Antimicrobial resistance genotypes and phenotypes of Campylobacter jejuni isolated in Italy from humans, birds from wild and urban habitats, and poultry

In vitro antimicrobial resistant pattern, plasmid profile and the survival of Campylobacter jejuni isolated from poultry sources

1. Infections due to Campylobacter spp. significantly contribute to bacterial gastroenteritis worldwide. This study aimed to investigate whether Campylobacter spp. can persist in poultry environments and how they survive in various sources from poultry farms and slaughterhouses.2. A total of 192 samples were collected from three different poultry farms and slaughterhouses and C. jejuni was detected in 47.4% of them. The prevalence of C. jejuni was higher in poultry slaughterhouses than in farms. A total of 69 C. jejuni were tested for their susceptibility to different antibiotics. From these 15 isolates from poultry farms and slaughterhouses, 50-70% exhibited antibiotic resistance. These isolates were analysed for plasmid profiling, identification of virulence genes and lipo-oligosaccharide characterisation.3. Nearly all C. jejuni isolates harboured plasmid sizes ranging from 2.3 to 23 kb. The virB11 gene of C. jejuni was characterised using PCR and there was no gene amplification in the isolated strains. All multidrug-resistant (MDR) isolates from poultry farms and slaughterhouses had full-length lipo-oligosaccharide molecules, based on their molecular weight.4. The MDR strain C. jejuni (LCJ5) was chosen for its survival rate from various sources, including lamb, chicken meat and eggs, as well as in the slaughterhouse environment, which contains materials like stainless steel, iron and wood. The findings suggested that the prevalence of Campylobacter can be reduced through improved hygiene practices and by raising awareness about the importance of consuming properly cooked meat products.

Molecular Tracing and Molecular Characteristics of Strains from Campylobacter jejuni Bacteremia in a 23-Day-Old Infant in China

Campylobacter jejuni (C. jejuni), a common foodborne zoonotic pathogen, usually causes gastroenteritis and rarely causes extraintestinal infections such as bacteremia. This study investigates a rare case of invasive C. jejuni bacteremia in a 23-day-old infant in Nanchang, China. Epidemiological data were collected from the infant's cohabitants (3). The cohabitants' anal swabs (3), milk powder (1), a feeding bottle (1), and kitchen items (3) were collected and screened for C. jejuni. Antimicrobial susceptibility testing was conducted, and whole genome sequencing was performed for genetic analysis, including whole genome multilocus sequence typing (wgMLST), single-nucleotide polymorphism, antimicrobial resistance (AMR) and virulence gene profiling. As a result, three C. jejuni strains were isolated from the infant, the infant's grandmother, and the feeding bottle. The results revealed that the three C. jejuni isolates were clonally related, sharing minimal genetic differences. The infant's grandmother, who had slaughtered a live chicken 4 days before the infant's illness, was identified as the likely source of transmission. AMR profiles showed resistance to fluoroquinolones and cephalosporins. The three isolates were found to carry the blaOXA-184 gene and a chromosomal mutation in gyrA (T86I). Additionally, 69 virulence genes were identified in all isolates, including those associated with adherence (4), glycosylation system (23), motility and export apparatus (38), cytolethal toxin (3), and invasion (1). This case represents the third reported instance of C. jejuni bacteremia in an infant in China. The analysis confirmed a transmission pathway from the grandmother.

Antimicrobial Resistance Profiles of Campylobacter spp. Recovered from Chicken Farms in Two Districts of Bangladesh

The rapid emergence of antimicrobial resistance (AMR) in Campylobacter has reinforced its status as a foodborne pathogen of significant public health concern. Resistant Campylobacter is typically transferred to humans via the consumption of contaminated animal products, particularly poultry. The genes associated with antimicrobial resistance in Campylobacter spp. are poorly understood. To address this knowledge gap, we conducted a prevalence survey of AMR Campylobacter across 84 chicken farms in two districts of Bangladesh. Pooled cloacal swabs were collected from chickens and underwent bacteriological testing for Campylobacter spp. with PCR confirmation. Antimicrobial susceptibility was tested against 14 antibiotics by disk diffusion method, and 12 resistance genes were screened in Campylobacter-positive isolates using multiplex PCR. A total of 34 (40.5%) farms were Campylobacter-positive of which 73.5% of isolates were resistant to at least 10 antibiotics. The antimicrobial susceptibility results indicate a high level of resistance against streptomycin (97.1%), clindamycin (97.1%), ampicillin (94.1%), tetracycline (94.1%), erythromycin (91.2%), ciprofloxacin (88.2%), nalidixic acid (85.3%), and imipenem (82.4%), and comparatively a low frequency of resistance to chloramphenicol (47.1%), ceftazidime (44.1%), and colistin (35.3%). Multidrug-resistant (MDR) and extensively drug-resistant Campylobacter were identified in 97.1%, and 50% of isolates, respectively. Ten resistance genes were identified including blaTEM (in 97.1% of isolates), strA-strB (85.9%), tetA (70.6%), tetB (32.4%), qnrS (23.5%), blaCTX-M-1 (20.6%), qnrB (20.6%), blaSHV (8.8%), aadB (5.9%), and qnrA (2.9%). Our findings demonstrate that resistance to ampicillin, tetracycline, and ceftazidime in Campylobacter isolates was significantly (p ≤ 0.05) associated with the presence of blaTEM, tetA, and blaSHV genes, respectively. The high rates of AMR in Campylobacter isolates from our study are not surprising given the liberal use of antimicrobials and incomplete biosecurity provisions on farms. Of particular concern are resistance rates to those classes of antibiotics that should be reserved for human use (azithromycin, ciprofloxacin, and colistin). AMR was more prevalent in chicken farms that used multiple antibiotics, engaged in prophylactic treatment of the birds, and improperly disposed of antibiotic packages. The high prevalence of MDR in chicken-derived Campylobacter isolates from the different regions of our study reinforces the need for more prudent use of antimicrobial compounds in Bangladeshi chicken farms.

Genome sequences of antimicrobial-resistant Campylobacter coli and Campylobacter jejuni, isolated from poultry in Ukraine

Genomes of a Campylobacter coli OR12-like strain ChP2023 (1,713,995 bp) isolated from broiler chicken and Campylobacter jejuni subsp. jejuni NCTC 11168R-like strain KF2023 (1,729,995 bp) isolated from turkey, from poultry production facilities in Ukraine in 2023, were sequenced using Oxford Nanopore Technologies. Both genomes included antibiotic resistance genes and other virulence factors.

Insights on the genomic diversity, virulence and resistance profile of a Campylobacter jejuni strain isolated from a hospitalized patient in Brazil

Campylobacteriosis is currently recognized as one of the major causes of foodborne bacterial diseases worldwide. In Brazil, there is insufficient data to estimate the impact of Campylobacter in public health. The aim of this present study was to characterize a C. jejuni CJ-HBSJRP strain isolated from a hospitalized patient in Brazil by its ability to invade human Caco-2 epithelial cells, to survive in U937 human macrophages, and to assess its phenotypic antimicrobial resistance profile. In addition, prophages, virulence and antimicrobial resistance genes were search using whole-genome sequencing data. The genetic relatedness was evaluated by MLST and cgMLST analysis by comparison with 29 other C. jejuni genomes isolated from several countries. The CJ-HBSJRP strain showed an invasion percentage of 50% in Caco-2 polarized cells, 37.5% of survivability in U937 cells and was phenotypically resistant to ampicillin, ciprofloxacin and nalidixic acid. A total of 94 virulence genes related to adherence, biofilm, chemotaxis, immune modulation, invasion process, metabolism, motility and toxin were detected. The resistance genes blaOXA-605 (blaOXA-61), cmeB and mutations in the QRDR region of gyrA were also found and none prophages were detected. The MLST analysis showed 23 different STs among the strains studied. Regarding cgMLST analysis, the CJ-HBSJRP strain was genetically distinct and did not group closely to any other isolate. The results obtained reinforce the pathogenic potential of the CJHBSJRP strain and highlighted the need for more careful attention to Campylobacter spp. infections in Brazil since this pathogen has been the most commonly reported zoonosis in several countries worldwide.

