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Sharma, L. (2020). Antibiotic Resistance, Gut Microbiome Communities and Species Identification in Retail
Shrimp. Retrieved from https://purl.lib.fsu.edu/diginole/2020_Summer_Fall_Sharma_fsu_0071N_16203
In the United States (US), farm-raised shrimp accounts for ~80% of the total shrimp market share. Farmed shrimp are cultivated as monoculture and are susceptible to infections. The aquaculture industry is dependent on the application of antibiotics for disease prevention, resulting in the selection of antibiotic-resistant (ABR) bacteria. We aimed to characterize the prevalence of ABR bacteria and gut microbiome communities in commercially available shrimp. Thirty-one raw and cooked shrimp samples were purchased from supermarkets in Florida and Georgia (US). The samples were processed for the isolation of ABR bacteria and isolates were characterized using an array of molecular and antibiotic susceptibility tests. Aerobic plate counts of the cooked samples (n=13) varied from 3 log CFU/g to 6.4 log CFU/g. The 110 isolates obtained in this study were spread across 18 bacterial genera, comprising of coliforms and opportunistic pathogens. Interestingly, isolates from cooked shrimp showed higher resistance towards chloramphenicol (18.6%) and tetracycline (20%) while those from raw shrimp exhibited low levels of resistance towards nalidixic acid (10%) and tetracycline (8.2%). Compared to wild-caught shrimp, the imported farm-raised shrimp harbored distinct gut microbiota communities. The presence of ABR strains in cooked shrimps calls for change in processing specifications for their mitigation.Penaeidae shrimp species are known to share morphology characteristics and identification based on morphological appearance becomes more challenging when shrimp is processed into cooked products. Misrepresentation of shrimp is common in commercially available shrimp. The objective of the study was to develop a high-resolution melting (HRM) RT PCR assay targeting the 16S rRNA gene fragment for specific identification of the top five penaeid species, Litopenaeus vannamei, Penaeus duorarum, Penaeus monodon, Litopenaeus setiferus, and Pleoticus muelleri. The applicability of assay was evaluated using two DNA extraction kits and two RT PCR master mixes. The HRM assay was evaluated using 43 shrimp samples using sequence known positive control, and results were validated by sequencing shrimp 16S rRNA gene fragment. Assay standardized in this study formed a distinct melt curve profile for each species in the normalized and differential melt curve plots. The assay using Apex qPCR 2× GREEN master mix showed 100% sensitivity and specificity. Further, species identification results obtained by HRM assay were in complete agreement with identification achieved by 16S rRNA gene sequencing. The HRM assay developed in this study can be used as a rapid, low-cost, and reliable method for the identification of the abovementioned shrimp species.
A Thesis submitted to the Department of Nutrition, Food, and Exercise Sciences in partial fulfillment of the requirements for the degree of Master of Science.
Sharma, L. (2020). Antibiotic Resistance, Gut Microbiome Communities and Species Identification in Retail
Shrimp. Retrieved from https://purl.lib.fsu.edu/diginole/2020_Summer_Fall_Sharma_fsu_0071N_16203