Published Academic Study Confirms Higher Prevalence of Anti-Microbial Resistant Bacteria in Imported, Farm-Raised Shrimp

On Tuesday, Nature’s Scientific Reports published an article by Laxmi Sharma, Dhruv Patel, Dr. Ravinder Nagpal, and Dr. Prashant Singh of Florida State University and Dr. Charlene Jackson of the Bacterial Epidemiology and Antimicrobial Resistance Research Unit of the U.S. Department of Agriculture (USDA), Agricultural Research Service characterizing the prevalence of antibiotic-resistant bacteria and gut microbiome communities in shrimp sold for consumption in the U.S. market.  Dr. Singh and his team found that there was a substantially higher prevalence of multi-drug resistant (MDR) strains of bacteria in imported shrimp than in U.S. wild-caught shrimp.  The researchers observed that “[t]he higher abundance of these antibiotic-resistance genes in farm-raised shrimp can be attributed to the application of antibiotics for aquaculture operations facilitating the selection of strains with resistance genes.”

For the study, the researchers took a total of thirty-one shrimp samples (thirteen cooked and eighteen raw shrimp) from eight different countries (seven U.S. wild-caught and twenty-four imported) and attempted to isolate and characterize antibiotic-resistant bacteria from these samples.  Their analysis found greater prevalence of multi-drug resistant pathogens in imported, cooked shrimp, with high aerobic plate counts (APC) for cooked shrimp imported from India and Vietnam.  Dr. Singh’s team also reported that they had isolated and identified strains of the pathogen Stenotrophomonas maltophilia in cooked shrimp from Vietnam, the first time that such bacteria had ever been isolated in cooked shrimp samples.

Although the study observes that “[c]ommercially available cooked shrimp samples with high APC are not likely to cause infection in healthy individuals,” it also warned that “the consumption of frozen shrimp harboring antibiotic-resistant strains of opportunistic pathogens can lead to serious illnesses, particularly in immunocompromised populations.”  The study explained that “FDA cooking recommendations are focused on mitigating Listeria monocytogenes in cooked shrimp, which may not be effective to eliminate antibiotic-resistant bacteria spread over multiple genera.”  The authors argued that their results required revisiting safety guidelines for cooked shrimp:

“The data demonstrate that the presence of [multi-drug resistant] bacterial strains and opportunistic pathogens in imported cooked shrimp products may pose a threat to human health and calls for the need for standardization of effective cooking time-temperature combination[s] for potential mitigation of antibiotic-resistant strains in cooked shrimp samples.”

The researchers made clear that the indiscriminate use of antibiotics in shrimp aquaculture overseas likely contributed to the development of antimicrobial-resistant pathogens: “The higher abundance of these antibiotic-resistance genes in farm-raised shrimp can be attributed to the application of antibiotics for aquaculture operations facilitating the selection of strains with resistance genes.”  Further, the study warned that “[t]he widespread trade of shrimp can act as a vehicle for the dissemination of antibiotic-resistant genes.”  Because “the FDA relies on only testing antibiotic residue in imported seafood . . the presence of [multi-drug resistant] strains in cooked shrimp samples points toward a gap in monitoring measures.”

The publication of this study comes on the heels of the release of a report last month by the Federation of Indian Animal Protection Organisations (FIAPO) (Aquaculture: An Investigation on Trends and Practices in India) summarizing that organization’s findings following the investigation of 241 aquaculture farms in India.  FIAPO reported discovering antibiotics being “used in 40% of the grow out farms prophylactically to prevent the incidence of diseases . . .”  Discussing its review of farms in the state of Andhra Pradesh, FIAPO observed that “[t]here were frequent disease outbreaks at shrimp farms” and that “farmers admitted to the use of antibiotics.”  FIAPO also found that they did not visit a single aquaculture farm that maintained effluent treatment facilities; “[t]he effluents were being released directly into the nearby estuaries/canals.”

FIAPO’s report rang alarm bells regarding the danger posed by the overuse of antibiotics in Indian aquaculture:

“Throughout the investigation we found that farmers heedlessly administer antimicrobial and growth promoters to the fish and shrimps.  Aquaculture is pushing us closer to the next AMR (antimicrobial resistance) catastrophe.  UN has declared AMR as a ‘global health emergency’.”

