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

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.

Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers

Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.

Prevalence of ciprofloxacin resistance and associated genetic determinants differed among Campylobacter isolated from human and poultry meat sources in Pennsylvania

Poultry is the primary source of Campylobacter infections and severe campylobacteriosis cases are treated with macrolides and fluoroquinolones. However, these drugs are less effective against antimicrobial-resistant strains. Here, we investigated the prevalence of phenotypic antimicrobial resistance and associated resistance genetic determinants in Campylobacter isolates collected from human clinical (N = 123) and meat (N = 80) sources in Pennsylvania in 2017 and 2018. Our goal was to assess potential differences in the prevalence of antimicrobial resistance in Campylobacter isolated from human and poultry meat sources in Pennsylvania and to assess the accuracy of predicting antimicrobial resistance phenotypes based on resistance genotypes. We whole genome sequenced isolates and identified genetic resistance determinants using the National Antimicrobial Resistance Monitoring System Campylobacter AMR workflow v2.0 in GalaxyTrakr. Phenotypic antimicrobial susceptibility testing was carried out using the E-Test and Sensititre CAMPYCMV methods for human clinical and poultry meat isolates, respectively, and the results were interpreted using the EUCAST epidemiological cutoff values. The 193 isolates were represented by 85 MLST sequence types and 23 clonal complexes, suggesting high genetic diversity. Resistance to erythromycin was confirmed in 6% human and 4% meat isolates. Prevalence of ciprofloxacin resistance was significantly higher in human isolates as compared to meat isolates. A good concordance was observed between phenotypic resistance and the presence of the corresponding known resistance genetic determinants.

Genotypic characterization, antimicrobial susceptibility and virulence determinants of Campylobacter jejuni and Campylobacter coli isolated from pastured poultry farms

Aim

Campylobacter is the leading bacterial pathogen that causes foodborne illnesses worldwide. Pasture farming is regarded as an important source of agricultural production for small farming communities. Consumer preference for pasture-raised animal products has increased; however, there is a paucity of information on the microbiological quality of pasture-raised poultry products. The purpose of this study was to explore genetic relatedness of thermophilic Campylobacter isolates, to assess antibiotic resistance phenotypically and genotypically, and to screen the presence of virulence determinants of Campylobacter isolates from pasture-raised poultry farms from southeastern United States.

Methods

Ninety-seven Campylobacter isolates previously identified by Q7 BAX® System Real-Time PCR were genotyped by multilocus sequence typing (MLST). Campylobacter isolates were then evaluated for their phenotypic antimicrobial susceptibility against nine antimicrobial agents using Sensititre plates. Additionally, Campylobacter isolates were tested for the presence of antimicrobial resistance-associated elements. Furthermore, Campylobacter isolates were screened for the presence of 13 genes encoding putative virulence factors by PCR. These included genes involved in motility (flaA and flhA), adhesion and colonization (cadF, docC, racR, and virB11), toxin production (cdtA, cdtB, cdtC, wlaN, and ceuE) and invasion (ciaB and iamA).

Results

Among 97 Campylobacter isolates, Campylobacter jejuni (n = 79) and Campylobacter coli (n = 18) were identified. By MLST, C. jejuni isolates were assigned to seven clonal complexes. Among them, ST-353, ST-607 and ST-21 were the most common STs recognized. All C. coli (n = 18) isolates were included in CC-828. Interestingly, eight STs identified were not belonging any previous identified clonal complex. Campylobacter isolates displayed a high resistance rate against tetracycline (81.4%), while a low rate of resistance was observed against macrolides (azithromycin and erythromycin), quinolones and fluoroquinolones (nalidixic acid and ciprofloxacin), aminoglycosides (gentamicin), ketolide (telithromycin), amphenicol (florfenicol) and lincomycin (clindamycin). Thirteen isolates (13.54%) were pan-susceptible to all tested antibiotics, while nine isolates were multi-antimicrobial resistant (MAR; resist to three or more antimicrobial classes). Interestingly, there were no isolates resistant to all antimicrobial classes. Thr86Ile mutation was identified in all quinolones resistant strains. Erythromycin encoding gene (ermB) was identified in 75% of erythromycin resistant isolates. The A2075 mutation was detected in one erythromycin resistant strain, while A2074 could not be identified. The tetO gene was identified in 93.7% of tetracycline resistant isolates and six tetracycline susceptible isolates. In conclusion, the results of this study revealed that Campylobacter isolates from pasture-raised poultry farms showed the ST relatedness to Campylobacter isolates commonly associated with humans, indicating pasture-raised broiler flocks, similar to conventionally-reared broiler flocks, as a potential vector for antibiotic-resistant and pathogenic strains of thermophilic Campylobacter to humans.