Campylobacter jejuni and Campylobacter coli in human stool samples: antibiotic resistance profiles, putative virulence determinants and molecular characterization of the isolates

Campylobacters, especially C. jejuni and C. coli, have become one of the leading causes of acute gastroenteritis in humans worldwide in recent years. We aimed to investigate the presence, antimicrobial resistance, putative virulence genes, and molecular characterization of C. jejuni and C. coli recovered from human acute gastroenteritis cases in the study. In the study, suspected Campylobacter spp. isolates were obtained in 43 (5%) feces samples collected from a total of 850 patients who applied to the Erciyes University Medical Faculty acute clinic between March 2019 and February 2020. As a result of the phenotypic tests, these isolates were determined to be Campylobacter spp. According to the multiplex PCR, 33 of 43 Campylobacter spp. isolates were identified as C. jejuni (76%) and ten isolates were as C. coli (24%). In the disc diffusion test, the highest resistance rate was found in the trimethoprim/sulfamethoxazole (90.1%) and ciprofloxacin (90.1%), and the lowest rate was found in the amoxicillin-clavulanic acid (9.3%). In Campylobacter spp. isolates, the virulence genes cdtA, virB11, cdtB, cadF, iam, ceu, and flaA were found to be positive at rates of 26 (60%), 28 (65.6%), 13 (30%), 4 (9%), 27 (62%), 17 (39%), and 7 (16%), respectively. However, the cdtC gene was not detected in any of the isolates. The study searched tetO gene to examine the genetic aspect of tetracycline resistance, which was found in all Campylobacter spp. isolates. In the PCR reactions to investigate A2074C and A2075G mutations of macrolide resistance, it was determined as 7 (16%) and 21 (48%) of the isolates. To detect quinolone resistance, the rates of quinolone resistance-determining regions (QRDR) were 20 (45.4%) and the gyrA gene mutations in the mismatch amplification mutation assay PCR (MAMA-PCR), were 19 (43.1%) of isolates. In addition, the quinolone resistance gene (qnr) carried by plasmid in Campylobacter isolates was not found in the study. BlaOXA-61 and CmeB (multi-drug efflux pump) genes were detected as 28 (63.6%) and 30 (68.1), respectively. The Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) used for typing the isolates revealed that the band profiles obtained from the isolates were different. In conclusion, this was a very comprehensive study revealing the presence of antibiotic-resistant C. jejuni and C. coli with various virulence genes in patients admitted to a university hospital with acute gastroenteritis. This is of utmost significance for public health. Since campylobacteria are foodborne, zoonotic pathogens and transmission occurs mostly through food. People should have detailed information about the transmission routes of campylobacteria and risky foods. In addition, staff, food processors and caterers, should be trained in hygiene.

Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers

The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.

Distribution of Virulence Genes in Campylobacter spp. Isolated from Agaricus Mushrooms in Iran

The white button mushroom (Agaricus) is a significant nutritional and therapeutic species utilized in the human diet and could transmit various bacterial infections. Campylobacter species are the most common cause of foodborne illness across the world. The present study has been planned to determine the frequency of virulence genes and antibiotic susceptibility test in Campylobacter spp. recovered from Agaricus mushroom. In this study, 740 Agaricus mushroom samples were gathered randomly from various markets from June 2020 to December 2020. Confirmation of Campylobacter spp. using biochemical analyses and 23S rRNA-based PCR was performed. The agar dilution technique was used to determine resistance to antibiotics using gentamicin (GM10μg), ciprofloxacin (CIP5μg), nalidixic acid (NA30μg), tetracycline (TE30μg), ampicillin (AM10μg), amoxicillin+ clavulanic acid (AMC30μg), erythromycine (E15μg), azithromycin (AZM15μg), clindamycin (CC2μg), and chloramphenicol (C30μg). Multiplex PCR was utilized to determine the prevalence of the recR, dnaJ, wlaN, virBll, cdtC, cdtB, cdtA, flaA, cadF, pidA, ciaB, ceuE, and cgtB genes. Campylobacter spp. were detected in 74 out of 740 Agaricus mushroom samples (10%). According to the data, Agaricus mushroom samples included 32 (4.32%) C. jejuni, 11 (1.48%) C. coli, and 31 (4.18%) other Campylobacter spp. Antimicrobial resistance was most common in C. jejuni isolates. C. jejuni isolates also had the lowest resistance rate to gentamycin, ciprofloxacin, and nalidixic acid. C. coli isolates were reported to have the highest antimicrobial resistance to ciprofloxacin, ampicillin, and erythromycine. Resistance to gentamycin and amoxicillin+ clavulanic acid was likewise lowest among C. coli strains. The flaA and ciaB genes were found in 100% of B-lactams-susceptible C. jejuni and C. coli strains. When examining the relationship between antibiotic resistance and the existence of virulence genes, it was observed that there is a statistically significant relationship (p < 0.001) between bacterial resistance and virulence genes. Our findings indicated that changes in resistance patterns in Campylobacter strains have emerged from multiple treatment approaches in Agaricus mushrooms.

Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis

Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq^® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0-26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain-Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (bla _OXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3')-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (bla _OXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.

Prevalence and Antimicrobial Resistance of Campylobacter spp. Isolated from Broilers Throughout the Supply Chain in Valencia, Spain

Campylobacter is a major foodborne pathogen and its antimicrobial resistance (AMR) has been described worldwide. The main objective of this study was to determine the occurrence and AMR of Campylobacter spp. isolated from broilers throughout the supply chain in Valencia, Spain. A total of 483 samples were included in the analysis: 430 from the slaughterhouse (chicken carcass and neck skin) and 53 from the point of sale (retail broiler and packaging). Taking into account the origin of the sample, the prevalence of Campylobacter spp. was 19% in carcass, 28.2% in neck skin, 36.7% in retail broiler, and 80% in packaging isolates. The prevalence of different species in the analyzed samples was 21.1% and 4.8% for Campylobacter jejuni and Campylobacter coli, respectively. AMR profiling of 125 Campylobacter isolates revealed that 122 (97.6%) of the isolates were resistant to one or more antimicrobials. C. jejuni samples presented high resistance to nalidixic acid and ciprofloxacin, 96.1% and 90.2% respectively, whereas C. coli showed 87% of resistance to both antimicrobials. Both species were resistant to tetracycline (C. jejuni 84.3% and C. coli 60.9%) and 26.1% of C. coli was resistant to streptomycin. These results showed no significant difference in the frequency of AMR (p ≥ 0.05) among isolates originated from different points in the food-processing chain at slaughterhouses and retail establishments. In contrast, three main patterns were detected: quinolone-tetracycline (64%), quinolone-only (17.6%), and quinolone-tetracycline-aminoglycosides (8%). Additionally, 12.8% of the isolates presented multidrug resistance, with significantly higher levels detected among C. coli (30.4%) isolates compared with C. jejuni (8.8%) and all the three strains were resistant to all six antibiotics tested. Therefore, these results indicate that broilers could be a source of antimicrobial-resistant Campylobacter in humans and consequently pose a risk to public health.

Prevalence and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli from Laying Hens Housed in Different Rearing Systems

Campylobacter (C.) jejuni and C. coli are responsible for food poisoning in humans. Laying hens may host the bacteria usually without developing symptoms. The aims of this paper were to evaluate the incidence of C. jejuni and C. coli infection in laying hen flocks housed in different rearing systems, the plasma levels of two welfare indicators (corticosterone and interleukin 6, IL-6) and the antimicrobial resistance of the detected Campylobacter strains. Two different flocks (1 and 2) from cage (A), barn (B) and aviary (C) farms were investigated. The highest (p < 0.05) levels of IL-6 were detected in laying hens housed in aviaries. A similar trend emerged in corticosterone level, although differences were found between C1 and C2. C. jejuni and C. coli were identified in 43.5% and 38.9% of birds, respectively. In total, 14 out of 177 (7.9%) hens simultaneously hosted C. jejuni and C. coli.C. jejuni was prevalently detected in hens housed in barns (B1: 53.3%; B2: 46.7%) and aviaries (C1: 34.6%; C2: 86.7%). Conversely, laying hens housed in cages were significantly exposed to infection of C. coli (A1: 41.9%; A2: 80%) while, regarding barns and aviaries, a significant prevalence emerged only in flocks B2 (40%) and C1 (54.8%). Simultaneous infection was statistically significant in barn B1 (36.7%). Antibiotic resistance was mainly detected among C. coli strains, and it was most frequent for fluoroquinolones and tetracycline. Multidrug resistance was also found in C. jejuni (19.7%) and C. coli (17.5%) strains. Based on the results of this study, we recommend increasing biosecurity and hygienic measures to manage hen flocks.

