This study analyzed various organic fertilizers for indicator microorganisms, pathogens, and antibiotic-resistant Escherichia coli, and evaluated the growth potential of E. coli O157:H7 and Salmonella in fertilizers. A microbiological survey was conducted on 103 organic fertilizers from across the United States. Moisture content ranged from approximately 1% to 86.4%, and the average pH was 7.77. The total aerobic mesophiles ranged from approximately 3 to 9 log colony-forming units (CFU)/g. Enterobacteriaceae populations were in the range of <1 to approximately 7 log CFU/g, while coliform levels varied from <1 to approximately 6 log CFU/g. Thirty samples (29%) were positive for E. coli, with levels reaching approximately 6 log CFU/g. There were no confirmed positives for E. coli O157:H7, Salmonella, or Listeria monocytogenes. The majority of E. coli isolates (n=73), confirmed by glutamate decarboxylase (gad) PCR, were from group B1 (48%) and group A (32%). Resistance to 16 antibiotics was examined for 73 E. coli isolates, with 11 isolates having resistance to at least one antibiotic, 5 isolates to ≥ 2 antibiotics, and 2 isolates to ≥ 10 antibiotics. In the presence of high levels of background aerobic mesophiles, Salmonella and E. coli O157:H7 grew approximately 1 log CFU/g within 1 day of incubation in plant-based compost and fish emulsion-based compost, respectively. With low levels of background aerobic mesophiles, Salmonella grew approximately 2.6, 3.0, 3.0, and 3.2 log CFU/g in blood, bone, and feather meals and the mixed-source fertilizer, respectively, whereas E. coli O157:H7 grew approximately 4.6, 4.0, 4.0, and 4.8 log CFU/g, respectively. Our results revealed that the microbiological quality of organic fertilizers varies greatly, with some fertilizers containing antibiotic resistant E. coli and a few supporting the growth of foodborne pathogens after reintroduction into the fertilizer.

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We compared the effectiveness of three PCR protocols for the detection of Bifidobacterium adolescentis and one PCR protocol for detecting Bacteroidales as indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration of B. adolescentis DNA was recovered from sewage samples on the 0.2 μm filters compared to the 0.45 μm filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999), B. adolescentis was detected only in undiluted sewage samples. The King method (2007) performed well and detected B. adolescentis in all of the sewage dilutions (from undiluted to 10−4). In contrast, the Bonjoch approach (2004) was effective at detecting B. adolescentis at lower dilutions (10−3) of sewage samples and it gave false positive results with some (3/8) pig fecal samples. Human-specific Bacteroidales (HuBacs) were detected in the lower diluents of sewage samples but was positive in pig (6/8) and cattle fecal samples. PCR detection of B. adolescentis in marine samples from Puerto Rico and freshwater samples from Georgia indicated that the PCR method of King et al. (2007) and the modified Layton method for HuBac were in agreement in detecting human fecal pollution in most sites.

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