Beta-lactam resistance in Campylobacter coli and Campylobacter jejuni chicken isolates and the association between blaOXA-61 gene expression and the action of β-lactamase inhibitors

Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru

OBJECTIVES

Antimicrobial resistant (AMR) Campylobacter is a global health threat; however, there is limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated genomic determinants of AMR using a collection of whole genome sequenced Campylobacter jejuni and C. coli isolates from Iquitos, Peru.

METHODS

Campylobacter isolates from two paediatric cohort studies enriched with isolates that demonstrated resistance to ciprofloxacin and azithromycin were sequenced and mined for AMR determinants.

RESULTS

The gyrA mutation leading to the Thr86Ile amino acid change was the only gyrA mutation associated with fluoroquinolone resistance identified. The A2075G mutation in 23S rRNA was present, but three other 23S rRNA mutations previously associated with macrolide resistance were not identified. A resistant-enhancing variant of the cmeABC efflux pump genotype (RE-cmeABC) was identified in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes. Mutations identified in the CmeR-binding site, an inverted repeat sequence in the cmeABC promoter region that increases expression of the operon, were identified in 24/97 C. jejuni and 14/67 C. coli genomes. The presence of these variants, in addition to RE-cmeABC, was noted in 18 of the 24 C. jejuni and 9 of the 14 C. coli genomes.

CONCLUSIONS

Both RE-cmeABC and mutations in the CmeR-binding site were strongly associated with the MDR phenotype in C. jejuni and C. coli. This is the first report of RE-cmeABC in Peru and suggests it is a major driver of resistance to the principal therapies used to treat human campylobacteriosis in this setting.

Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter

IMPORTANCE

Campylobacter is a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat. Campylobacter is common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity of Campylobacter strains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show that Campylobacter jejuni and Campylobacter coli differ in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiating Campylobacter strains.

Combined genomic-proteomic approach in the identification of Campylobacter coli amoxicillin-clavulanic acid resistance mechanism in clinical isolates

Introduction

Aminopenicillins resistance among Campylobacter jejuni and Campylobacter coli strains is associated with a single mutation in the promoting region of a chromosomal beta-lactamase blaOXA61, allowing its expression. Clavulanic acid is used to restore aminopenicillins activity in case of blaOXA61 expression and has also an inherent antimicrobial activity over Campylobacter spp. Resistance to amoxicillin-clavulanic acid is therefore extremely rare among these species: only 0.1% of all Campylobacter spp. analyzed in the French National Reference Center these last years (2017-2022).

Material and methods

Whole genome sequencing with bioinformatic resistance identification combined with mass spectrometry (MS) was used to identify amoxicillin-acid clavulanic resistance mechanism in Campylobacters.

Results

A G57T mutation in blaOXA61 promoting region was identified in all C. jejuni and C. coli ampicillin resistant isolates and no mutation in ampicillin susceptible isolates. Interestingly, three C. coli resistant to both ampicillin and amoxicillin-clavulanic acid displayed a supplemental deletion in the promoting region of blaOXA61 beta-lactamase, at position A69. Using MS, a significant difference in the expression of BlaOXA61 was observed between these three isolates and amoxicillin-clavulanic acid susceptible C. coli.

Conclusion

A combined genomics/proteomics approach allowed here to identify a rare putative resistance mechanism associated with amoxicillin-clavulanic acid resistance for C. coli.

First report of phenotypic and genotypic (blaOXA-61) beta-lactam resistance in Campylobacter jejuni from broilers in Indonesia

Background and Aim

Campylobacter is a zoonotic bacterium that is a major source of foodborne diseases. In humans, most cases of campylobacteriosis are caused by Campylobacter jejuni. Poultry is the main reservoir of Campylobacter for humans, because Campylobacter is part of the normal flora of the digestive tract of poultry. Antimicrobial resistance to several antibiotics in Campylobacter isolated from humans and food animals has increased rapidly. Beta-lactam is an antibiotic with a high prevalence of resistance in Campylobacter. This study aimed to investigate phenotypic and genotypic (blaOXA-61) beta-lactam resistance in C. jejuni from broilers in Indonesia.

