RATHNAMMA)M. NASIM2024-01-092024-01-092022https://krishikosh.egranth.ac.in/handle/1/5810206018A study was conducted to monitor the presence, antimicrobial resistance (AMR) phenotype and genotype of Salmonella and E. coli in the entire commercial broiler supply by collecting 232 samples from Broiler breeder farms (BBF), hatcheries, commercial broiler farms (CBF) and retail meat shops (RMS). It was evident that enrichment in TTB followed by colony PCR was rapid and specific; however, BGA and XLT4 were more specific media for isolation of Salmonella. The overall presence of Salmonella and E. coli in complete poultry supply chain was 20 and 72 per cent, respectively. A significant higher (P<0.05) presence of Salmonella was observed in RMS (46%) followed by CBF (19%), and hatcheries (10%). The presence of E. coli in BBF, hatcheries, CBF and RMS were 48, 83, 70 and 91 per cent, respectively. Antimicrobial resistance based on disc diffusion assay and MIC revealed that all the E. coli and Salmonella isolates were resistant to at least one of the antibiotics and 75 & 76 per cent of the isolates were multidrug resistant (MDR) respectively. In complete poultry supply chain E. coli and Salmonella showed highest resistance to doxycycline (97 & 94%), followed by fluoroquinolone, gentamicin, β lactam, sulphonamides and colistin and lesser resistance to phenicols and neomycin. All E. coli and Salmonella isolates were screened for the presence of 35 antimicrobial resistant (AMR) genes belonging to seven groups of antibiotics by PCR and it was observed that the overall presence of AMR genes among the E. coli and Salmonella isolates was 69 and 60 per cent respectively. Among the AMR genes, highest presence was recorded for tetA (69%), followed by blaTEM, mcr2-5, aac(6’)-Ib-cr, qnrS, qnrD, cmlA1, sul1, catA2, qnrB, blaCTX-M, blaSHV, mcr-1, catA1, blaOXA and OqxAB in Salmonella and qnrB, qnrS, blaTEM, aac(6’)-Ib-cr, blaCTX-M, mcr1-5 (19.59%), qepA, mcr-4, cmlA1, sul1, catA1, blaSHV, catA2, qnrD, blaOXA and sul2, blaCTXM group2, gropu9, &gropu8/25 in E. coli. There was fair to significant correlation between AMR phenotype and genotype. AMR E. coli and Salmonella and genes encoding AMR were present throughout the poultry supply chain, however CBF and RMS were the major focal points of AMR. No significant difference in presence of AMR E. coli could be observed during the crop cycles in CBF, as presence was observed at all the intervals indicating the need for efficient monitoring and control strategies for effective prevention of AMR in complete poultry supply chain.EnglishThesis