Prevalence of tetracycline-resistant Campylobacter in organic broilers during a production cycle

Campylobacter Diversity Along the Farm-to-Fork Continuum of Pastured Poultry Flocks in the Southeastern United States

INTRODUCTION

Consumer demand for pasture raised, antibiotic-free poultry products has led to an increase in pastured poultry operations within the United States. Given the level of environmental interaction and the potential increase in exposure to foodborne pathogens in these settings, a greater understanding of the prevalence and diversity of Campylobacter populations inherent within pastured poultry flocks is needed.

METHODS

To achieve this, 40 pastured poultry flocks from nine farms were sampled using a farm-to-fork strategy, and Campylobacter was isolated and characterised from preharvest (faeces, soil) through postharvest (caeca, whole carcass rinse) to the final product the consumer would purchase (whole carcass rinse).

RESULTS

Campylobacter was isolated from 872 of 1820 samples, showing an overall prevalence of 47.91%. The caeca showed the highest (p < 0.05) Campylobacter load (4.64 log10 CFU/mL) and prevalence (95.5%), while the final product whole carcass rinses had the lowest (p < 0.05) Campylobacter load (0.32 log10 CFU/mL) and prevalence (15.45%), suggesting that the Campylobacter load in the caeca may not be indicative of the Campylobacter load on the final product. Of the 872 positive samples, 337 Campylobacter isolates were selected for further characterisation. Campylobacter jejuni and Campylobacter coli comprised 74.18% (250/337) and 21.95% (74/337) of the selected isolates respectively. While the Campylobacter isolates displayed resistance to several antibiotics, the most common resistance for both C. jejuni and C. coli was against tetracycline (55.86% and 70.31% respectively). Multidrug resistance phenotypes (≥ 3 antibiotic classes) were relatively low for both C. jejuni (2.80%) and C. coli (9.45%).

CONCLUSIONS

Campylobacter load, prevalence and diversity were more affected by farm location than by the type of sample from which the Campylobacter was isolated. Overall, these results indicated a need for farm-specific Campylobacter mitigation strategies to ensure the safety of these increasingly in-demand poultry products.

Prevalence and Antimicrobial Resistance of Campylobacter in Conventional and No Antibiotics Ever Broiler Farms

Campylobacter is a leading cause of enteric disease worldwide. No antibiotics ever (NAE) poultry has become increasingly popular, yet little is known about the incidence and antimicrobial resistance (AMR) of Campylobacter in this production system. This study was conducted to determine the prevalence, concentration, and AMR of Campylobacter in conventional (CV) and NAE-raised broilers. Two CV and two NAE commercial broiler flocks were included in this study. Cecum (n = 420) and ileum (n = 420) of chickens were collected at different stages during the broiler grow-out phase and following transportation to the processing plant. Samples of litter (n = 24), feed (n = 24), and water (n = 24) were also collected. Screening for Campylobacter was conducted using real-time PCR assay, and enumeration was performed by direct plating on Campy Cefex agar. Campylobacter isolates were confirmed by real-time PCR, and antimicrobial susceptibility was evaluated following the National Antimicrobial Resistance Monitoring System (NARMS) methods. Whole Genome Sequencing (WGS) was used to identify AMR genes carried by the resistant isolates. Campylobacter prevalence reached 100% within the first 3 weeks of summer production under both NAE and CV rearing. A lower Campylobacter prevalence was detected in conventionally raised broilers during fall (P ≤ 0.05), yet no change in prevalence was observed in NAE birds (P > 0.05). Populations were high in the cecum, carrying an average of 6.6 Log10 CFU/g after transportation, and antimicrobial-resistant Campylobacter was isolated from CV broilers during the fall. Three isolates (1.2%), identified as C. coli, carrying the gyrA and tet(O) genes, exhibited simultaneous resistance to ciprofloxacin, tetracycline, and nalidixic acid. Results from this study can help identify important shifts in gut microbial community dynamics and Campylobacter prevalence associated with antibiotic administration within commercial poultry operations.