Materials and Methods

A total of 100 samples of broiler intestinal contents were obtained from 10 broiler farms in Pasuruan Regency, Indonesia. Campylobacter jejuni was identified using conventional and polymerase chain reaction (PCR)-based methods. Phenotypic detection of beta-lactam resistance was performed using an antimicrobial susceptibility test with antibiotic disks of aztreonam, ampicillin, and amoxicillin-clavulanic acid. Genotypic detection by PCR was performed using the blaOXA-61 gene, which encodes beta-lactamase.

Results

Campylobacter jejuni was identified in 23% of the samples. Phenotypically, 100% (23/23) and 73.9% (17/23) C. jejuni isolates had high resistance to aztreonam and ampicillin, respectively, but all isolates were susceptible to amoxicillin-clavulanic acid. Genotypically, all isolates carried blaOXA-61, indicated by the presence of a 372-bp PCR product.

Conclusion

Campylobacter jejuni is highly resistant to beta-lactams and is a serious threat to human health. Resistance to beta-lactams should be monitored because beta-lactamase genes can be transferred between bacteria. Public awareness must also be increased on the importance of using antibiotics rationally in humans and animals.

Genetic characteristics, antimicrobial susceptibility, and virulence genes distribution of Campylobacter isolated from local dual-purpose chickens in central China

Food-borne antibiotic-resistant Campylobacter poses a serious threat to public health. To understand the prevalence and genetic characteristics of Campylobacter in Chinese local dual-purpose (meat and eggs) chickens, the genomes of 30 Campylobacter isolates, including 13 C. jejuni and 17 C. coli from Jianghan-chickens in central China, were sequenced and tested for antibiotic susceptibility. The results showed that CC-354 and CC-828 were the dominant clonal complexes of C. jejuni and C. coli, respectively, and a phylogenetic analysis showed that three unclassified multilocus sequence types of C. coli were more closely genetically related to C. jejuni than to other C. coli in this study. Of the six antibiotics tested, the highest resistance rates were to ciprofloxacin and tetracycline (100%), followed by lincomycin (63.3%), erythromycin (30.0%), amikacin (26.7%), and cefotaxime (20.0%). The antibiotic resistance rate of C. coli was higher than that of C. jejuni. The GyrA T86I mutation and 15 acquired resistance genes were detected with whole-genome sequencing (WGS). Among those, the GyrA T86I mutation and tet(O) were most prevalent (both 96.7%), followed by the blaOXA-type gene (90.0%), ant(6)-Ia (26.7%), aac(6')-aph(3'') (23.3%), erm(B) (13.3%), and other genes (3.3%). The ciprofloxacin and tetracycline resistance phenotypes correlated strongly with the GyrA T86I mutation and tet(O)/tet(L), respectively, but for other antibiotics, the correlation between genes and resistance phenotypes were weak, indicating that there may be resistance mechanisms other than the resistance genes detected in this study. Virulence gene analysis showed that several genes related to adhesion, colonization, and invasion (including cadF, porA, ciaB, and jlpA) and cytolethal distending toxin (cdtABC) were only present in C. jejuni. Overall, this study extends our knowledge of the epidemiology and antibiotic resistance of Campylobacter in local Chinese dual-purpose chickens.

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.

Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution

Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presence of ARGs in multiple mobile elements distributed among different Cff lineages highlights the risk for spread and further emergence of AMR in C. fetus. Surveillance for these resistances requires the establishment of ECOFFs for C. fetus.

Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors of Campylobacter

Campylobacter infections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir for Campylobacter. Here, we characterized the genetic diversity of Campylobacter species detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed on Campylobacter jejuni (n = 39) and Campylobacter coli (n = 5) isolates. All C. jejuni isolates were susceptible to all antibiotics tested while C. coli (n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates' flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3 C. jejuni isolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates' multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected for Campylobacter strains that are less likely to colonize the chicken host.

