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Chickens are the primary reservoirs of Campylobacterspp., mainly C. jejuniand C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacterspp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuniand 5 C. coliisolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobactersequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuniand 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 gyrAgene (Threonine-86-Isoleucine) and another in the rpsLgene (Lysine-43-Arginine) were detected. The blaOXAresistance gene was present in all isolates, the gyrAmutations was in 95.2% of C. jejuniand 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuniand 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuniisolates 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. coliisolates were resistant to all tested antimicrobials, while 1 C. coliwas 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 Campylobacterisolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacterspp. in Thai chicken production systems.

Many studies have examined avian pathogenic Escherichia coli(APEC) from commercial broilers but few have examined isolates from native chickens. This study compared APEC isolates from commercial broilers and native chickens in regard to the phylogenetic group and the phenotypic and genotypic antimicrobial resistance profiles. From 100 suspect colibacillosis cases in both commercial broilers and native chickens, a total of 90 broiler isolates and 42 native chicken isolates were identified as E. coliby biochemical tests. Phylogenetic grouping revealed that 90 broiler APEC isolates belonged to A group (5.56%), B1 group (22.22%), B2 group (31.11%), and D group (41.11%). The 42 native chicken APEC isolates belonged to A group (35.71%), B1 group (26.19%), B2 group (30.95%), and D group (7.14%). The difference in the allocation to groups A and D of the 2 isolate types was significant (P< 0.05). The APEC broiler isolates had a significantly higher multidrug-resistant (MDR) rate (80%) than the native chicken isolates (14.29%) (P< 0.05). The APEC broiler isolates demonstrated significantly higher resistance rates than the native chicken isolates for amoxicillin (98.89%; 78.57% respectively), chloramphenicol (42.2%; 9.5%), enrofloxacin (68.9%; 7.1%), gentamicin (11.1%; 0%), nalidixic acid (72.2%; 7.1%), sulfamethoxazole + trimethoprim (45.6%; 2.4%), and tetracycline (88.9%; 76.2%) (P< 0.05). The APEC broiler isolates had a significantly higher presence compared with the native chicken isolates of the following resistance genes:- by blaTEM(43.3%; 21.4%, respectively), cml-A(34.4%; 2.4%), tetA(76.7%; 40.5%), tetB(26.7%; 0%), sul2(23.3%; 14.3%), and dhfrI(13.3%; 0%) (P< 0.05). The qnrBand qnrSgenes were detected (12.16%; 72.97% respectively), in the APEC broiler isolates resistant to nalidixic acid and/or enrofloxacin while only qnrSgenes was detected in all 3 APEC native chicken isolates. Regarding the point mutations of gyrAand parC, all isolates were positive to gyrA83S, gyrA87D, gyrA87L, gyrA87NY, parC80S and parC80I except that gyrA83S was not present in 20 APEC broiler isolates. Antimicrobial stewardship programs should be targeted at the backyard poultry sector as well as the commercial poultry sector.