Introduction: Escherichia fergusonii is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of E. fergusonii.Methods: Six E. fergusonii strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulo-mobilome analyses and pangenomics were performed for E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database.Results and discussion: Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E. fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR.

In light of the significant public health and food safety implications associated with Clostridium perfringens, this study aimed to isolate and characterize C. perfringens in samples obtained from broiler chicken retail points in Meghalaya, northeastern India. A total of 280 samples comprising meat, intestinal contents, water, and hand swabs were processed to detect contamination by C. perfringens. The isolates were subjected to toxinotyping, antimicrobial susceptibility testing, and biofilm-forming ability test. The overall occurrence of C. perfringens was 22.5% (17.74–27.85, 95% CI) with the highest recovery from intestine samples (31%; 22.13–41.03, 95% CI), followed by meat (23%, 15.17–32.49, 95% CI) and water samples (18%, 8.58–31.44, 95% CI). Type A was the predominant toxinotype (71.43%, 58.65–82.11, 95% CI), followed by Type A with beta2 toxin (17.46%, 9.05–29.10, 95% CI), Type C (7.94%, 2.63–17.56, 95% CI), and Type C with beta2 toxin (3.17%, 0.39–11.0, 95% CI). Nearly all (95.24%) isolates were multidrug resistant and 68.25% were biofilm formers. The predominance of multidrug-resistant and virulent Type A and Type C C. perfringens in retail broiler meat and intestines in the tribal-dominated northeastern region of India is of great concern from food safety and public health perspectives.

Toxoplasma gondii and Trichinella spp. are critical tissue-dwelling foodborne zoonotic parasites associated with pork consumption and pig rearing. Despite being a major pig-rearing region in the country, Northeastern India has not undergone any investigation regarding the presence of T. gondii and Trichinella spp. in pigs. Therefore, this study aims to determine the seroprevalence of T. gondii and Trichinella spp. and identify associated risk factors in pigs reared by tribal communities and small-holder livestock farmers in the northeastern region of India. In a cross-sectional serological survey, 400 pigs from 400 households across five northeastern states of India underwent testing for the seroprevalence of porcine toxoplasmosis and trichinellosis. Serum samples (80 from each state) were analyzed using commercially available ELISA assays. Data on backyard farm characteristics and various management aspects were collected, and risk factors linked with prevalence were analyzed through univariate and multivariate logistic regression analysis. The findings revealed that the apparent and true prevalence of anti-T. gondii antibodies were 45% (40.12–49.88, 95% CI) and 45.7% (40.7–50.69, 95% CI), respectively. As for anti- Trichinella antibodies, both the apparent and true prevalence were 0.75% (-0.1–1.6, 95% CI). The univariate and multivariate analyses indicated that age above 24 months (OR 7.20, 95% CI 2.45–23.71), exposure to cats (OR = 5.87, 95% CI 2.55–14.05), and farms operating for breeding purposes (OR = 5.60, 95% CI 3.01–11.04) were significant risk factors associated with the seroprevalence of T. gondii. This study marks the initial documentation of the seroprevalence of T. gondii and Trichinella spp. in pigs reared by tribal communities in Northeastern India. The results emphasize the significance of these parasites as foodborne zoonotic threats in the region, potentially posing substantial public health risks, especially within tribal and rural communities. The insights derived from this research could be valuable in formulating targeted preventive and control strategies against T. gondii and Trichinella spp. in pigs, not only in this region but also in areas with similar rearing practices.