Low-Level Tetracycline Resistance Gene tet(O)_3 in Campylobacter jejuni

Campylobacter (C.) spp. are the most important foodborne, bacterial, and zoonotic pathogens worldwide. Resistance monitoring of foodborne bacterial pathogens is an important tool to control antimicrobial resistance as a part of the “One Health” approach. The detection and functionality of new resistance genes are of paramount importance in applying more effective screening methods based on whole genome sequencing (WGS). Most tetracycline-resistant C. spp. isolates harbor tet(O), a gene that encodes a ribosomal protection protein. Here we describe tet(O)_3, which has been identified in two food isolates of C. jejuni and is very similar to the tet(O) gene in Streptococcus pneumoniae, having a truncated promoter sequence. This gene confers resistance to tetracycline below 1 mg/L, which is the epidemiological cut-off value. We have analyzed the entire genome of these two isolates, together with a C. jejuni isolate found to have high-level resistance to tetracycline. In contrast to the highly resistant isolate, the promoter of tet(O)_3 is highly responsive to tetracycline, as observed by reverse transcription polymerase chain reaction (RT-PCR). In addition, the two isolates possess a CRISPR repeat, fluoroquinolone resistance due to the gyrA point mutation C257T, a β-lactamase resistance gene blaOXA-184, a multidrug efflux pump CmeABC and its repressor CmeR, but no plasmid. Low-level antibiotic resistant C. jejuni might therefore have an advantage for surviving in non-host environments.

Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains

Recently, there has been a consumer push for natural and organic food products. This has caused alternative poultry production, such as organic, pasture, and free-range systems, to grow in popularity. Due to the stricter rearing practices of alternative poultry production systems, different types of levels of microbiological risks might be present for these systems when compared to conventional production systems. Both conventional and alternative production systems have complex supply chains that present many different opportunities for flocks of birds or poultry meat to be contaminated with foodborne pathogens. As such, it is important to understand the risks involved during each step of production. The purpose of this review is to detail the potential routes of foodborne pathogen transmission throughout the conventional and alternative supply chains, with a special emphasis on the differences in risk between the two management systems, and to identify gaps in knowledge that could assist, if addressed, in poultry risk-based decision making.

Prevalence of Salmonella and Campylobacter spp. in Alternative and Conventionally Produced Chicken in the United States: A Systematic Review and Meta-Analysis

ABSTRACT

The burden of foodborne illness linked to the consumption of contaminated broiler meat is high in the United States. With the increase in popularity of alternative poultry rearing and production systems, it is important to identify the differences in food safety risks presented by alternative systems compared with conventional methods. Although many studies have been conducted that surveyed foodborne pathogen prevalence along the broiler supply chain, a systematic overview of all of the results is lacking. In the current study, a systematic review and meta-analysis were conducted to quantify the differences in prevalence of Salmonella and Campylobacter spp. in farm environment, rehang, prechill, postchill, and retail samples between conventional and alternative production systems. A systematic search of Web of Science and PubMed databases was conducted to identify eligible studies. Studies were then evaluated by inclusion criteria, and the included studies were qualitatively and quantitatively analyzed. In total, 137 trials from 72 studies were used in the final meta-analysis. Meta-analysis models were individually constructed for subgroups that were determined by sample type, pathogen, and production type. All subgroups possessed high amounts of heterogeneity (I2 > 75%). For environmental sample subgroups, Campylobacter prevalence was estimated to be 15.8 and 52.8% for conventional and alternative samples, respectively. Similar prevalence estimates for both production types were observed for Salmonella environmental samples and all retail samples. For conventional samples, Campylobacter and Salmonella prevalence was highest in prechill samples followed by rehang and postchill samples, respectively. The results herein will be useful in future quantitative microbial risk assessments for characterizing the differences in foodborne illness risks presented by different broiler production systems.