Prevalence and Antimicrobial Resistance of Campylobacter coli and Campylobacter jejuni Isolated from Pig Guts, Pig Feces, and Surface Swabs from the Cutting Tables at Slaughterhouse and Taverns in Southern Benin

Campylobacter food-borne infections are a serious public health problem. In Benin, there is a proliferation of pork consumption in several forms. This study aims to determine the prevalence and the antimicrobial resistance of Campylobacter coli and Campylobacter jejuni strains isolated from pig guts, pig feces, and surface swabs from the cutting tables in southern Benin. For this purpose, 200 samples of pig guts, 40 samples of swabs from the cutting table surface, and 8 samples of pig feces were collected and subjected to bacteriological examination. The method used for the identification of bacteria was microbiological culture combined with molecular identification by PCR. The identified strains were then subjected to antibiotic susceptibility testing according to the methodology recommended by the EUCAST. Antibiotic profiles were compared between strains isolated from pig guts, pig feces, and cutting table surfaces on the one hand and among the different sampling sites on the other hand. The results obtained show that 47.6% of the samples analyzed were contaminated by Campylobacter spp. Molecular identification revealed 34.7% of Campylobacter coli and 9.3% of Campylobacter jejuni. The study of antimicrobial susceptibility showed resistance to ciprofloxacin, 44% to ampicillin, 23.9% to erythromycin, 11% to gentamicin, and 10.1% to amoxicillin + clavulanic acid. In total, 90.8% of the isolated Campylobacter strains were multidrug resistant. The use of antimicrobials in livestock production systems has increased considerably, which could explain, at least partially, the prevalence of Campylobacter and the resistance of strains to antibiotics. To limit the risk of Campylobacter food-borne infections, it is therefore important to include Campylobacter in the list of pathogens to be tested during sanitary quality control of meat and meat products in Benin.

Systematic Review and Meta-Analysis of Integrated Studies on Salmonella and Campylobacter Prevalence, Serovar, and Phenotyping and Genetic of Antimicrobial Resistance in the Middle East—A One Health Perspective

Background:Campylobacter and Salmonella are the leading causes of foodborne diseases worldwide. Recently, antimicrobial resistance (AMR) has become one of the most critical challenges for public health and food safety. To investigate and detect infections commonly transmitted from animals, food, and the environment to humans, a surveillance–response system integrating human and animal health, the environment, and food production components (iSRS), called a One Health approach, would be optimal. Objective: We aimed to identify existing integrated One Health studies on foodborne illnesses in the Middle East and to determine the prevalence, serovars, and antimicrobial resistance phenotypes and genotypes of Salmonella and Campylobacter strains among humans and food-producing animals. Methods: The databases Web of Science, Scopus, and PubMed were searched for literature published from January 2010 until September 2021. Studies meeting inclusion criteria were included and assessed for risk of bias. To assess the temporal and spatial relationship between resistant strains from humans and animals, a statistical random-effects model meta-analysis was performed. Results: 41 out of 1610 studies that investigated Campylobacter and non-typhoid Salmonella (NTS) in the Middle East were included. The NTS prevalence rates among human and food-producing animals were 9% and 13%, respectively. The Campylobacter prevalence rates were 22% in humans and 30% in food-producing animals. The most-reported NTS serovars were Salmonella Enteritidis and Salmonella Typhimurium, while Campylobacter jejuni and Campylobacter coli were the most prevalent species of Campylobacter. NTS isolates were highly resistant to erythromycin, amoxicillin, tetracycline, and ampicillin. C. jejuni isolates showed high resistance against amoxicillin, trimethoprim–sulfamethoxazole, nalidixic acid, azithromycin, chloramphenicol, ampicillin, tetracycline, and ciprofloxacin. The most prevalent Antimicrobial Resistance Genes (ARGs) in isolates from humans included tetO (85%), Class 1 Integrons (81%), blaOXA-61 (53%), and cmeB (51%), whereas in food-producing animals, the genes were tetO (77%), Class 1 integrons (69%), blaOXA-61 (35%), and cmeB (35%). The One Health approach was not rigorously applied in the Middle East countries. Furthermore, there was an uneven distribution in the reported data between the countries. Conclusion: More studies using a simultaneous approach targeting human, animal health, the environment, and food production components along with a solid epidemiological study design are needed to better understand the drivers for the emergence and spread of foodborne pathogens and AMR in the Middle East.

Prevalence and Characterization of Quinolone Resistance in Campylobacter spp. Isolates in Chicken Livers from Retail Stores in Georgia, USA

ABSTRACT

Campylobacter is a bacterial pathogen that causes human foodborne illnesses worldwide, and outbreaks have been associated with consumption of undercooked chicken livers. The objectives of this study were to compare two PCR assays of 250 Campylobacter isolates for identification to species, to assess antibiotic resistance of the isolates, and to analyze genetic diversity of the quinolone resistance determining regions (QRDRs) of the isolates. A double-blind design was used to identify the species of Campylobacter; 181 (72%) of the isolates were identified as Campylobacter jejuni, and 69 (28%) isolates were identified as Campylobacter coli by both PCR assays. A total of 93 (37.2%) isolates were resistant to at least one antibiotic. Among 88 C. jejuni isolates, 33 (18%) were resistant to nalidixic acid (NAL) and ciprofloxacin (CIP), 25 (14%) were resistant to tetracycline (TET), and 18 (10%) were resistant to NAL and TET. Two C. jejuni isolates were resistant to four of the tested antibiotics, and one isolate was resistant to five antibiotics. Two C. coli isolates were resistant to TET, and two were resistant to NAL, CIP, and TET. The amino acid sequences of the QRDRs for the isolates had eight point mutations and could be classified into 12 groups. Thirty-eight C. jejuni isolates resistant to NAL and CIP had a point mutation at residue 86 (substitution from threonine to isoleucine). However, six isolates without this substitution were resistant to NAL and/or CIP. Ten isolates with a point mutation at residue 86 were susceptible to NAL and CIP. This observation suggests that in addition to the substitution at residue 86 other mechanisms may confer resistance to quinolones. Further studies are needed to elucidate mechanisms for quinolone resistance in Campylobacter. The Campylobacter spp. isolated from chicken livers in this study were resistant to quinolones and other classes of antibiotics.

HIGHLIGHTS

Campylobacter spp. in Eggs and Laying Hens in the North-East of Tunisia: High Prevalence and Multidrug-Resistance Phenotypes

Despite the importance of eggs in the human diet, and unlike other products, for which food safety risks are widely investigated, information on the occurrence of Campylobacter and antimicrobial resistance in eggs and layer hen flocks is lacking in Tunisia. This study was conducted to determine the occurrence of Campylobacter and the antimicrobial resistance in layer hens and on eggshells. Thus, 366 cloacal swabs and 86 eggshell smear samples were collected from five layer hen farms in the North-East of Tunisia. The occurrence of Campylobacter infection, and the antimicrobial resistance rates and patterns, were analyzed. The occurrence rates of Campylobacter infection in laying hens and eggshells were 42.3% and 25.6%, respectively, with a predominance of C. jejuni (68.4%, 81.9%), followed by C. coli (31.6%, 18.2%). The antimicrobial susceptibility testing revealed high resistance rates against macrolides, tetracycline, quinolones, β-lactams, and chloramphenicol, with percentages ranging from 35.5% to 100%. All isolates were multidrug resistant (MDR) and five resistance patterns were observed. These results emphasized the risk to consumer health and the need to establish a surveillance strategy to control and prevent the emergence and the spread of resistant strains of Campylobacter in poultry and humans.

