Campylobactermulti-locus sequence types and antimicrobial susceptibility of broiler cecal isolates: A two year study of 143 commercial flocks

Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing

Chickens are the primary reservoirs of Campylobacter spp., mainly C. jejuni and C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacter spp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuni and 5 C. coli isolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobacter sequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuni and 5 ST in C. coli. The prominent ST was ST 2274 (5 isolates, 19.2%), followed by ST 51, 460, 2409, and 6455 (2 isolates in each ST, 7.7%), while all remaining ST (464, 536, 595, 2083, 6736, 6964, 8096, 10437, 828, 872, 900, 8237, and 13540) had 1 isolate per ST (3.8%). Six types of antimicrobial resistance genes (ant(6)-Ia, aph(3')-III, blaOXA, cat, erm(B), and tet(O)) and one point mutations in the gyrA gene (Threonine-86-Isoleucine) and another in the rpsL gene (Lysine-43-Arginine) were detected. The blaOXA resistance gene was present in all isolates, the gyrA mutations was in 95.2% of C. jejuni and 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuni and 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuni isolates were all resistant to ciprofloxacin, enrofloxacin, and nalidixic acid, with lower levels of resistance to tetracycline (76.2%), tylosin (52.3%), erythromycin (23.8%), azithromycin (22.2%), and gentamicin (11.1%). Most C. coli isolates were resistant to all tested antimicrobials, while 1 C. coli was pan-susceptible except for tylosin. Single-nucleotide polymorphisms concordance varied widely, with differences of up to 13,375 single-nucleotide polymorphisms compared to the reference Campylobacter isolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacter spp. in Thai chicken production systems.

Correlation between Multilocus Sequence Typing and Antibiotic Resistance, Virulence Potential of Campylobacter jejuni Isolates from Poultry Meat

Campylobacter jejuni is a major foodborne pathogen and can be transmitted to human beings via the consumption of poultry products. This study aimed to determine antibiotic resistance and virulence potential of one hundred C. jejuni isolates from poultry meat and to explore the correlation between them and the multilocus sequence types (MLST). A total of 29 STs and 13 CCs were identified by MLST, of which 8 STs were first identified. The dominant ST was ST583 (21%), followed by ST42 (15%), ST61 (12%), and ST2276 (10%). Eighty-eight isolates showed resistance to at least one antibiotic. The resistance rate to fluoroquinolones was the highest (81%), followed by tetracycline (59%), whereas all the isolates were susceptible to erythromycin and telithromycin. Multi-antibiotic resistance was detected in 18 C. jejuni isolates. Great variability in the adhesion and invasion ability to Caco-2 cells was observed for the 100 isolates, with adhesion rates varying between 0.02% and 28.48%, and invasion rates varied from 0 to 6.26%. A correlation between STs and antibiotic resistance or virulence was observed. The ST61 isolates were significantly sensitive to CIP, while the TET resistance was significantly associated with ST354 and ST6175 complex. ST11326 showed substantially higher resistance to gentamicin and higher adhesion and invasion abilities to Caco-2 cells. The results helped improve our understanding of the potential hazard of different genotypes C. jejuni and provided critical information for the risk assessment of campylobacteriosis infection.

Identification of the first erm(B)-positive Campylobacter jejuni and Campylobacter coli associated with novel multidrug resistance genomic islands in Australia

OBJECTIVES

This report describes the first identification of two Campylobacter isolates harbouring erm(B) in Australia.

METHODS

Two erm(B)-positive isolates, Campylobacter coli 18V1065H1 and Campylobacter jejuni 19W1001H1, were isolated from diarrhoeal faecal samples from two travellers who had recently returned from Southeast Asia. Isolates underwent whole-genome sequencing using an Illumina NextSeq system and were analysed with the Nullarbor pipeline. Antimicrobial resistance genes were identified using AMRFinderPlus and sequence types (STs) were determined by multilocus sequence typing and the PubMLST Campylobacter jejuni/coli typing scheme.

RESULTS

Besideserm(B), C. jejuni 19W1001H1 possessed six other resistance genes [aad9, aadE, aph(3')-Illa, bla_OXA-185, catA13 and tet(O)], the gyrA T86I mutation and the RE-CmeABC multidrug efflux pump variant. Campylobacter coli 18V1065H1 also possessed six resistance genes [aad9, aadE, aph(3')-IIIa, bla_OXA-61, sat4 and tet(O)] in addition to erm(B); however, this isolate lacked genetic evidence for resistance to fluoroquinolones (no gyrA mutation). The erm(B) locus differed between isolates and neither was identical to previously identified erm(B) multidrug resistance genomic island (MDRGI) types. Both erm(B)-bearing isolates belonged to novel sequence types: ST9967 (C. jejuni 19W1001H1) and ST10161 (C. coli 18V1065H1).