Prevalence and antimicrobial resistance of Campylobacter jejuni and C. coli identified in a slaughterhouse in Argentina

The aim of this study was to evaluate the percentage of Campylobacter (C. jejuni and C. coli) from samples collected at the slaughterhouse to describe the prevalence of resistance to selected antimicrobials, and to characterize the genetic determinants. In total, from 333 samples analyzed, 31% were positive for Campylobacter. More positive samples were detected before the chiller (46%) than after the chiller (16%). C. coli (59%) was more prevalent than C. jejuni (41%). Antimicrobial resistance differences between C. jejuni and C. coli were found (p < 0.001). Multidrug resistance was found in 72% of C. coli isolates and 69% of C. jejuni isolates (p < 0.001). Most C. jejuni isolates (57%) had the three genes of the cmeABC efflux pump. The tet(O) gene and resistance-associated point mutations within both the gyrA and 23S rRNA genes were detected in 100% of C. coli isolates. On the other hand, C. jejuni only had more prevalence of the bla_OXA-61 gene than C. coli (p < 0.001), and most of the C. jejuni isolates (70–80%) had the tet(O) and gyrA point mutation. These results could contribute to knowledge about the status of thermotolerant Campylobacter resistant to antimicrobials isolated from food animals in Argentina and to develop an antimicrobial resistance surveillance system.

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From samples analyzed, 31% were positive for Campylobacter.

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More positive samples were detected before the chiller (46%) than after it (16%).

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Multidrug resistance was found in 72% of C. coli isolates and 69% of C. jejuni isolates.

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The tet(O) gene was detected in 100% of the tetracycline-, resistantC. coliisolates.

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C.jejuni only had more prevalence of the bla_OXA-61 gene than C. coli (p < 0.001).

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.

Resistance to Antibiotics in Thermophilic Campylobacters

Campylobacter jejuni (C. jejuni) is one of the most frequent causes of bacterial enterocolitis globally. The disease in human is usually self-limiting, but when complications arise antibiotic therapy is required at a time when resistance to antibiotics is increasing worldwide. Mechanisms of antibiotic resistance in bacteria are diverse depending on antibiotic type and usage and include: enzymatic destruction or drug inactivation; alteration of the target enzyme; alteration of cell membrane permeability; alteration of ribosome structure and alteration of the metabolic pathway(s). Resistance of Campylobacter spp. to antibiotics, especially fluoroquinolones is now a major public health problem in developed and developing countries. In this review the mechanisms of resistance to fluoroquinolones, macrolides, tetracycline, aminoglycoside and the role of integrons in resistance of Campylobacter (especially at the molecular level) are discussed, as well as the mechanisms of resistance to β-lactam antibiotics, sulphonamides and trimethoprim. Multiple drug resistance is an increasing problem for treatment of campylobacter infections and emergence of resistant strains and resistance are important One Health issues.

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.

New and alternative strategies for the prevention, control, and treatment of antibiotic-resistant Campylobacter

Campylobacter is an enteric pathogen and a leading bacterial cause of diarrhea worldwide. It is widely distributed in food animal species and is transmitted to humans primarily through the foodborne route. While generally causing self-limited diarrhea in humans, Campylobacter may induce severe or systemic infections in immunocompromised or young/elderly patients, which often requires antibiotic therapy with the first-line antibiotics including fluoroquinolones and macrolides. Over the past decades, Campylobacter has acquired resistance to these clinically significant antibiotics, compromising the effectiveness of antibiotic treatments. To address this concern, many studies have been conducted to advance novel and alternative measures to control antibiotic-resistant Campylobacter in animal reservoirs and in the human host. Although some of these undertakings have yielded promising results, efficacious and reliable alternative approaches are yet to be developed. In this review article, we will describe Campylobacter-associated disease spectrums and current treatment options, discuss the state of antibiotic resistance and alternative therapies, and provide an evaluation of various approaches that are being developed to control Campylobacter infections in animal reservoirs and the human host.