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

Campylobacteriosis continues to be one of the leading causes of foodborne bacterial zoonotic infections worldwide. Despite its public health importance, the status of this disease in wild birds and the possibility of transmission from wild birds to domestic animals and humans have not been clearly elucidated yet. This article reviews the available literature with the aim of making a comprehensive manuscript on this disease status in wild birds and the possibility of interspecies transmission. Campylobacter has been isolated from various species of wild birds worldwide, with C. jejuni being the most commonly isolated species. The prevalence of Campylobacter in wild birds may vary depending on several factors like geographical location, season, the bird’s health status, bird species, sample type, the method used, and ecological factors. Molecular studies over the past two to three decades have characterized Campylobacter strains isolated from wild birds and have come up with results that fall into two categories. The first are those that report overlapping strains among human, domestic animal, and wild bird isolates. The results of the studies under this category emphasize that wild birds carry strains of Campylobacter, which are indistinguishable from domestic animals and humans and are therefore an important public and animal health concern. In contrast, the studies under the second category highlight significant differences in Campylobacter population structure among these hosts. Despite the controversiality and the inadequacy of current research to draw a full conclusion, the role of wild birds in the epidemiology of Campylobacter should not be undermined as drug-resistant strains, especially resistance to tetracycline and fluoroquinolones, are increasingly documented. In addition, source attribution studies have linked human cases of Campylobacter infections to wild birds. Therefore, the role of wild birds in the epidemiology of Campylobacter infection should not be neglected. However, in order to determine disease status in wild birds and the precise role of wild birds in domestic animals and human health, detail-oriented epidemiological investigations characterizing the genetic relatedness of isolates from the respective species and environment through one health approach are warranted.

Systematic Evaluation of Whole-Genome Sequencing Based Prediction of Antimicrobial Resistance in Campylobacter jejuni and C. coli

The increasing prevalence of antimicrobial resistance (AMR) in Campylobacter spp. is a global concern. This study evaluated the use of whole-genome sequencing (WGS) to predict AMR in Campylobacter jejuni and C. coli. A panel of 271 isolates recovered from Canadian poultry was used to compare AMR genotype to antimicrobial susceptibility testing (AST) results (azithromycin, ciprofloxacin, erythromycin, gentamicin, tetracycline, florfenicol, nalidixic acid, telithromycin, and clindamycin). The presence of antibiotic resistance genes (ARGs) was determined for each isolate using five computational approaches to evaluate the effect of: ARG screening software, input data (i.e., raw reads, draft genome assemblies), genome coverage and genome assembly software. Overall, concordance between the genotype and phenotype was influenced by the computational pipelines, level of genome coverage and the type of ARG but not by input data. For example, three of the pipelines showed a 99% agreement between detection of a tet(O) gene and tetracycline resistance, whereas agreement between the detection of tet(O) and TET resistance was 98 and 93% for two pipelines. Overall, higher levels of genome coverage were needed to reliably detect some ARGs; for example, at 15X coverage a tet(O) gene was detected in >70% of the genomes, compared to <60% of the genomes for bla(OXA). No genes associated with florfenicol or gentamicin resistance were found in the set of strains included in this study, consistent with AST results. Macrolide and fluoroquinolone resistance was associated 100% with mutations in the 23S rRNA (A2075G) and gyrA (T86I) genes, respectively. A lower association between a A2075G 23S rRNA gene mutation and resistance to clindamycin and telithromycin (92.8 and 78.6%, respectively) was found. While WGS is an effective approach to predicting AMR in Campylobacter, this study demonstrated the impact that computational pipelines, genome coverage and the genes can have on the reliable identification of an AMR genotype.

Occurrence and multidrug resistance of Campylobacter spp. at duck farms and associated environmental and anthropogenic risk factors in Bangladesh

Background

The alarming rise in multi-drug resistant (MDR) zoonotic pathogens, including Campylobacter spp., has been threatening the health sector globally. In Bangladesh, despite rapid growth in poultry sector little is known about the potential risks of zoonotic pathogens in homestead duck flocks. The aim of this study was to understand the occurrence, species diversity, and multi-drug resistance in Campylobacter spp., and identify the associated risk factors in duck farms in Bangladesh.

Methods

The study involved 20 duck farms at 6 sub-districts of Mymensingh, Bangladesh. Monthly occurrence of Campylobacter spp. in potential sources at the farms during February-September, 2018, was detected by culture and PCR-based methods. Campylobacter isolates were examined for resistance to different antimicrobials. Risk factors, concerning climatic and environmental disposition, farm management, and anthropogenic practices, of Campylobacter infection were estimated by participatory epidemiological tools.

Results

Occurrence of Campylobacter spp. was detected in overall 36.90% (155/420) samples, more frequently in drinking water (60%, 30/50), followed by cloacal swab (37.50%, 75/200), egg surface swab (35%, 35/100) and soil of the duck resting places (30%, 15/50) but was not detected in feed samples (n = 20). PCR assays distinguished the majority (61.30%, 95/155) of the isolates as C. coli, while the rest (38.70%, 60/155) were C. jejuni. Notably, 41.7% (25/60) and 31.6% (30/95) strains of C. jejuni and C. coli, respectively, were observed to be MDR. The dynamics of Campylobacter spp., distinctly showing higher abundance during summer and late-monsoon, correlated significantly with temperature, humidity, and rainfall, while sunshine hours had a negative influence. Anthropogenic management-related factors, including, inadequate hygiene practices, use of untreated river water, wet duck shed, flock age (1–6 months), and unscrupulous use of antimicrobials were identified to enhance the risk of MDR Campylobacter infection.

Conclusion

The present study clearly demonstrates that duck farms contribute to the enhanced occurrence and spread of potentially pathogenic and MDR C. coli and C. jejuni strains and the bacterial dynamics are governed by a combined interaction of environmental and anthropogenic factors. A long-term holistic research at the environment-animal-human interface would be integral to divulge health risk reduction approaches tackling the spread of Campylobacter spp. from duck farms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06834-w.

A systematic review from basics to omics on bacteriophage applications in poultry production and processing

The growing human population is currently facing an unprecedented challenge on global food production and sustainability. Despite recognizing poultry as one of the most successful and rapidly growing food industries to address this challenge; poultry health and safety remain major issues that entail immediate attention. Bacterial diseases including colibacillosis, salmonellosis, and necrotic enteritis have become increasingly prevalent during poultry production. Likewise, outbreaks caused by consumption of undercooked poultry products contaminated with zoonotic bacterial pathogens such as Salmonella, Campylobacter and Listeria, are a serious public health concern. With antimicrobial resistance problem and restricted use of antibiotics in food producing animals, bacteriophages are increasingly recognized as an attractive natural antibacterial alternative. Bacteriophages have recently shown promising results to treat diseases in poultry, reduce contamination of carcasses, and enhance the safety of poultry products. Omics technologies have been successfully employed to accurately characterize bacteriophages and their genes/proteins important for interaction with bacterial hosts. In this review, the potential of using lytic bacteriophages to mitigate the risk of major poultry-associated bacterial pathogens are explored. This study also explores challenges associated with the adoption of this technology by industries. Furthermore, the impact of omics approaches on studying bacteriophages, their host interaction and applications is discussed.

Detection of Campylobacter jejuni and Salmonella typhimurium in chicken using PCR for virulence factor hipO and invA genes (Saudi Arabia)

Campylobacter jejuni and Salmonella typhimurium are the leading causes of bacterial food contamination in chicken carcasses. Contamination is particularly associated with the slaughtering process. The present study isolated C. jejuni and S. typhimurim from fifty chicken carcass samples, all of which were acquired from different companies in Riyadh, Saudi Arabia. The identification of C. jejuni was performed phenotypically by using a hippurate test and genetically using a polymerase chain reaction with primers for 16S rRNA and hippurate hydrolase (hipO gene). For the dentification of S. typhimurim, a serological Widal test was carried out using serum anti-S. typhimurium antibodies. Strains were genetically detected using invA gene primers. The positive isolates for C. jejuni showed a specific molecular size of 1448 bp for 16S rRNA and 1148 bp for hipO genes. However, the positive isolates of the invA gene exhibited a specific molecular size at 244 bp using polymerase chain reaction (PCR). Comparing sequencing was performed with respect to the invA gene and the BLAST nucleotide isolates that were identified as Salmonella enterica subsp. enterica serovar typhimurium strain ST45, thereby producing a similarity of 100%. The testing identified C.jejuni for hippuricase, GenBank: Z36940.1. While many isolates of Salmonella spp. that contained the invA gene were not necessarily identified as S. typhimurim, the limiting factor for the Widal test used antiS. typhimurum antibodies. The multidrug resistance (MDR) of C. jejuni isolates in chickens was compared with the standard C. jejuni strain ATCC 22931. Similarly, S. typhimurium isolates were compared with the standard S. typhimurium strain ATCC 14028.

