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The main objective of the study was to assess the microbiological quality of milk at different stages of the dairy value chain from farm to the factory in Bangladesh. A total of 438 raw milk samples (387 from primary producers, 32 from collectors, 15 from chilling plants, 4 from local restaurants) and 95 commercially processed milk samples were collected from northern part of Bangladesh. Almost 72% (n = 280) of samples at producer level and 100% from both collectors (n = 32) and chilling plants (n = 15) were contaminated with coliforms while 57% (n = 220) of samples from producers, 91% (n = 29) of samples from collectors and 100% (n = 15) from chilling plants were contaminated with fecal coliforms. Around 31% (n = 119) of samples from producers were positive for E. coli whereas >60% (n = 20) and 100% (n = 15) samples from collectors and chilling plants, respectively were positive for E. coli . One quarter of samples from collectors were positive for B. cereus and coagulase positive staphylococci and 33% (n = 5) of samples from chilling plants were positive for both of these microorganisms. In case of commercially processed milk, 77% (n = 46) and 37% (n = 22) of pasteurized milk samples had a high aerobic plate count (APC) (10 4  CFU/ml) and coliform count (>10 CFU/ml), respectively. None of the samples was positive for Shigella spp., Salmonella spp., and Campylobacter spp. Among 158 E. coli positive raw milk samples, 9% (n = 14) contained pathogenic E. coli , and enteroaggregative E. coli (EAEC) and Shiga-toxin producing E. coli (STEC) were found to be the predominant pathotypes. Of the 23 pathogenic E. coli identified from 14 samples based on their gene contents, >95% (n = 22) were resistant to at least one antibiotic and 13% (n = 3) of isolates were resistant to ≥3 classes of antibiotics. Several factors including the time of milking, hygiene practices of the producers, cow breed and amount of milk produced by the cow were found to be significantly associated with high APC of milk samples. In conclusion, both raw and commercially pasteurized milk are highly contaminated with fecal organisms. For intervention, more emphasis should be given at producer's level as microorganisms introduced to milk at this stage get the longest time for survival and multiplication. [ABSTRACT FROM AUTHOR]