HIGHLIGHTS

Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland

OBJECTIVES

We characterized clinical isolates of Campylobacter using whole-genome sequencing (WGS) for detection of virulence genes, antimicrobial resistance markers and phylogenetic analysis in order to increase the knowledge on the molecular epidemiology of Campylobacter in Ireland, where there are significant gaps due to the widespread in the use of culture independent methods for the diagnosis of campylobacteriosis.

METHODS

WGS was applied to 122 Campylobacter human isolates collected over a 10-years period, from diarrhoeal stool samples submitted for routine enteric screening.

RESULTS

Genes associated with cytotoxin production such as cdtA, cdtB and cdtC were found in 88%, 89% and 89% isolates, respectively; adherence, colonization and invasion genes such as cadF, dnaJ, racR, iam, virB11 and ciaB were found in 99%, 99%, 98%, 99%, 1% and 80% isolates, respectively. Genetic markers associated with resistance to quinolones (C257T in gyrA), beta-lactams (blaoxa-61) and tetracycline (tet(O)) were present in 43%, 71% and 25% isolates, respectively. The cmeABC operon was present in 94% of isolates. No macrolide or aminoglycoside resistance markers were detected. Phylogenetic analysis showed that 112 isolates were assigned to 29 sequence types grouped into 17 clonal complexes. Four clusters previously unidentified were detected. These results shown the similarity of Irish data compared to what has been described globally.

CONCLUSIONS

WGS has shown a high discriminatory power for cluster detection, demonstrating that its integration in routine laboratory surveillance could improve the detection and management of outbreaks. In addition we were able to demonstrate that virulence genes in clinical Campylobacter infections in Ireland were similar to those known previously. High prevalence of quinolone resistance markers has been found, which has implications for antimicrobial stewardship.

Ecological Dynamics of Campylobacter in Integrated Mixed Crop-Livestock Farms and Its Prevalence and Survival Ability in Post-Harvest Products

This study investigated the ecological distribution of zoonotic bacterial pathogen, Campylobacter, in mixed crop-livestock (MCL) farms compared to conventional farms and their products at pre- and post-harvest levels. A total of 222 Campylobacter isolates were identified. At pre-harvest level, a total of 1287 samples from seven MCL farms, four conventional poultry farms, four organic produce-only and five conventional produce-only farms from Maryland and the DC metropolitan area were analysed from 2012 to 2014. Campylobacter was detected in 11.16% and 3.6% of MCL and conventional farm samples, respectively, but none from produce-only farm samples. Tetracycline resistance was observed in 51.02% of MCL farm isolates but none among conventional farm isolates. For post-harvest analysis, a total of 1281 food products from seven farmers markets, three organic retail supermarkets and three conventional retail supermarkets were collected from the same area. Campylobacter was isolated in 87.5%, 71.43% and 33.33% of whole chicken carcasses in farmers markets, organic and conventional retail supermarkets, respectively. No Campylobacter was detected in post-harvest produce samples due in part to the inability of Campylobacter to survive in absence of sufficient water activity. Overall, this study reveals public health concerns regarding the MCL farm environment and their products that are sold in retail and farmers markets.

Antibiotic Resistance Patterns of Major Zoonotic Pathogens from All-Natural, Antibiotic-Free, Pasture-Raised Broiler Flocks in the Southeastern United States