Occurrence and antimicrobial resistance of Campylobacter isolates from broiler chicken and slaughter house environment in India

Campylobacteriosis is among the most frequently reported foodborne zoonoses. A total of 848 samples were screened for Campylobacter spp. and occurrence was found to be 8.7%, 2.3% and 1.65% in broiler cecum samples, chicken meat samples and slaughter house environment swabs, respectively. High level of antimicrobial resistance was found against tetracycline (64.1%), doxycycline (54.4%), ampicillin (46.6%), nalidixic acid (42.7%), kanamycin (35.9%), and ciprofloxacin (33.33%). Resistance to co-amoxiclav (19.4%) and erythromycin (21.4%) was less common. The MAR index of the isolates was in the range of 0.11-0.78. Multi-drug resistance was observed in 54.4% of the isolates, with 53.2% C. jejuni and 55.3% C. coli isolates found resistant against three or more classes of antimicrobials. Presence of mutations in gyrA and 23S rRNA genes was investigated, which revealed that all the fluoroquinolone resistant isolates possessed Thr-86-Ile point mutation, whereas only 68% of erythromycin resistant isolates had A2075G mutation. The tetO gene was present in 91.7% tetracycline resistant isolates and bla_OXA-61 gene was detected in 97.9% of the ampicillin resistant isolates. The occurrence of antimicrobial resistant Campylobacter spp. in broiler chicken samples and slaughter house settings is a public health risk and calls for judicial use of antimicrobials.

Honeybee and Plant Products as Natural Antimicrobials in Enhancement of Poultry Health and Production

The quality and safety attributes of poultry products have attracted increasing widespread attention and interest from scholarly groups and the general population. As natural and safe alternatives to synthetic and artificial chemical drugs (e.g., antibiotics), botanical products are recently being used in poultry farms more than 60% of the time for producing organic products. Medicinal plants, and honeybee products, are natural substances, and they were added to poultry diets in a small amount (between 1% and 3%) as a source of nutrition and to provide health benefits for poultry. In addition, they have several biological functions in the poultry body and may help to enhance their welfare. These supplements can increase the bodyweight of broilers and the egg production of laying hens by approximately 7% and 10% and enhance meat and egg quality by more than 25%. Moreover, they can improve rooster semen quality by an average of 20%. Previous research on the main biological activities performed by biotics has shown that most research only concentrated on the notion of using botanical products as growth promoters, anti-inflammatory, and antibacterial agents. In the current review, the critical effects and functions of bee products and botanicals are explored as natural and safe alternative feed additives in poultry production, such as antioxidants, sexual-stimulants, immuno-stimulants, and for producing healthy products.

Genotypic analyses and antimicrobial resistance profiles of Campylobacter jejuni from crows (Corvidae) of United States and India reflect their respective local antibiotic burdens

AIM

The study examined the hypothesis that crow-borne Campylobacter can function as environmental reservoirs and indicators of antibiotic resistance (AR) determinants circulating in a human population.

METHODS AND RESULTS

Two species of crows from Washington (WA), United States, and Kolkata, India, respectively, were examined for their ability to carry antibiotic resistant Campylobacter. Campylobacter jejuni was the only species isolated by selective agar plating from crow faecal samples. Disk diffusion method used to compare the AR profile of the isolates showed tetracycline (TET) resistance to be the most prevalent (27%) among WA isolates, followed by ciprofloxacin (CIP; 24%). Among Kolkata isolates, nalidixic acid resistance was most common (36%), followed by CIP (27%). The AR profile demonstrated by crow isolates of WA reflects those reported by the US National Antimicrobial Resistance Monitoring System for human isolates (2007-2011), where resistance to TET was most prevalent (≈45%), followed by quinolones (≈24%). The Kolkata crow isolates reflected the AR profile of human clinical isolates from India, where 97% resistance was shown to quinolones, followed by TET (18%). Multilocus sequence typing of 37 isolates, including 11 water isolates from the crow roost area, showed 24 different sequence types (STs). Seventeen of these were previously found in wild birds, 2 in human diarrhoea, 4 in poultry and 8 in environmental water. One isolate was found in both water and faeces, though from different sites within WA.

CONCLUSIONS

The results indicate that crows most likely acquire the AR from anthropogenic sources. Although they are colonized by specific STs, rarely isolated from humans, they can facilitate the spread of AR.

SIGNIFICANCE AND IMPACT OF THE STUDY

By studying two areas in different continents, this research demonstrates that Campylobacter borne by crows can function as environmental reservoirs and indicators of AR determinants that circulate in a human population. This information will be of importance to scientists from the medical and poultry industries.

High-throughput sequencing reveals genetic determinants associated with antibiotic resistance in Campylobacter spp. from farm-to-fork

Campylobacter species are one of the most common causative agents of gastroenteritis worldwide. Resistance against quinolone and macrolide antimicrobials, the most commonly used therapeutic options, poses a serious risk for campylobacteriosis treatment. Owing to whole genome sequencing advancements for rapid detection of antimicrobial resistance mechanisms, phenotypic and genotypic resistance trends along the "farm-to-fork" continuum can be determined. Here, we examined the resistance trends in 111 Campylobacter isolates (90 C. jejuni and 21 C. coli) recovered from clinical samples, commercial broiler carcasses and dairy products in Cairo, Egypt. Multidrug resistance (MDR) was observed in 10% of the isolates, mostly from C. coli. The prevalence of MDR was the highest in isolates collected from broiler carcasses (13.3%), followed by clinical isolates (10.5%), and finally isolates from dairy products (4%). The highest proportion of antimicrobial resistance in both species was against quinolones (ciprofloxacin and/or nalidixic acid) (68.4%), followed by tetracycline (51.3%), then erythromycin (12.6%) and aminoglycosides (streptomycin and/or gentamicin) (5.4%). Similar resistance rates were observed for quinolones, tetracycline, and erythromycin among isolates recovered from broiler carcasses and clinical samples highlighting the contribution of food of animal sources to human illness. Significant associations between phenotypic resistance and putative gene mutations was observed, with a high prevalence of the gyrA T86I substitution among quinolone resistant isolates, tet(O), tet(W), and tet(32) among tetracycline resistant isolates, and 23S rRNA A2075G and A2074T mutations among erythromycin resistant isolates. Emergence of resistance was attributed to the dissemination of resistance genes among various lineages, with the dominance of distinctive clones. For example, sub-lineages of CC828 in C. coli and CC21 in C. jejuni and the genetically related clonal complexes 'CC206 and CC48' and 'CC464, CC353, CC354, CC574', respectively, propagated across different niches sharing semi-homogenous resistance patterns.

