Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which is an economically important disease in the poultry industry worldwide. The present study investigated O-serogroups, phylogenetic groups, antimicrobial resistance, and the existence of virulence-associated genes (VAGs) and antimicrobial resistance genes in 125 APEC isolates between 2018 and 2019 in Korea. The phylogenetic group B2 isolates were confirmed for human-related sequence types (STs) through multi-locus sequence typing (MLST). O-serogroups O2 (12.5%) and O78 (10.3%) and phylogenetic group B1 (36.5%) and A (34.5%) were predominant in chicken and duck isolates, respectively. Out of 14 VAGs, iucD, iroN, hlyF, and iss were found significantly more in chicken isolates than duck isolates (p < 0.05). The resistance to ampicillin, ceftiofur, ceftriaxone, and gentamicin was higher in chicken isolates than duck isolates (p < 0.05). The multidrug resistance (MDR) rates of chicken and duck isolates were 77.1% and 65.5%, respectively. One isolate resistant to colistin (MIC 16 μg/mL) carried mcr-1. The B2-ST95 APEC isolates possessed more than 9 VAGs, and most of them were MDR (82.4%). This report is the first to compare the characteristics of APEC isolates from chickens and ducks in Korea and to demonstrate that B2-ST95 isolates circulating in Korea have zoonotic potential and pose a public health risk.

The past two decades have seen the emergence of highly pathogenic avian influenza (HPAI) infections that are characterized as extremely contagious, with a high fatality rate in chickens, and humans; this has sparked considerable concerns for global health. Generally, the new variant of the HPAI virus crossed into various countries through wild bird migration, and persisted in the local environment through the interactions between wild and farmed birds. Nevertheless, no studies have found informative cases associated with connecting local persistence and long-range dispersal. During the 2016–2017 HPAI H5N6 epidemic in South Korea, we observed several waterfowls with avian influenza infection under telemetric monitoring. Based on the telemetry records and surveillance data, we conducted a case study to test hypotheses related to the transmission pathway between wild birds and poultry. One sedentary wildfowl naturally infected with HPAI H5N6, which overlapped with the home range of one migratory bird with H5-specific antibody-positive, showed itself to be phylogenetically close to the isolates from a chicken farm located within its habitat. Our study is the first observational study that provides scientific evidence supporting the hypothesis that the HPAI spillover into poultry farms is caused by local persistence in sedentary birds, in addition to its long-range dispersal by sympatric migratory birds.

Mycoplasma gallisepticum (MG) can cause respiratory disease in chickens and result in serious economic losses in the chicken industry. The use of live vaccines has been a favorable option for the control of MG infection in multi-age commercial layers and broiler breeders. There are three live vaccines, including ts-11, 6/85, and F strain, that have been commonly used in various parts of the world, including South Korea. The definitive diagnosis of the infection, therefore, requires the differentiation of wild-type field strains of MG from the vaccine strains used. Thus, we aimed to develop a novel multiplex PCR assay to discriminate between vaccine strains (ts-11, 6/85, and F strain) and wild-type field strains of MG isolated from infected chickens. We designed four novel primer sets that are each specific to MG species, ts-11, 6/85, and F strain. The multiplex PCR assay using the primer sets differentially identified wild-type and vaccine strains of MG but did not detect other avian bacteria. The detection limit of this assay was 250 fg/μL of genomic DNA of each strain tested. In addition, this assay was applied to 36 MG strains isolated from chickens over the past 20 years in South Korea. As a result, the assay identified 22 wild-type strains and 14 vaccine strains. Consequently, the novel multiplex PCR assay can discriminate between vaccine and wild-type field strains of MG and could be a valuable tool for the diagnosis of MG infection in MG-vaccinated chicken flocks.

Fowl typhoid, caused by Salmonella Gallinarum (SG), remains an important poultry disease. We characterized 136 SG isolates, one per farm, from diagnostic submissions of diseased chickens to the national veterinary laboratory in South Korea from 2002 to 2026, comparing two periods (2002–2010 and 2011–2026). Antimicrobial susceptibility was determined by broth microdilution, the spvB polyproline linker (PPL; the region joining the two functional domains of the SpvB virulence factor) was sequenced, and genetic relatedness was assessed by XbaI–pulsed-field gel electrophoresis (PFGE). Resistance to nalidixic acid was most frequent (93.4%), followed by streptomycin (83.1%) and ciprofloxacin (71.3%). Resistance to ampicillin, tetracycline, and nalidixic acid was less frequent in 2011–2026 (false discovery rate-adjusted p < 0.05), and these associations persisted after adjustment for chicken type. Multidrug resistance was detected in 52.2% of isolates, without significant change between periods. However, 13 of the 34 multidrug-resistant isolates from 2002–2010 were resistant to four or more antimicrobial classes, whereas all 37 from 2011–2026 were resistant to exactly three classes. Five PPL lengths of 13–21 prolines were identified, and their distribution differed between periods (p = 0.016). Isolates carrying ≥17 prolines were more frequent in 2011–2026 than in 2002–2010 (p < 0.01). PFGE yielded 61 pulsotypes in 27 clusters, with two dominant clusters detected across years and chicken types. These findings indicate that the PFGE-defined SG population showed temporal phenotypic changes within Korean poultry flocks, underscoring the need for continued surveillance of resistance and genotype.

Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum (SG) causes fowl typhoid, an important poultry disease, but the genetic diversity and phylogenetic relationships among Korean SG isolates remain insufficiently investigated. We analyzed 26 Korean SG isolates collected between 2002 and 2026 and compared them with 57 publicly available SG genomes from other countries using whole-genome sequencing. Using a cutoff of 100 core-genome single-nucleotide polymorphisms, 83 isolates were classified into eight clusters and ten singletons, with all Korean isolates assigned to the same cluster. Five sequence types (ST78, ST331, ST13540, ST14504, ST14529) were identified. ST78 was predominant, whereas ST14504 and ST14529 were identified exclusively among Korean isolates. Bayesian phylogenetic analysis estimated the time to the most recent common ancestor of the Korean isolates to be approximately 1990. Genomic analyses revealed differences in Salmonella pathogenicity islands, virulence genes, plasmid replicons, antimicrobial resistance genes, and quinolone resistance-determining region mutations. A resistance profile comprising aac(3)-VIa, aadA1, sul1, and qacEΔ1 was observed exclusively in 12 Korean isolates; of these, eleven harbored only the IncFII(S) plasmid replicon, and IncX1 was also detected in one isolate, together with bla_TEM-1B and tet(A). These findings provide valuable genomic and epidemiological insights into SG and may contribute to improved control of fowl typhoid.