Antibiotic usage, residues and resistance genes from

Journal of Environmental Chemical Engineering xxx (xxxx) xxx–xxx

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Antibiotic usage, residues and resistance genes from food animals to human and environment: An Indian scenario Krishnasamy Sivagami, Vijayan Jaya Vignesh, Ramya Srinivasan, Govindaraj Divyapriya, ⁎ Indumathi M. Nambi Environmental and Water Resources Engineering Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, 600036, India

A R T I C L E I N F O

A B S T R A C T

Keywords: Antibiotics Resistance genes Food animals Indian scenario Super bugs

Antibiotics are majorly used in food animals for growth promotion and prophylactic purposes in public health and environment. The aim of this review is mainly to discuss about the antibiotics usage in poultry, livestock and aquaculture sectors, particularly in India, and the identification of antibiotic resistance in animals, their corresponding antibiotic resistance genes (ARGs) (if investigated) and their dissemination among environmental compartments in various parts of the country. It also discusses about the classification and mechanism of action of different antibiotics. It reports the risks, benefits, ARGs development mechanisms from food animals to humans and to the environment. Most of the current studies are done in the medical field on regulating/restricting antibiotic usage and tracking the propagation of ARGs in bacterial samples of sick patients and also report the identification of antibiotics and ARGs in wastewater treatment plant effluents across various countries. This study mainly reviews the evolution and transportation of ARGs in detail for Indian scenario.

1. Introduction In recent times, the occurrence and detection of pharmaceutically active compounds in the aquatic environment is a serious health concern. Rampant use of antibiotics in hospitals, livestock, poultry and aquaculture farms, indiscriminate disposal of waste and wastewater from municipalities, animal farms and pharmaceutical industries into rivers, lakes and other water bodies over the years, have contributed to the development of the mammoth problem of antibiotic resistance. Further, animal protein intake grew in Asia, it increased from seven to twenty-five grams per capita in five decades [1]. Consequently, the quantity of diet obtained from rice and wheat progressively decreased. To meet the growing demand, developing countries have moved towards highly cost-efficient and vertically integrated intense poultry, livestock and aquaculture production systems. Moreover, a study conducted by Ramanan Laxminarayanan states that, the antibiotic use in food animals will increase by 82 per cent in India by 2030 [2], which would be quite an alarming increase. Most of the antibiotic dose (30–80%) given to food animals are excreted because of partial metabolization of antibiotics. In addition, animal feed-containing antibiotics that are not consumed by animals will reach the soil sediments directly. Another source of antibiotics entering the environment is through manure. Solid waste generated from animal farms is mostly used as manure (called as farm yard ⁎

manure) to fertilize the soil [3]. However, most of the antibiotics leach during run off and end up in aquatic systems such as rivers and lakes. In spite of knowing the fact that antibiotics have been entering the environment through various sources, only a very few research investigations have been done on the fate and transport of antibiotics present in storage-manure or animal excreta. It is also known that the natural soil microbial communities get affected severely due to the presence of broad spectrum antibiotics in soil. It results in the emergence of ARGs in the soil bacteria and creates “super bugs” which severely impact the human and environmental health [4]. Aquaculture sector uses antibiotics for prophylactic purposes, as therapeutic measures and as feed additives [5]. Very few drugs like oxytetracycline hydro chloride, sulfamerazine and a combined preparation that contains sulfadimethozine and ormetoprim have been approved by FDA for use in aquaculture in developed countries. On the other hand, less stringent guidelines in developing countries like India have led to rampant and reckless use of unapproved drugs in aquaculture [6]. It is a fact that 70–80% of the antibiotics used in aquatic farming end up in the environment. The reason for these antibiotics to end up in environmental compartments is partial/incomplete metabolism, which leads to development of antimicrobial resistance (AMR) in the exposed bacteria [7]. Hence, there is a need to track the fate and transformation of antibiotics during their metabolism and transfer into the food chain and to identify forms of antibiotics in animal products

Corresponding author. E-mail address: [email protected] (I.M. Nambi).

https://doi.org/10.1016/j.jece.2018.02.029 Received 15 November 2017; Received in revised form 7 February 2018; Accepted 16 February 2018 2213-3437/ © 2018 Elsevier Ltd. All rights reserved.