Campylobacter jejuni ST50, a pathogen of global importance: A comparative genomic analysis of isolates from Australia, Europe and North America

Campylobacter jejuni is the leading cause of bacterial gastroenteritis globally, and infections are often transmitted through consumption of raw or undercooked poultry. Campylobacter jejuni ST50 is among the top ten sequence types (STs) reported in the collected isolates listed at PubMLST records from poultry, food and clinical sources for Asia, Europe, North America, Oceania and South America. This study was designed to determine the most commonly reported C. jejuni STs globally using the PubMLST database and assess similarities between genomes of C. jejuni ST50 isolates from geographically distinct locations. To gain a better understanding of C. jejuni diversity, we compared draft genome sequences of 182 ST50 isolates recovered from retail or caecal poultry samples in Oceania, Europe and North America that were collected over a period of 9 years (2010 to 2018). Overall, phylogenetic analysis revealed that isolates from geographically distinct locations tended to cluster based on the continent where the sample was collected. Among ST50 isolates from Europe and North America, we identified resistance determinants associated with phenotypic resistance to beta-lactams (EU: 55%; GB: 43.1%), tetracyclines (CA: 77.3%; EU: 37.5%; GB: 9.8%; US: 43.5%) and fluoroquinolones (EU: 60.0%; GB: 15.7%); no resistance determinants were identified in isolates from Australia. In general, the majority of the virulence genes, with rare exceptions such as wlaN, cj1138, hddA and rfbC, were evenly distributed throughout the genomes of all ST50 isolates in this study. Genomic-based characterization of C. jejuni ST50 isolates from poultry on three continents highlighted that geographically distinct isolates have evolved independently but only represent a glimpse into the diversity of C. jejuni.

The impact of essential oils on antibiotic use in animal production regarding antimicrobial resistance - a review

Population growth directly affects the global food supply, demanding a higher production efficiency without farmland expansion - in view of limited land resources and biodiversity loss worldwide. In such scenario, intensive agriculture practices have been widely used. A commonly applied method to maximize yield in animal production is the use of subtherapeutic doses of antibiotics as growth promoters. Because of the strong antibiotic selection pressure generated, the intense use of antibiotic growth promoters (AGP) has been associated to the rise of antimicrobial resistance (AMR). Also, cross-resistance can occur, leading to the emergence of multidrug-resistant pathogens and limiting treatment options in both human and animal health. Thereon, alternatives have been studied to replace AGP in animal production. Among such alternatives, essential oils and essential oil components (EOC) stand out positively from others due to, besides antimicrobial effectiveness, improving zootechnical indexes and modulating genes involved in resistance mechanisms. This review summarizes recent studies in essential oils and EOC for zoonotic bacteria control, providing detailed information about the molecular-level effects of their use in regard to AMR, and identifying important gaps to be filled within the animal production area.

Host-Dependent Clustering of Campylobacter Strains From Small Mammals in Finland

Small mammals are known to carry Campylobacter spp.; however, little is known about the genotypes and their role in human infections. We studied intestinal content from small wild mammals collected in their natural habitats in Finland in 2010-2017, and in close proximity to 40 pig or cattle farms in 2017. The animals were trapped using traditional Finnish metal snap traps. Campylobacter spp. were isolated from the intestinal content using direct plating on mCCDA. A total of 19% of the captured wild animals (n = 577) and 41% of the pooled farm samples (n = 227) were positive for C. jejuni, which was the only Campylobacter species identified. The highest prevalence occurred in yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) which carried Campylobacter spp. in 66.3 and 63.9% of the farm samples and 41.5 and 24.4% of individual animals trapped from natural habitats, respectively. Interestingly, all house mouse (Mus musculus) and shrew (Sorex spp.) samples were negative for Campylobacter spp. C. jejuni isolates (n = 145) were further characterized by whole-genome sequencing. Core genome multilocus sequence typing (cgMLST) clustering showed that mouse and vole strains were separated from the rest of the C. jejuni population (636 and 671 allelic differences, 94 and 99% of core loci, respectively). Very little or no alleles were shared with C. jejuni genomes described earlier from livestock or human isolates. FastANI results further indicated that C. jejuni strains from voles are likely to represent a new previously undescribed species or subspecies of Campylobacter. Core-genome phylogeny showed that there was no difference between isolates originating from the farm and wild captured animals. Instead, the phylogeny followed the host species-association. There was some evidence (one strain each) of livestock-associated C. jejuni occurring in a farm-caught A. flavicollis and a brown rat (Rattus norvegicus), indicating that although small mammals may not be the original reservoir of Campylobacter colonizing livestock, they may sporadically carry C. jejuni strains occurring mainly in livestock and be associated with disease in humans.

Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry

Aliarcobacter butzleri is an emerging foodborne and zoonotic pathogen that is usually transmitted via contaminated food or water. A. butzleri is not only the most prevalent Aliarcobacter species, it is also closely related to thermophilic Campylobacter, which have shown increasing resistance in recent years. Therefore, it is important to assess its resistance and virulence profiles. In this study, 45 Aliarcobacter butzleri strains from water poultry farms in Thuringia, Germany, were subjected to an antimicrobial susceptibility test using the gradient strip diffusion method and whole-genome sequencing. In the phylogenetic analysis, the genomes of the German strains showed high genetic diversity. Thirty-three isolates formed 11 subgroups containing two to six strains. The antimicrobial susceptibility testing showed that 32 strains were resistant to erythromycin, 26 to doxycycline, and 20 to tetracycline, respectively. Only two strains were resistant to ciprofloxacin, while 39 strains were resistant to streptomycin. The in silico prediction of the antimicrobial resistance profiles identified a large repertoire of potential resistance mechanisms. A strong correlation between a gyrA point mutation (Thr-85-Ile) and ciprofloxacin resistance was found in 11 strains. A partial correlation was observed between the presence of the bla3 gene and ampicillin resistance. In silico virulence profiling revealed a broad spectrum of putative virulence factors, including a complete lipid A cluster in all studied genomes.

Comparison of antimicrobial resistance in thermophilic Campylobacter strains isolated from conventional production and backyard poultry flocks

1. The aim of this study was to compare the resistance pattern of thermophilic Campylobacter spp. isolated from conventional production (n = 34) and backyard poultry flocks (n = 36) from Rio de Janeiro State, Brazil. The disc diffusion method and statistical tests were used for investigation and analysis of the resistance pattern of Campylobacter spp. isolated from different rearing systems.2. Antimicrobial resistance percentages to amoxycillin with clavulanic acid (AMC), ampicillin (AMP), ceftiofur (CTF), ciprofloxacin (CIP), enrofloxacin (ENO), erythromycin (ERI), gentamicin (GEN) and tetracycline (TET) were 32.4%, 44.1%, 67.6%, 97.1%, 82.4%, 26.5%, 5.9% and 38.2% in conventional production flocks respectively, while the backyard flock's resistance levels were 0.0%, 13.9%, 69.4%, 100.0%, 91.7%, 5.6%, 0.0% and 16.7%, respectively.3. Campylobacter spp. from conventional poultry production was more resistant to AMC, AMO, ERI and TET (P > 0.05) when compared to strains from backyard poultry. A higher frequency of resistance to fluoroquinolones (FLQ), CIP and ENO, was observed in strains from both systems, demonstrating the spread of resistant strains among poultry production environments.

First Report of aacC5-aadA7Δ4 Gene Cassette Array and Phage Tail Tape Measure Protein on Class 1 Integrons of Campylobacter Species Isolated from Animal and Human Sources in Egypt

Simple Summary

Campylobacter species are among the major causes of bacterial foodborne infections. Here, we investigate, for the first time, class 1 integrons and associated gene cassettes among pan drug-resistant (PDR), extensively drug-resistant (XDR), and multidrug-resistant (MDR) Campylobacter species isolated from livestock animals and humans in Egypt. Our results revealed alarming PDR (2.55%) and inordinate XDR (68.94%) and MDR (28.5%) Campylobacter isolates. None of the examined isolates were pan-susceptible. The existence of a novel gene cassette array, namely aacC5-aadA7Δ4 and a putative phage tail tape measure protein on class 1 integrons of Campylobacter species is the most highlighted novelty of the current study. Evidence from this study showed the possibility of Campylobacter–bacteriophage interactions as well as treatment failure in animals and humans due to horizontal gene transfer mediated by class 1 integrons.

