The dairy industry, comprising 50% of the global livestock units (Baker et al., 2022; FAO, 2020) is a significant source of environmental dissemination and proliferation of antibiotic resistance (Baker et al., 2022). The current regulatory approaches have been ineffective in curbing the misuse of antibiotics in dairy farms (Gelband & Delahoy, 2014; Klein et al., 2021; Tacconelli & Diletta Pezzani, 2019), particularly in resource-constrained settings of low- and middle-income countries (LMICs), indicating the need to shift towards a disease prevention-based approach to reduce the need for antibiotic therapy (Pinto Jimenez et al., 2023; H. Singh et al., 2023). Since the disease prevalence in dairy farms is linked with infrastructural factors (floor type and ventilation) (A. K. Singh et al., 2020; Witkowska & Ponieważ, 2022) and operational practices (hygiene and footbaths) (Jacobs et al., 2019; Lindahl et al., 2019) improving infrastructure and operations could be key to controlling antibiotic resistance in the dairy environment. However, knowledge on the kind of infrastructure and operations that affect antibiotic resistance potential in dairy environment is missing, especially in resource-constrained dairy farms that are distinct and peculiar to top dairy producing countries, India and Pakistan (OECD/FAO, 2022).
Despite being the largest in the world (Global Livestock Populations, 2020; OECD/FAO, 2022) the Indian dairy sector, comprising primarily small homestead farms, has unique infrastructural features and relies mostly on manual labour, and is challenged by limited access to trained veterinary care, underdiagnosis of diseases, and easy access to antibiotics, which are frequently marketed directly to farmers (Chauhan et al., 2018, 2019; Jani et al., 2021; Mutua et al., 2020a; Tiseo et al., 2020; Van Boeckel et al., 2015). As a result, Indian dairy farms find themselves simultaneously susceptible to under treatment of sick animals (Chauhan et al., 2018; Sharma et al., 2020a) and misuse of antibiotics, including third- and fourth-generation antibiotics (Jindal et al., 2057; Ranjalkar & Chandy, 2019).
In 2020–2030, the dairy industry expects its highest growth in production in India and Pakistan (OECD/FAO, 2022). Concurrently, antibiotic consumption is also estimated to rise by 67%, with India emerging as the largest consumer of antibiotics by 2030 (Laxminarayan et al., 2020; Van Boeckel et al., 2015). Being among the largest dairy producers and antibiotic consumers, the Indian dairy industry could become a fertile ground for the emergence and selection of antibiotic resistance (Holmes et al., 2016; Laxminarayan et al., 2013). Up to 90% of the antibiotics used in dairy farms are excreted in whole or metabolized form (Wallace et al., 2018; Zhao et al., 2010). The co-selectors that are released from dairy farms can exert selection pressure on local bacteria (Peng et al., 2015, 2017; Sivagami et al., 2020; Tasho & Cho, 2016; Wichmann et al., 2014; Wu et al., 2023; Zainab et al., 2020; Zhang et al., 2019). Subsequent enrichment of the environmental resistome could present a public health challenge (Berendonk et al., 2015a) if the antibiotic resistance transfers to clinically relevant pathogens (Berendonk et al., 2015b; Brinkac et al., 2017; Smith et al., 2002). Exposure to livestock is a known risk factor for acquiring antibiotic resistance and is a threat to public health.(Landers et al., n.d.). In LMICs, such as India, where the dairy farms are usually very close to the human dwellings (N. Kumar et al., 2021), the risk of zoonotic transmission of antibiotic resistant pathogens and resistome is high (Dafale et al., 2020; Garcia et al., 2019; J. Li et al., 2019; Swarthout et al., 2022) and presents an occupational hazard for the exposed dairy farm workers and agricultural farmers (Kraemer et al., 2019; Xiong et al., 2018).
We investigated the effect of infrastructure type (herd size, housing system, ventilation level, type of floor, drain lining) and operations (dung and wastewater disposal and veterinary consultation) in dairy farms on the levels of ARGs in excrements and manure-amended soil. We collected dung, manure, wastewater, manure-amended soil, and control soil from sixteen dairy farms in Dehradun district, India during summer, monsoon, and winter. These sixteen dairy farms had varying herd sizes and distinct infrastructure and operations. We checked for the presence of twenty ARGs conferring resistance to sulfonamides (sul1, sul2), fluoroquinolones (parC, gyrA, qnrA), tetracyclines (tetA, tetO, tetW, tetM), polymyxin (mcr1, mcr2, mcr3, mcr4, mcr5), macrolides (ermF), glycopeptides (vanA), β-lactams (blaOXA1, blaTEM), multi-drug efflux pump (acrA, acrB) and one integron integrase gene cassette intI1, of which only eight ARGs (sul1, sul2, parC, mcr5, ermF, tetW, blaOXA1, blaTEM) and class 1 integrase-integron gene, intI1, were detected. The following were quantified using quantitative polymerase chain reaction (qPCR): mcr5, tetW, ermF, parC, sul1, sul2, intI1, and 16S rRNA gene copies. Some ARGs were associated with infrastructure (herd size, floor type, and ventilation) and operational practices (dung management and veterinary consultation). The ARG levels were higher during monsoon and summer than in winter, with animal-associated matrices (dung, manure, wastewater, and manure-amended soil) having higher potential for horizontal gene transfer. Dairy farm workers had greater ARG exposure while handling dung than manure and manure-amended soil.