Please cite this article as: Krishnasamy, S., Journal of Environmental Chemical Engineering (2018), https://doi.org/10.1016/j.jece.2018.02.029


K. Sivagami et al.

mechanisms are summarized in Table 1 [15].

and waste. Antibiotic resistant bacteria (ARB) thrive in soil all over the world because soil contains a lot of antibiotic-producing strains. For instance, Actinomycetes is the most ubiquitous soil bacteria, and has the potential to synthesize more than half of the world’s antibiotics (such as erythromycin, streptomycin and tetracycline) [8]. If the soil is laden with antibiotics, then that is the best possible route for spreading antibiotic resistance through manure and other agricultural practices. Especially, opportunistic pathogens like Acinetobacter and Pseudomonas when present in the soil, due to their intrinsic capability to develop resistance, acquire ARGs from the natural environment (soil) and they become ARBs [9]. [10] stated that 480 Streptomyces strains cultured from soil were tested for 21 antimicrobials and it was found that the strains were multi-drug resistant, on an average, to 8 antimicrobials. The most interesting revelation was that 2 strains were resistant to about 15 drugs. Thus, in nature, soil presents a single high potential reservoir of ARGs; if the resistance can be passed on to pathogens, there will be a linkage between the environment and human health to a great extent [11]. ARGs are often positioned on mobile genetic elements like plasmids and transposons, which ensure the spread by horizontal gene transfer. Mobile elements like plasmids harbor a lot of ARGs which have been found in clinically relevant pathogens found in soil and water like Salmonella, Shigella, Escherichia, Aeromonas, Pseudomonas and Klebsiella [12].

3. Antibiotics and ARGs Residues of antibiotics are released into the environment due to incomplete absorption and metabolic activities of food animals. Antibiotics from food supplement may be lost either through leaching or elimination by urine and feces. The possibility of antibiotics reaching the environment depends on their properties, bio-availability and surrounding environmental characteristics [71]. Development of antibiotic resistance is considered to be a major risk factor in addition to possible toxicity, allergy or carcinogenicity to humans [6]. The bacteria which have acquired resistance against antibiotics are called Antibiotic Resistant Bacteria (ARB) [29]. ARBs are capable of transferring their resistance gene to other bacteria through plasmid DNAs by Horizontal Gene Transfer (HGT) by disseminating the ARG among other bacteria. ARBs also use genetic elements such as integrons, transposons and bacteriophages to disseminate the ARG. ARGs are considered to be emerging environmental contaminants because once they are into the system; they are capable of spreading the antibiotic resistance to other bacterial cells in the system as well. This dissemination of antibiotic resistance may happen by one or more of the following ways [30,15]. (i). Horizontal gene transfer (HGT) (occurs between pathogens, non-pathogens and also between distantly related bacterial species). (ii). Multiple antibiotic resistant (MAR) integron – one antibiotic co-selecting for resistance to other antibiotics (iii). Persistent nature of DNA – on the death of ARG-containing cells, there occurs the release of DNA into the surrounding environment. The DNA which has been released is quite persistent and protected due to certain soil compositions. Thus, the DNA is transformed into other bacterial cells which are alive and hence resistance is further passed on. iv) Another way of transmission of resistance is, DNA sending messages to the ribosome (rRNA 50S and 30S sub units) to produce poly peptides or proteins for growth. When the bacterium is ready to divide, the DNA uncoils, and the rapid prolific bacteria has more chance to develop mutants which also increases the antibiotic resistance.

2. Classification and mechanism of action of antibiotics Food animals are injected with antibiotics to take care of the clinical disease, to avoid general disease events and to promote growth. The use of antibiotics in food animals are classified as prophylactic and subtherapeutic use. Following are the twelve classes of antibiotics that are used during the life cycle of food animals, (1) arsenicals, (2) polypeptides, (3) glycolipids, (4) tetracyclines, (5) elfamycins, (6) macrolides, (7) lincosamides, (8) polyethers, (9) beta-lactams, (10) quinoxalines, (11) streptogramins, and (12) sulfonamides [13]. World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Drug Administration (FDA) stated that fluoroquinolones, 3rd and 4th generation cephalosporins and macrolides as “critically important” antimicrobial agents [14]. Antimicrobial agents are frequently used to treat various epidemic events and used for various purposes in livestock populations. Each family or subgroup of antimicrobials has its own purpose and mode of action to target species. Hence, each microbial species counters the antimicrobial agents with specific defense/ resistance mechanism(s) for its survival. The main antimicrobial families, their mode of action and their general resistance development

3.1. Antibiotic resistance – occurrence and dissemination The contamination issue does not stop at the point of occurrence of antibiotics; it includes the presence of ARGs as well in the environment which is becoming a major global threat in recent years. The antibiotics widely used in livestock, poultry and aquaculture have been studied, are listed in the table below (Table. 2), to understand the possible direct impacts of improper use and/or disposal of antibiotics. It is important to

