Data generated on AMR trends will be helpful to inform policy and decision making for AMR containment
Photo for representation: iStock The Food and Agriculture Organization of the United Nations (FAO) and the Indian Council of Agricultural Research (ICAR) published the surveillance data of the Indian Network for Fishery and Animal Antimicrobial Resistance (INFAAR) for 2019-22. This is the first report on antimicrobial resistance (AMR) surveillance trends in fisheries and livestock sector from India.
INFAAR, a network of laboratories established under ICAR, along with technical support from FAO and the United States Agency for International Development (USAID), is dedicated to AMR surveillance in fisheries and livestock sectors. Currently, encompassing 20 laboratories, including 17 ICAR Research Institute Laboratories, one Central Agriculture University Laboratory, one State Agriculture University Laboratory, and one State Veterinary University, INFAAR aims for further expansion.
Antibiotic use in food animal production is known to be a driver for AMR. In this context, data generated on AMR trends will be helpful to inform policy and decision making for AMR containment.
Within the fisheries sector, three key production systems were covered — freshwater, brackish-water and marine. According to FAO definitions of aquaculture environments, freshwater systems include freshwater bodies like rivers or lakes, where salinity is typically below 0.5 per cent. Brackish-water systems involve sources such as estuaries and bays, where salinity ranges between 0.5 per cent and full-strength seawater. Marine production systems involve seawater environments, with salinity typically exceeding 20 per cent.
The panel of antibiotics tested included amikacin, ampicillin, amoxicillin-clavulanic acid, aztreonam, cefotaxime, cefepime, cefoxitin, ceftazidime, chloramphenicol, co-trimoxazole, enrofloxacin, gentamicin, imipenem, meropenem and tetracycline.
Two types of samples were collected across the three aquaculture systems: Fish or shrimp samples and pond or seawater samples. In total, 3,087 farms spanning 42 districts in 12 states of India were included in the survey.
Across all three systems, resistance was profiled for Staphylococcus aureus, coagulase-negative Staphylococcus species (CONS) and Escherichia coli. Additionally, freshwater systems were analysed for Aeromonas species, while both shrimp aquaculture and mariculture were assessed for Vibrio parahaemolyticus and Vibrio sp. Total number of bacterial isolates analysed were 6,789, which included 4,523 freshwater, 1,809 shrimp and 457 mariculture isolates.
Isolates of S aureus, known to cause a broad spectrum of infections in humans, exhibited high resistance against penicillin across all systems — shrimp (94.3 per cent), freshwater fish (91.4 per cent), marine fish (79.2 per cent). Erythromycin resistance was also observed in freshwater (34.3 per cent), shrimp (40.8 per cent), and marine isolates (18.8 per cent). Additionally, freshwater fish showed notable resistance to ciprofloxacin (54.8 per cent).
For CONS isolates, penicillin resistance across all systems was in the range of 76-91.5 per cent. Resistance to cefoxitin ranged from 18-38.5 per cent, while resistance to erythromycin varied from 22.6-36.1 per cent. CONS isolates are implicated in a range of clinically significant human infections, including skin and bloodstream infections.
In case of E coli, which also causes a range of common infections in humans, while isolates from freshwater were susceptible to most antimicrobials, they exhibited moderate resistance mainly against ampicillin (39.2 per cent) in shrimps. In marine samples, they showed higher resistance to cefotaxime (54.1 per cent) and cefpodoxime (66.9 per cent) as compared to freshwater and shrimp samples.
In addition, resistance patterns for Vibrio sp, which are prevalent in saltwater environments and associated with foodborne infections, were also documented in the shrimp and marine fish samples. Vibrio parahaemolyticus, a type of Vibrio species, was also specifically assessed.
In both cases, notable resistance was observed against ampicillin (56-59 per cent) in shrimp samples, while highest resistance was observed against cefotaxime (around 56 per cent) in marine samples. Aeromonas species, which was only studied in the freshwater fish samples, mainly showed resistance against cefoxitin (42.7 per cent).
The major food-producing animals included in this surveillance were cattle, buffalo, goat, sheep, pig and poultry. Out of a total of 5,983 samples across 32 districts which were collected, 2,076 E coli and 1,244 Staphylococcus isolates were characterised for their AMR profile using the same antibiotic panel as in the fisheries surveillance.
In E coli isolates, notable resistance was against cefotaxime (46 per cent) and ampicillin (41 per cent). Both S aureus and CONS isolates showed around 75 per cent resistance to penicillin. In addition, 41 of the total S aureus isolates (452) were found to be methicillin-resistant S aureus (MRSA), a drug-resistant variant of Staphylococcus.
For both E coli and Staphylococci, isolates from poultry origin exhibited higher resistance rates for all the tested antibiotics as compared to all the other food animals — ampicillin (53 per cent), cefotaxime (51 per cent), tetracycline (approximately 50 per cent), and nalidixic acid (47 per cent) and enrofloxacin (41 per cent).
The report analysed multidrug resistance (MDR) patterns in E coli isolates of aquaculture origin, revealing that 39 per cent of isolates exhibited MDR, which indicates resistance to three or more antimicrobial classes.
MDR was also detected in E coli isolates from food animal samples. The most prominent MDR was observed against a combination of cefotaxime-enrofloxacin and tetracycline (12.6 per cent), with approximately 15.8 per cent of poultry isolates exhibiting this simultaneous resistance.
Overall, 370 isolates of extended spectrum β-lactamase (ESBL) producing E coli and 292 isolates of AmpC type β-lactamase producers were also identified in the study. These pathogens are associated with MDR.
The report highlighted the conclusions and recommendations put forth by the INFAAR Advisory Board. While acknowledging the limited coverage of all regions in India in this surveillance, the report underscored that it provides a baseline data for further understanding AMR trends in India in the animal food sector and for evaluating the effectiveness of interventions.
The report showed low levels of resistance in both the fisheries and animal sectors to certain less commonly used antibiotics (such as chloramphenicol). It also documented notable levels of resistance to macrolides like erythromycin, quinolones such as ciprofloxacin, and third and fourth-generation cephalosporins like cefotaxime and cefpodoxime. All these are critically important antimicrobials with quinolones and third and fourth-generation cephalosporins being highest priority critically important antimicrobials. These observations suggest the need for judicious antibiotic use in food animal production systems like aquaculture and livestock.
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