Abstract

Campylobacter species are common commensals in the gastrointestinal tract of livestock animals; thus, animal-to-human transmission occurs frequently. We investigated for the first time, class 1 integrons and associated gene cassettes among pan drug-resistant (PDR), extensively drug-resistant (XDR), and multidrug-resistant (MDR) Campylobacter species isolated from livestock animals and humans in Egypt. Campylobacter species were detected in 58.11% of the analyzed chicken samples represented as 67.53% Campylobacter jejuni(C. jejuni) and 32.47% Campylobacter coli (C. coli). C. jejuni isolates were reported in 51.42%, 74.28%, and 66.67% of examined minced meat, raw milk, and human stool samples, respectively. Variable antimicrobial resistance phenotypes; PDR (2.55%), XDR (68.94%), and MDR (28.5%) campylobacters were reported. Molecular analysis revealed that 97.36% of examined campylobacters were integrase gene-positive; all harbored the class 1 integrons, except one possessed an empty integron structure. DNA sequence analysis revealed the predominance of aadA (81.08%) and dfrA (67.56%) alleles accounting for resistance to aminoglycosides and trimethoprim, respectively. This is the first report of aacC5-aadA7Δ4 gene cassette array and a putative phage tail tape measure protein on class 1 integrons of Campylobacter isolates. Evidence from this study showed the possibility of Campylobacter–bacteriophage interactions and treatment failure in animals and humans due to horizontal gene transfer mediated by class 1 integrons.

Occurrence of tet(O/M/O) Mosaic Gene in Tetracycline-Resistant Campylobacter

Campylobacter is one of the most important microorganisms responsible for foodborne diseases in the EU. In this study, we investigated resistance to tetracycline in 139 Campylobacter jejuni and Campylobacter coli samples isolated from human clinical cases. From these, 110 were resistant to tetracycline, with MIC (minimal inhibitory concentration) varying in a range of 1 to >512 μg/mL, and 109 (78.4%) carried tet(O), a gene that confers resistance to tetracycline through the expression of a protein that confers protection to the ribosome. Amongst the tetracycline-resistant isolates, one C. jejuni (HCC30) was the only tet(O)-negative sample, presenting an MIC of 256 μg/mL. Instead, the mosaic gene tet(O/M/O) was found in HCC30 and, as far as we know, this is the first description of this chimeric gene originating from homologous recombination between tet(O) and tet(M). The previously described mosaic gene tet(O/32/O), also found in Campylobacter, presents a chimeric structure very similar to that of tet(O/M/O), affecting domains II and III of encoded proteins distantly related to the elongation factor G (EF-G). The tet(O/M/O) mosaic gene has been found in nucleotide databases in several genomes of Campylobacter isolated from different origins, indicating its frequent acquisition, even though it can be undetected through screening by PCR with specific tet(O) primers. In this work, we address the improvement of classical PCR to efficiently diagnose the most prevalent tetracycline resistance determinants in Campylobacter, including tet(O/M/O), which should be taken into account in the optimization of campylobacteriosis treatments.

Genotyping and Antibiotic Resistance Traits in Campylobacter jejuni and coli From Pigs and Wild Boars in Italy

The present study investigated the genomic constitution and antimicrobial resistance (AMR) of 238 Campylobacter from pigs and wild boars in Italy between 2012 and 2019. Campylobacter strains were genotyped using multilocus sequence typing (MLST) and whole genome MLST (wgMLST), screened for antimicrobial resistance genes, and tested for phenotypic susceptibility to six different antibiotics. C. coli was detected in 98.31% and 91.66% of pigs and wild boars, while C. jejuni was isolated in the remaining cases. MLST assigned 73 STs and 13 STs in pigs and wild boars, respectively, including 44 novel STs. The predominant ST in pigs was ST-854 (12.36%), followed by ST-9264 (6.18%). ST-1055 and ST-1417 were predominant in wild boars (30% and 13.33%, respectively). The minimum spanning tree using 1,121 global MLST profiles showed specific Italian clusters and a clear separation between pig and wild boar profiles. The wgMLST confirmed the MLST clustering and revealed a high genetic diversity within C. coli population in Italy. Minimum inhibitory concentrations (MIC) of six antibiotics revealed higher resistance in pigs to ciprofloxacin, nalidixic acid, streptomycin and tetracycline, compared to wild boar. In contrast, most strains were susceptible to gentamicin. Worrying levels of multidrug resistance (MDR) were observed mostly in pig isolates. Molecular screening of AMR mechanisms revealed the predominance of gyrA T86I substitution among fluoroquinolone- and quinolone-resistant isolates, and the 23S rRNA A2075G mutation among macrolide-resistant isolates. Other resistance determinants were observed: (i) tet(O) gene was present among tetracycline-resistant isolates; (ii) rpsL and aph(3')-III genes conferring resistance to aminoglycosides, were identified only in streptomycin or gentamicin-resistant pig isolates; (iii) cmeA, cmeB, cmeC, cmeR genes responsible of pump efflux mechanisms, were observed in almost all the strains; (iv) OXA-61, encoding β-lactamase, was found in the half of the strains. Genotypic and phenotypic AMR profiling was fairly correlated for quinolones/fluoroquinolones. Campylobacter infection is common also in wild boar populations in Italy, suggesting that wild boars could be a reservoir of resistant and multi-resistant Campylobacter species, which may be of public health concern. The present study adds to our knowledge on the epidemiological and ecological traits of this pathogen in domesticated and wild swine.

Occurrence of Campylobacter jejuni in Gulls Feeding on Zagreb Rubbish Tip, Croatia; Their Diversity and Antimicrobial Susceptibility in Perspective with Human and Broiler Isolates

Campylobacteriosis is the most common gastrointestinal bacterial disease in the European Union (EU). Wild birds are one of the natural reservoirs of these pathogens. In this study we tested cloacal swabs of 643 gulls captured on rubbish tip in Zagreb, Croatia for the presence of Campylobacter spp. and found 168 Campylobacter positive samples. We used multilocus sequence typing (MLST) to genotype 62 random C. jejuni isolates from gulls, 24 isolates from broiler caeca, 27 isolates from broiler neck skins and 23 human isolates. Altogether, we identified 44 different STs, from which 19 were newly described. Most of the new STs (14) originate from gulls. Although humans and broilers share the majority of STs and isolates from gulls are separated from these, there was one ST present in all three hosts: 45. Additionally antimicrobial susceptibility to six antimicrobials was performed on 123 C. jejuni strains isolated from broiler caeca (n = 22), neck skins of broilers (n = 20), gulls cloacal swabs (n = 50) and human faeces (n = 31) by the broth microdilution method. Results show lower resistance of gull isolates to NAL and CIP, while resistance to TET was as high as in human and broiler isolates.

Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.

Antimicrobial Susceptibility and Clonality of Vaginally Derived Multidrug-Resistant Mobiluncus Isolates in China

Here, the antimicrobial susceptibility, resistance mechanisms, and clonality of Mobiluncus sp. isolates recovered from gynecological outpatients in China were investigated. Compared to M. mulieris, M. curtisii exhibited higher antimicrobial resistance to metronidazole, clindamycin, and tetracycline. Whole-genome sequencing indicated that the clindamycin resistance gene erm(X) was located on a transposable element, Tn5432, which was composed of two IS1249 sequences. Phylogenetic analysis indicated that Mobiluncus spp. had high diversity, with isolates being grouped into several sporadic clades.

Prevalence and susceptibility to antibiotics from Campylobacter jejuni and Campylobacter coli isolated from chicken meat in southern Benin, West Africa

Objective

Poultry is commonly considered to be the primary vehicle for Campylobacter infection in humans. The aim of this study is to assess the risk of Campylobacteriosis in chicken meat consumers in southern Benin by assessing the prevalence and resistance profile of Campylobacter coli and Campylobacter jejuni isolated from chicken thigh in Southern Benin.

Results

The contamination rate of Campylobacter in the samples was 32.8%. From this percentage, 59.5% were local chicken thighs and 40.5% of imported chicken thighs (p = 0.045). After molecular identification, on the 256 samples analyzed, the prevalence of C. jejuni was 23.4% and 7.8% for C. coli, with a concordance of 0.693 (Kappa coefficient of concordance) with the results from phenotypic identification. Seventy-two-point seven percent of Campylobacter strains were resistant to Ciprofloxacin, 71.4% were resistant to Ampicillin and Tetracycline. 55.8% of the strains were multi-drug resistant.