Table 1 Classification of antibiotics used in food animals [15]. Drugs Classification

Mode of action

Resistance mechanism

Sulfonamides Sulfadiazine

Purine synthesis of DNA which interferes folic synthesis rRNA binds with 50S sub-unit which prevents protein production

Chromosome mutation, plasmid and integron mediated resistance Methylation of 23S sub-unit of rRNA prevents binding and drug inactivation Inducible efflux in E. coli (Tet A, Tet B) Binding site changes (Tet O, Tet M) β lactamase production primarily changes cell wall proteins so that they cannot bind to penicillin binding proteins. Target modification − DNA gyrase Decreased permeability- outer membrane porins mutation Methylation of rRNA in gram positive organisms and inhibits binding Phosphorylation and adenylation of amino glucoside stops the binding Resistance mechanism varies depending upon the type of antibiotics

Lincosamide Macrolides,Tialmulin Tetracyclines Penicillin, Beta lactamase sensitive, Other penicillins, cephalosporins Quinolones, Flouro quinolones Macrolides/ Azalides Aminoglycosides

Others

Inhibits cell wall production and binds enzymes which help form peptidoglycans Interfere in DNA breakage −reunion step by binding DNA-gyrase Binding of rRNA to 50S sub unit which inhibits transpeptidation and production of protein

rRNA binds to sub units which inhibits protein and cell wall production

2

3

Salmonella

S. aureus Shiga toxin producing E. coli (STEC) and non-STEC isolates

35 Enterococcus isolates

Non-typhal salmonella isolates E. coli

Poultry

Bovine Bovine

Ducks

Poultry Poultry, humans, bovine, equine, sheep Piglets

82 Vibrio parahaemolyticus isolates

Fin fish

In addition, referred to CDDEP, 2017.

34 isolates Salmonella 770 isolates of Vibrio cholerae

40 salmonella isolates

240 salmonella isolates

704 salmonella strains

Cuttlefish and prawn Fin fish, shell fish and crustaceans

SeafoodFish and crustace

E. coli

Livestock-Bovine

774 isolates of E. coli

Micro-organisms

Animal

Table 2 Representative studies on antibiotic resistance in India.

Ampicillin, cefpodoxime, streptomycin, carbenicillin, cephalothin, amoxicillin, colistin, tetracycline, naxidic acid

16 antibiotics were tested Polymyxin-B, cephalothin, chloramphenicol, streptomycin, tetracycline, oxytetrcycline, sulfadiazene

Bacitracin (98.7%), chloramphenicol (6.7%), gentamycin (16.2%), nalixidic acid (11.7%), neomycin (53.3%), novobiocin (90%), oxytetracycline (46.2%), penicillin G (92.9%), polymixin B (18.8%), streptomycin (19.6%) Multiple antibiotic resistance genes were tested for their presence

Oxytetracycline Cloxacillin, cephaloridine, oxytetracycline, ampicillin, amoxicillin, chloramphenicol, trimethoprim-sulphamethaxazole, doxycycline, chloramphenicol Ampicillin, erythromycin, nalidixic acid, oxytetracycline, sulfadiazine, cefixine, lincomycin, roxythromycin, penicillin chloramphenicol

Chloramphenicol, gentamycin sulphate. Lincosamide and macrolidebased antibiotics were also tested

Levoflaxin, chloramphenicol, norfloxacin, ciprofloxacin, gentamycin, oxytetracycline Erythromycin, tetracycline, gentamycin, lincomycin Tetracycline,cephalexin, enrofloxacin, kanamysin, cephaloridine, ampicillin, amikacin

Nitrofurantoin, co-trimoxazole, tetracycline,ampicillin

Antibiotics tested

25% of the drugs were multidrug resistant and 67.5% were resistant to 2 or more of the tested antibiotics All the salmonella strains were susceptible Polymyxin-B, cephalothin andchloramphenicol were found to be sensitive. Streptomycin, tetracycline, oxytetrcycline, sulfadiazine had greater than 25% resistant strains. Significant number of tested finfish samples had ARB. Greater than 80% of the isolates showed resistance against ampicillin, cefpodoxime, streptomycin, carbenicillin, cephalothin. 63% and 77% of the isolates displayed resistance against amoxicillin, colistin. All the isolates were sensitive to tetracycline and naxidic acid

95.4% of the isolates were found to be resistant to the antibiotics tested 98.7% of the strains were resistant to Bactracin, Novobiocin and penicillin G