The use of antibiotics in agroecosystems has been implicated in the rise in antibiotic resistance (AR), which can affect environmental, animal, and human health. To determine the environmental impact of antibiotic use in agroecosystems, appropriate background levels of AR in agricultural environments in the absence of antibiotic application must be determined. Therefore, to determine background levels of AR in broiler production, four target microbes (, , , and ) were isolated from 15 all-natural, antibiotic-free, pasture-raised broiler flocks from six farms within the southeastern United States. The AR profiles of these isolates were characterized using the CDC National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), and these resistance patterns were compared across target microbes and farms and throughout the life cycle of the flocks along the farm-to-fork continuum. Antibiotic resistances were most prevalent in and and least prevalent in . Although and were isolated from the same farms and characterized using the same NARMS plates, they exhibited distinct AR profiles, with demonstrating clear farm-specific resistance patterns. Multidrug resistance rates (three or more antibiotics), in order of prevalence, were (63.9%), (36.0%), (12.7%), and (1.4%). The results of this study demonstrate the variability in background AR among major food safety-related microbes, even when isolated from similar production and processing samples from the same farms, and indicate the need for the proper design of future broiler production studies to account for this highly dynamic background AR.

Resistance to β-lactam and tetracycline in Campylobacter spp.isolated from broiler slaughterhouses in southern Brazil

Abstract The study was carried out to screen and analyze the genetic characteristics of antimicrobial resistance in Campylobacter spp. from poultry sources. A total of 141 strains of Campylobacter isolated from samples of broilers of slaughterhouses in southern Brazil was identified by phenotypic and genotypic methods. Campylobacter isolates were evaluated for its antimicrobial susceptibility and the presence of resistance genes. The strains were investigated for antimicrobial susceptibility against two agents (ampicillin and tetracycline) by disk diffusion method. PCR assay was used to confirm the specie and the presence of ampicillin (blaOXA-61), tetracycline tet(O), and the energy-dependent multi-drug efflux pump (cmeB) genes. Campylobacter jejuni was the most ubiquitous; its presence was determined in 140 samples out of 141 (99.3%), whereas Campylobacter coli was found only in one of the contaminated samples (0.70%). The results obtained showed 65% and 35.5% of Campylobacter isolates resistant to β-lactams and tetracyclines, respectively. The cmeB gene responsible for multidrug resistance was detected in 26 isolates out 141 strains (18.5%). Moreover, 36 out of 141 Campylobacter strains (25.6%) were found to be resistant to at least two different antimicrobia resistance markers (β-lactams and tetracyclines).

Chromosomal tet(O)-harboring regions in Campylobacter coli isolates from turkeys and swine

In turkey-derived Campylobacter coli isolates of a unique lineage (cluster II), the tetracycline resistance determinant tet(O) was chromosomal and was part of a gene cassette (transposon) interrupting a Campylobacter jejuni-associated putative citrate transporter gene. In contrast, the swine-derived C. coli strain 6461 harbored a chromosomal tet(O) in a different genomic location.

Antimicrobial susceptibilities and resistance genes in Campylobacter strains isolated from poultry and pigs in Australia

AIMS

To evaluate the phenotypic and genotypic profiles of Campylobacter spp. from poultry faecal samples from free range or intensively raised meat chickens and free range egg layers. In addition, a case-comparison study of antibiotic resistance genes from different groups of poultry and some pig strains previously collected was carried out.

METHODS

Resistance to different antibiotics was assessed using the agar dilution method. In addition, all the strains were tested for ampicillin (bla(OXA-61) ), erythromycin (aph-3-1), tetracycline tet(O), streptomycin (aadE), and the energy-dependent multi-drug efflux pump (cmeB) resistance genes using multiplex polymerase chain reaction.

RESULTS

The evaluation of phenotypic resistance revealed all of the strains from poultry were sensitive to ciprofloxacin, gentamicin, erythromycin or tylosin. But, widespread resistance to lincomycin (51-100%), extensive resistance to ampicillin (33·3-60·2%) and less resistance to tetracycline (5·6-40·7%) were observed in the different groups of chickens. Antibiotic resistance genes bla(OXA-61,) cmeB and tet(O) were found in 82·6-92·7%, 80·3-89% and 22·3-30·9% Camp. coli isolates from pigs, whilst 59-65·4% and 19·2-40·7% Camp. jejuni from chickens were found to encode bla(OXA-61) and tet(O), respectively.