However, FIAPO also found that there were signs that Indian shrimp aquaculture, in particular, was capable of remedying antibiotic abuse provided that strong measures prohibiting the presence of antibiotic residues in shrimp were enforced by the markets to which Indian shrimp was exported:

 “As the majority of the shrimp produced is exported, we found that shrimp farms had good potential to self-regulate the water quality.  Other factors contributing to this were the involvement of wealthy entrepreneurs who can afford basic and advanced requirements of shrimp farming, [and] strict regulations imposed by EU, Japan, US and other countries importing shrimp from India.”

Beyond the findings made by Dr. Singh and his team regarding antimicrobial resistant pathogens in imported shrimp sold in the U.S. market, their study published earlier this week additionally sought to characterize and compare the gut microbiome diversity of wild-caught shrimp from the United States and farm-raised shrimp from Ecuador.  The researchers found that, compared to domestic wild-caught shrimp, imported farm-raised shrimp “showed clearly distinct microbiome composition . . .,” and, as such, might provide an ability to distinguish between wild-caught and farm-raised shrimp (“These differentially abundant markers could be considered as potential metagenomic biomarkers for the identification of shrimp from Ecuador (farm-raised) and the U.S. (wild-caught).”).

This finding follows the publication of an earlier study in the journal LWT – Food Science and Technology in August 2020 conducted by Dr. Singh, Laxmi Sharma, and Dr. Evelyn Watts of Louisiana State University in which the authors, building on the published work of European researchers in 2017, developed and confirmed an assay test that “can be used as rapid, low-cost, and reliable method for the identification” of different shrimp species commonly found in the U.S. market (Litopenaeus vannamei; Penaeus duorarum; Penaeus monodon; Litopenaeus setiferus; and Pleoticus muelleri).  As the researchers explain, the development of this rapid test potentially provides a powerful weapon through which to combat seafood fraud:

“To the best of our knowledge, this is the first real-time [polymerase chain reaction (PCR)] assay for specific identification and [differentiation of] Atlantic white shrimp, Pink shrimp, Pacific white shrimp, Black tiger shrimp, and Argentine red shrimp.  This low-cost assay can be useful for identification of shrimp species, prevention of misrepresentation of commercially available shrimp and suitable for implementation by [the] NOAA SIMP program.”

Dr. Singh, along with Laxmi Sharma, Dr. Charlene Jackson of the USDA, and Dr. Nagaraju Indugu of the University of Pennsylvania, additionally announced a draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a sample of farm-raised Ecuadorian shrimp in a notice published in December 2020 in the American Society for Microbiology’s Microbiology Resource Announcements.

Last year, prior to the formal publication of any of these studies and findings, Dr. Singh attended the Southern Shrimp Alliance’s annual meeting, describing the work being conducted in his laboratory.  “Even though there are a lot of words in these studies that I could not pronounce, much less spell, with a gun to my head, it is clear that Dr. Singh and his collaborators are doing cutting edge research,” said John Williams, the Executive Director of the Southern Shrimp Alliance.  “Our industry and the U.S. consuming public is fortunate that this incredible team of PhDs and graduate students have turned their attention to addressing the grave global health threat posed by the unwarranted use of antibiotics in shrimp aquaculture overseas.”

Read L. Sharma, R. Nagpal, C.R. Jackson, D. Patel, & P. Singh’s Antibiotic-Resistant Bacteria and Gut Microbiome Communities Associated with Wild-Caught Shrimp from the United States Versus Imported Farm-Raised Retail Shrimp, Scientific Reports (Nature) (Feb. 8, 2021) here:

Read N. Indugu, L. Sharma, C.R. Jackson, & P. Singh’s Whole-Genome Sequence Analysis of Multidrug-Resistant Enterobacter Hormaechei Isolated from Imported Retail Shrimp, American Society for Microbiology’s Microbiology Resource Announcements (Dec. 10, 2020) here:

Read the abstract of L. Sharma, E. Watts, and P. Singh’s High Resolution Real-Time PCR Melting Curve Assay for Identification of Top Five Penaeidae Shrimp Species, LWT – Food Science and Technology (Aug. 1, 2020) here:

Read the Federation of Indian Animal Protection Organisations’ (FIAPO) Aquaculture: An Investigation on Trends and Practices in India (Jan. 2020) here:


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