CONCLUSIONS

This study detected the presence oferm(B) in Campylobacter for the first time in Australia. This novel mechanism of macrolide resistance is a major concern both for human and animal health and warrants close surveillance as macrolides are often the drug of choice for treating campylobacteriosis. The erm(B) gene is associated with several MDRGIs and dissemination of this resistance mechanism will likely limit treatment options for Campylobacter infections.

Emergence of Fluoroquinolone-Resistant Campylobacter jejuni and Campylobacter coli among Australian Chickens in the Absence of Fluoroquinolone Use

In a structured survey of all major chicken-meat producers in Australia, we investigated the antimicrobial resistance (AMR) and genomic characteristics of Campylobacter jejuni (n = 108) and C. coli (n = 96) from cecal samples of chickens at slaughter (n = 200). The majority of the C. jejuni (63%) and C. coli (86.5%) samples were susceptible to all antimicrobials. Fluoroquinolone resistance was detected among both C. jejuni (14.8%) and C. coli (5.2%), although this only included three sequence types (STs) and one ST, respectively. Multidrug resistance among strains of C. jejuni (0.9%) and C. coli (4.1%) was rare, and fluoroquinolone resistance, when present, was never accompanied by resistance to any other agent. Comparative genome analysis demonstrated that Australian isolates were found dispersed on different branches/clusters within the international collection. The major fluoroquinolone-resistant STs of C. jejuni (ST7323, ST2083, and ST2343) and C. coli (ST860) present in Australian chickens were similar to those of international isolates and have been reported previously in humans and animals overseas. The detection of a subpopulation of Campylobacter isolates exclusively resistant to fluoroquinolone was unexpected since most critically important antimicrobials such as fluoroquinolones are excluded from use in Australian livestock. A number of factors, including the low level of resistance to other antimicrobials, the absence of fluoroquinolone use, the adoption of measures for preventing spread of contagion between flocks, and particularly the genomic identities of isolates, all point to humans, pest species, or wild birds as being the most plausible source of organisms. This study also demonstrates the need for vigilance in the form of surveillance for AMR based on robust sampling to manage AMR risks in the food chain.IMPORTANCECampylobacter is one of the most common causes of gastroenteritis in humans, with infections frequently resulting from exposure to undercooked poultry products. Although human illness is typically self-limiting, a minority of cases do require antimicrobial therapy. Ensuring that Campylobacter originating from meat chickens does not acquire resistance to fluoroquinolones is therefore a valuable outcome for public health. Australia has never legalized the use of fluoroquinolones in commercial chickens and until now fluoroquinolone-resistant Campylobacter has not been detected in the Australian poultry. This structured survey of meat chickens derived from all major Australian producers describes the unexpected emergence of fluoroquinolone resistance in Campylobacter jejuni and C. coli Genetic characterization suggests that these isolates may have evolved outside the Australian poultry sector and were introduced into poultry by humans, pest species, or wild birds. The findings dramatically underline the critical role of biosecurity in the overall fight against antimicrobial resistance.

Antimicrobial Resistance and Virulence-Associated Traits of Campylobacter jejuni Isolated From Poultry Food Chain and Humans With Diarrhea

The objective of this study was to test the prevalence of virulence-associated markers and antimicrobial resistance in 624 C. jejuni isolated from poultry food chain, i. e., chicken feces (n = 160), poultry carcasses (n = 157), poultry meat (n = 152) and from humans (n = 155). All human strains were positive for 9 out of 13 putative virulence genes responsible for expression of pathogenic factors involved in different stages of the infection. The presence of all markers was also high in strains from chicken feces, carcasses and meat although not all of them were identified in 100% of the isolates. On the other hand, the virB11, wlaN, and iam putative pathogenic genes were detected in only 1.9, 15.2, and 20.5% of strains, respectively. C. jejuni isolates, irrespective of the origin, were highly resistant to ciprofloxacin (92.5% isolates), followed by nalidixic acid (88.9%) and tetracycline (68.4%). In case of ciprofloxacin, significantly more isolates from poultry feces, carcasses and meat were resistant than those obtained from humans and the same relationship was observed for tetracycline where the isolates from chicken feces were more often resistant than C. jejuni of carcasses and meat origin. A low number of strains was resistant to streptomycin (18.4% isolates) and only 5 strains (0.8%) displayed resistance to erythromycin. A relationship between resistance to fluoroquinolones and presence of selected pathogenic markers was observed, e.g., from 83.3% strains with the virB11 to 93.4% with the docA genes were resistant to ciprofloxacin. The isolates that did not possess any of the pathogenic traits were also mainly resistant to this antimicrobial, although the number of such strains was usually low, except virB11 (612 isolates), wlaN (529 strains), and iam (496 isolates). Furthermore, resistance to tetracycline was somehow associated with the presence of the virulence associated genes wlaN and virB11 (56.8 and 75.0% isolates, respectively). The present study shows a high antimicrobial resistance to quinolones and tetracycline of C. jejuni isolated along poultry food chain and from patients with diarrhea, which was closely correlated with the presence of several virulence genes playing a role in the pathogenesis of Campylobacter infection.