CONCLUSION

No significant difference between isolates from free range egg layers and meat chickens (P < 0·05) was found. However, there were significant differences between the pig strains and all the groups of poultry strains (P < 0·05) with regard to carriage of resistance genes. In addition, pulsed field gel electrophoresis of selected resistant isolates from the poultry and pig revealed closely related clonal groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggest the resistant strains are persisting environmental isolates that have been acquired by the different livestock species. Furthermore, the different treatment practices in poultry and pigs have resulted in differences in resistance profiles in Campylobacter isolates.

Campylobacter species occurrence within internal organs and tissues of commercial caged Leghorn laying hens

Campylobacter spp. are frequently present in the intestinal tract and internal tissues of broiler breeder and broiler chickens. Campylobacter spp. ecology in commercial Leghorn laying hens has not been extensively studied. The objectives of the current study were to determine 1) Campylobacter spp. presence in the reproductive tract, lymphoid organs, liver-gallbladder, and ceca of commercial Leghorn laying hens; 2) species of Campylobacter present; and 3) antimicrobial resistance pattern of Campylobacter isolates. In study 1, three flocks ranging from 94 to 105 wk of age were sampled from a commercial laying complex. In study 2, two flocks, 82 and 84 wk of age, were sampled from a separate complex. Hens were killed, defeathered, aseptically necropsied, and the spleen, liver-gallbladder, ovarian follicles, and upper (infundibulum, magnum, and isthmus) and lower (shell gland and vagina) reproductive tracts were aseptically removed before the ceca. Samples were packed on ice and transported to the laboratory for evaluation. For speciation, a standard BAX real-time PCR method was used while susceptibility testing was performed using US National Antimicrobial Resistance Monitoring System (NARMS) standards and recommended quality control organisms. Isolates were examined for susceptibility using a semi-automated testing system (Sensititer) to the following 9 antimicrobials: azithromycin, clindamycin, ciprofloxacin, erythromycin, florfenicol, gentamicin, nalidixic acid, telithromycin, and tetracycline. In study 1, the isolation rate was 13, 67, 53, 3, 13, and 57% from the ovarian follicles, lower reproductive tract, upper reproductive tract, spleen, liver-gallbladder, and ceca, respectively. In study 2, the isolation rate was 17, 43, 33, 20, 17, and 73% from the ovarian follicles, lower reproductive tract, upper reproductive tract, spleen, liver-gallbladder, and ceca, respectively. Overall, 50% of isolates were Campylobacter jejuni, 49% Campylobacter coli, and 1% Campylobacter lari. In study 1, all of the isolates were pan-susceptible. In study 2, thirty-seven percent of the isolates were resistant to tetracycline. Commercial table egg laying hens housed in colony cages on wire floors had diverse Campylobacter spp. recovered from different tissues and these isolates were not resistant to a broad range of antimicrobials.

Antibiotic resistance in Campylobacter: emergence, transmission and persistence

Campylobacter is a leading foodborne bacterial pathogen, which causes gastroenteritis in humans. This pathogenic organism is increasingly resistant to antibiotics, especially fluoroquinolones and macrolides, which are the most frequently used antimicrobials for the treatment of campylobacteriosis when clinical therapy is warranted. As a zoonotic pathogen, Campylobacter has a broad animal reservoir and infects humans via contaminated food, water or milk. Antibiotic usage in both animal agriculture and human medicine, can influence the development of antibiotic-resistant Campylobacter. This review will describe the trend in fluoroquinolone and macrolide resistance in Campylobacter, summarize the mechanisms underlying the resistance to various antibiotics and discuss the unique features associated with the emergence, transmission and persistence of antibiotic-resistant Campylobacter. Special attention will be given to recent findings and emphasis will be placed on Campylobacter resistance to fluoroquinolones and macrolides. A future perspective on antibiotic resistance and potential approaches for the control of antibiotic-resistant Campylobacter, will also be discussed.