Whole-Genome Sequencing

Thermophilic Campylobacter species of poultry origin have been associated with up to 80% of human campylobacteriosis cases. Layer chickens have received less attention as possible reservoirs of Campylobacter species. Initially, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of two archived Campylobacter isolates (Campylobacter jejuni strain 200605 and Campylobacter coli strain 200606) from layer chickens to five antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, tetracycline, and gentamicin) were determined using broth microdilution while the presence of selected antimicrobial resistance genes was performed by polymerase chain reaction (PCR) using specific primers. Whole-genome sequencing (WGS) was performed by the Illumina HiSeq X platform. The analysis involved antimicrobial resistance genes, virulome, multilocus sequence typing (MLST), and phylogeny. Both isolates were phenotypically resistant to ciprofloxacin (MIC: 32 vs. 32 µg/mL), nalidixic acid (MIC: 128 vs. 64 µg/mL), and tetracycline (MIC: 64 vs. 64 µg/mL), but sensitive to erythromycin (MIC: 1 vs. 2 µg/mL) and gentamicin (MIC: 0.25 vs. 1 µg/mL) for C. jejuni strain 200605 and C. coli strain 200606, respectively. WGS confirmed C257T mutation in the gyrA gene and the presence of cmeABC complex conferring resistance to FQs in both strains. Both strains also exhibited tet(O) genes associated with tetracycline resistance. Various virulence genes associated with motility, chemotaxis, and capsule formation were found in both isolates. However, the analysis of virulence genes showed that C. jejuni strain 200605 is more virulent than C. coli strain 200606. The MLST showed that C. jejuni strain 200605 belongs to sequence type ST-5229 while C. coli strain 200606 belongs to ST-5935, and both STs are less common. The phylogenetic analysis clustered C. jejuni strain 200605 along with other strains reported in Korea (CP028933 from chicken and CP014344 from human) while C. coli strain 200606 formed a separate cluster with C. coli (CP007181) from turkey. The WGS confirmed FQ-resistance in both strains and showed potential virulence of both strains. Further studies are recommended to understand the reasons behind the regional distribution (Korea, China, and Vietnam) of such rare STs.

Antimicrobial Resistance Profiles, Virulence Genes, and Genetic Diversity of Thermophilic Campylobacter Species Isolated From a Layer Poultry Farm in Korea

Thermophilic Campylobacter species are among the major etiologies of bacterial enteritis globally. This study aimed at assessing the antimicrobial resistance (AMR) profiles, virulence genes, and genetic diversity of thermophilic Campylobacter species isolated from a layer poultry farm in South Korea. One hundred fifty-three chicken feces were collected from two layer poultry farms in Gangneung, South Korea. The Campylobacter species were isolated by cultural techniques, while PCR and sequencing were used for species confirmation. Antimicrobial susceptibility testing for six antimicrobials [ciprofloxacin (CIP), nalidixic acid (NAL), sitafloxacin (SIT), erythromycin (ERY), tetracycline (TET), and gentamicin (GEN)] was carried out by broth microdilution. Three AMR and nine virulence genes were screened by PCR. Genotyping was performed by flaA-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). Of the 153 samples, Campylobacter spp. were detected in 55 (35.9%), with Campylobacter jejuni and Campylobacter coli being 49 (89.1%) and six (10.9%), respectively. High-level resistance was observed for CIP (100%), NAL (100%), and TET (C. jejuni, 93.9%; C. coli: 83.3%). No resistance was observed for SIT. The missense mutation (C257T) in gyrA gene was confirmed by sequencing, while the tet(O) gene was similar to known sequences in GenBank. The rate of multidrug-resistant (MDR) strains was 8.2%, and they all belonged to C. jejuni. All Campylobacter isolates possessed five virulence genes (cdtB, cstII, flaA, cadF, and dnaJ), but none possessed ggt, while the rates for other genes (csrA, ciaB, and pldA) ranged between 33.3 and 95.9%. The flaA-RFLP yielded 26 flaA types (C. jejuni: 21 and C. coli: five), while the MLST showed 10 sequence types (STs) for C. jejuni and three STs for C. coli, with CC-607 (STs 3611) and CC-460 (ST-460) being predominant. Among the 10 STs of C. jejuni, three were newly assigned. The findings of this study highlight the increased resistance to quinolones and TET, the virulence potential, and the diverse genotypes among Campylobacter strains isolated from the layer poultry farm.

Biofilm-forming ability of poultry Campylobacter jejuni strains in the presence and absence of Pseudomonas aeruginosa

The aims of this study were to evaluate the ability of Campylobacter jejuni isolated from a poultry slaughterhouse to form biofilm in the presence and absence of Pseudomonas aeruginosa, and the effect of surface (stainless steel, polystyrene), temperature (7, 25, and 42 °C), and oxygen concentration (microaerophilic and aerobic conditions) on the formation of biofilm. The genes ahpC, cadF, clpP, dnaJ, docA, flaA, flaB, katA, kpsM, luxS, racR, and sodB, related to biofilm formation by C. jejuni, were also investigated. All isolates formed biofilm on stainless steel and on polystyrene, in both aerobic and microaerophilic atmospheres, including temperatures not optimal for C. jejuni growth (7 and 25 °C), and biofilm also was formed in the presence of P. aeruginosa. In dual-species biofilm on stainless steel, biofilm formation was 2-6 log CFU·cm^-2 higher at 7 °C for all isolates, in comparison with monospecies biofilm. Ten genes (ahpC, cadF, clpP, dnaJ, docA, flaA, flaB, luxS, racR, and sodB) were detected in all isolates, but katA and kpsM were found in four and six isolates, respectively. The results obtained are of concern because the poultry C. jejuni isolates form biofilm in different conditions, which is enhanced in the presence of other biofilm formers, such as P. aeruginosa.

Optimization of a Method for Extraction and Determination of Residues of Selected Antimicrobials in Soil and Plant Samples Using HPLC-UV-MS/MS

The residues of antimicrobials used in human and veterinary medicine are popular pollutants of anthropogenic origin. The main sources of introducing antimicrobials into the environment are sewage treatment plants and the agricultural industry. Antimicrobials in animal manure contaminate the surrounding soil as well as groundwater, and can be absorbed by plants. The presence of antimicrobials in food of plant origin may pose a threat to human health due to their high biological activity. As part of the research, a procedure was developed for the extraction and determination of ciprofloxacin, enrofloxacin, cefuroxime, nalidixic acid and metronidazole in environmental samples (soil and parsley root). An optimized solid-liquid extraction (SLE) method was used to separate antimicrobials from the solid samples and a mixture of citrate buffer (pH = 4): methanol (1:1; v/v) was used as the extraction solvent. Solid phase extraction (SPE) with OASIS^® HLB cartridges was used to purify and pre-concentrate the sample. The recovery of the developed method was in the range of 55–108%. Analytes were determined by high-performance liquid chromatography coupled with an ultraviolet (UV) detector and a tandem mass spectrometer (HPLC-UV-MS/MS). The procedure was validated and applied to the determination of selected antimicrobials in soil and parsley root samples. Five types of soil and five types of parsley roots of different origins were analyzed. The presence of nalidixic acid in the parsley root samples was found in the concentration range of 0.14–0.72 ng g⁻¹. It has been shown that antimicrobials are absorbed by the plant and can accumulate antimicrobials in its edible parts.