Characterization and Prevalence of Campylobacter spp. From Broiler Chicken Rearing Period to the Slaughtering Process in Eastern China

Campylobacter is one of the most important foodborne pathogens worldwide, and poultry is regarded as the main reservoir of Campylobacter. The contamination of Campylobacter in broiler chickens at the farm level is closely related to the transmission of Campylobacter in the poultry production chain. This study identified 464 Campylobacter isolates from 1,534 samples from broiler rearing period and slaughtering process including 233 Campylobacter jejuni isolates and 231 Campylobacter coli isolates. We have observed a dynamic distribution of Campylobacter during broiler chicken production, that 66.3% of Campylobacter isolates were C. jejuni during broiler rearing period, while C. coli occupied 60.4% of Campylobacter isolates during the broiler slaughtering process. A tag-label method allowed us to track the dynamic of Campylobacter in each broiler chicken from 31-day age at rearing to the partition step in the slaughterhouse. At the 31-day during rearing, 150 broiler chicken were labeled, and was tracked for Campylobacter positive from rearing period to slaughtering process. Among the labeled broiler, 11 of the tracking broiler samples were able to detect Campylobacter from rearing period to slaughtering. All Campylobacter isolates from the 11 tracking samples were sequenced and analyzed. C. jejuni isolates were divided into four STs and C. coli isolates were divided into six STs. Isolates with identical core genome were observed from the same tag-labeled samples at different stages indicating a vertical transmission of Campylobacter in the early broiler meat production. Meanwhile, the core genome analysis elucidated the cross-contamination of Campylobacter during the rearing period and the slaughtering process. The virulotyping analysis revealed that all C. jejuni isolates shared the same virulotypes, while C. coli isolates were divided into three different virulotypes. The antimicrobial resistance gene analysis demonstrated that all Campylobacter isolates contained at least two antibiotic resistance genes (ARGs), and the ARG profiles were well-corresponding to each ST type. Our study observed a high prevalence of Campylobacter during the early chicken meat production, and further studies will be needed to investigate the diversity and transmission of Campylobacter in the poultry production chain.

Molecular Characterization and Antimicrobial Susceptibility of C. jejuni Isolates from Italian Wild Bird Populations

Poultry is considered a major reservoir of human campylobacteriosis. It also been reported that not only poultry, but also wild birds, are capable of carrying C. jejuni, thus demonstrating to be a risk of spreading the bacteria in the environment. To gain insight into the population structure and investigate the antimicrobial resistance genotypes and phenotypes, we analyzed a collection of 135 C. jejuni from 15 species of wild birds in Italy. MLST revealed the presence of 41 sequence types (STs) and 13 clonal complexes (CCs). ST-179 complex and the generalist ST-45 complex were the most prevalent. Core genome MLST revealed that C. jejuni from ST-45 complex clustered according to the bird species, unlike the ST-179 complex which featured 3 different species in the same cluster. Overall we found a moderate prevalence of resistance to tetracycline (12.5%), ciprofloxacin and nalidixic acid (10%). The novel ST isolated from one pigeon showed resistance to all the antibiotics tested. The ST-179 complex (33.3%) was identified with significantly higher nalidixic acid resistance relative to other tested STs. Nine AMR genes (tet(O), cmeA, cmeB, cmeC, cmeR, aad, blaOXA-61, blaOXA-184 and erm(B)) and 23S rRNA and gyrA-associated point mutations were also described, indicating a concordance level between genotypic and phenotypic resistance of 23.3%, 23.4% and of 37.5% for streptomycin, tetracycline and quinolones/fluoroquinolones, respectively. We recommend that particular attention should be given to wild birds as key sentinel animals for the ecosystem contamination surveillance.

Risk of multi-drug resistant Campylobacter spp. and residual antimicrobials at poultry farms and live bird markets in Bangladesh

BACKGROUND

Understanding potential risks of multi-drug resistant (MDR) pathogens from the booming poultry sector is a crucial public health concern. Campylobacter spp. are among the most important zoonotic pathogens associated with MDR infections in poultry and human. This study systematically examined potential risks and associated socio-environmental factors of MDR Campylobacter spp. in poultry farms and live bird markets (LBMs) of Bangladesh.

METHODS

Microbial culture and PCR-based methods were applied to examine the occurrence and MDR patterns of Campylobacter spp. in potential sources (n = 224) at 7 hatcheries, 9 broiler farms and 4 LBMs in three sub-districts. Antimicrobial residues in broiler meat and liver samples (n = 50) were detected by advanced chromatographic techniques. A questionnaire based cross-sectional survey was conducted on socio-environmental factors.

RESULTS

Overall, 32% (71/ 224) samples were found contaminated with Campylobacter spp. In poultry farms, Campylobacter spp. was primarily found in cloacal swab (21/49, 43%), followed by drinking water (8/24, 33%), and meat (8/28, 29%) samples of broilers. Remarkably, at LBMs, Campylobacter spp. was detected in higher prevalence (p < 0.05) in broiler meat (14/26, 54%), which could be related (p < 0.01) to bacterial contamination of drinking water (11/21, 52%) and floor (9/21, 43%). Campylobacter isolates, one from each of 71 positive samples, were differentiated into Campylobacter jejuni (66%) and Campylobacter coli (34%). Alarmingly, 49 and 42% strains of C. jejuni and C. coli, respectively, were observed as MDR, i.e., resistant to three or more antimicrobials, including, tetracycline, amoxicillin, streptomycin, fluoroquinolones, and macrolides. Residual antimicrobials (oxytetracycline, ciprofloxacin and enrofloxacin) were detected in majority of broiler liver (79%) and meat (62%) samples, among which 33 and 19%, respectively, had concentration above acceptable limit. Inadequate personal and environmental hygiene, unscrupulously use of antimicrobials, improper waste disposal, and lack of health surveillance were distinguishable risk factors, with local diversity and compound influences on MDR pathogens.

CONCLUSION

Potential contamination sources and anthropogenic factors associated with the alarming occurrence of MDR Campylobacter, noted in this study, would aid in developing interventions to minimize the increasing risks of poultry-associated MDR pathogens under 'One Health' banner that includes poultry, human and environment perspectives.

Thermotolerant Campylobacter spp. in chicken and bovine meat in Italy: Prevalence, level of contamination and molecular characterization of isolates

Campylobacter species are common foodborne pathogens associated with cases of human gastroenteritis worldwide. A detailed understanding of the prevalence, contamination levels and molecular characteristics of Campylobacter spp. in cattle and chicken, which are likely the most important sources of human contamination, is imperative. A collection of 1243 poultry meat samples (665 chicken breasts and 578 chicken thighs) and 1203 bovine meat samples (689 hamburgers and 514 knife-cut meat preparations) were collected at retail outlets, in randomly selected supermarkets located in different Italian regions during one year. Of these samples, 17.38% of the poultry meat and 0.58% of the bovine meat samples tested positive for Campylobacter, of which 131 were Campylobacter jejuni (57.96%) and 95 were Campylobacter coli (42.03%). Campylobacter isolates were genotyped with the aim of assessing the genetic diversity, population structure, source distribution and Campylobacter transmission route to humans. All isolates were molecularly characterized by pulse field gel electrophoresis (PFGE), and further genotyped using multilocus sequence typing (MLST) and fla-SVR sequencing to gain better insight into the population structure. Antibiotic resistance was also investigate. The highest levels of resistance among chicken strains were observed for ciprofloxacin (88.25%), nalidixic acid (81.45%) and tetracycline (75.6%). PFGE analysis revealed 73 pulsotypes for C. jejuni and 54 pulsotypes for C. coli, demonstrating the existance of different and specific clones circulating in Italy. MLST of C.jejuni isolates mainly clustered in the CC353, CC354, CC21, CC206 and CC443; while C.coli isolates clustered only in CC828. The most common flaA alleles were 287 for C. jejuni and 66 for C. coli. Our study confirms that poultry meat is the main source of Campylobacteriosis, whereas red meat had a low level of contamination suggesting a minor role in transmission. The high presence of Campylobacter in retail chicken meat, paired with its increased resistance to antimicrobials with several multidrug resistance profiles detected, is alarming and represents a persistent threat to public health.