Greater than 80% resistant to the antibiotics tested

Out of 111 isolates, about 20–30% were resistant Out of the STEC strains, 17% were found to have eaeA gene and among non-STEC strains, 14.28% had eaeA. All STEC were resistant to 3 or more of the antibiotics tested. All of them were non-sensitive to cephalexin and kanamycin Lincosamide and macrolide antibiotics were not effective. Enterococcus isolates were found to be susceptible to gentamycin sulphate and chloramphenicol All the strains were resistant to oxytetracycline 63.2% of the isolates displayed resistance towards atleast one drug and out of which multi-resistant were 41%

10 out of the total (14) tested isolates were resistant to either one or more of these antibiotics 100% of the isolates were resistant to the antibiotics of concern

Details

[21]

Assam

Cochin

Parangipettai

Mangalore

Various locations in India Tamil Nadu

Mizoram

[28]

[76] [27]

[26]

[75]

[25]

[24]

[22] [23]

[18,19] [20]

– Gujarat

South India Lucknow

[17]

[16]

Ref.

West Bengal

West Bengal

Location

K. Sivagami et al.



K. Sivagami et al.

Fig. 1. Sources of antibiotic usage, its spread and transfer of resistance genes to humans.

resistance to sulfadiazine and larger part of the isolates displayed resistance against penicillin, erythromycin, amikacin and carbenicillin. On the other hand, 74% isolates were susceptible to chloramphenicol. Similarly, [38] examined isolates from Salmonella enterica and found that majority of the isolates was resistant to numerous antibiotics such as β-lactam. Besides these, numerous studies have been reported on antibiotic resistance based on isolates from poultry [1,39,40]. [1] has also dealt with antibiotic resistance among food animals in detail. Antibiotic resistance can be transferred from animals/plants to humans by food chain, direct/indirect link with animal health workers/livestock industry and in agriculture through manure application. The spread of resistance between different ecosystems rely on the concentrations of antibiotic resistance genes (ARGs) and their responsible host bacteria present in an ecosystem and also largely vary on the rate of their exchange between ecosystems.

study the link between the illegitimate use of antibiotics, exposure to antibiotics-containing water and the gain of resistance. 3.2. Antibiotic resistance studies in India As mentioned earlier, pharmaceuticals such as antibiotics pose a great global threat due to build-up of antibiotic resistance in the environment, leading to untreatable infections which used to be treatable previously, due to the formation of super bugs. Antibiotic resistance is an emerging environmental and health crisis and requires immediate research attention and understanding of its occurrence and dissemination. The dissemination of antibiotic resistance involves three compartments, namely, (i) various sources, (ii) environmental pathways and exposure routes, and (iii) receptors. Fig. 1 gives a representation of the compartments and how the sub-compartments are inter-related. Due to the excessive usage of antibiotics as growth promoters in livestock and other animals, animal excreta have significant concentrations of antibiotics, which when washed off with water and trickles down into the aquifers along with rainwater, results in contaminating the environment (Fig. 1a). Similarly, excessive and inappropriate use of antibiotics by humans can lead to contamination of sewage treatment plants (Fig. 1b). Hospital and pharmaceutical industry-wastes are also illegally let into sewage systems, further contaminating the wastewater treatment plants (WWTPs) (Figs. 1c and d). Improper disposal of unused and/or expired antibiotic pills by flushing down the drain and overuse of unprescribed antibiotics due to over-the-counter sales, can also result in polluting the WWTPs (Figs. 1e and f). Eventually, by the above-mentioned ways, various components of the environment are contaminated by antibiotics and finally lead to ARBs and ARGs in the sewage. These result in further contaminating the water bodies due to discharge of treated sewage. Subsequently, humans encounter a similar circumstance (as that of animals) through various modes like oral ingestion of contaminated drinking water, inhalation of microbial aerosol and become a major vector for dissemination. Some of the major works since the seventies on the occurrence of antibiotic resistance in cattle, other livestock forms and poultry have been tabulated in Table 2 [1]. Besides the works mentioned in the table, several research works have been reported as listed below. Resistance has been identified against many antibiotics in several of the E. coli [31–33] and S. aureus [24,34–36] isolates obtained from bovine animals. Similarly, antibiotic resistance present in isolates from poultry had also been reported. [37] examined 123 isolates from chickens in various parts of India and found that all isolates exhibited complete

4. Massive use of antibiotics in veterinary medicine Antibiotics used in veterinary and human medicine are from the same class and sometimes similar in structure. A study reported in the Proceedings of the National Academy of Sciences, found that the antibiotic consumption between 2010 and 2030 is expected to rise by a staggering 67% [2]. More than 66% of the worldwide rise in antimicrobial consumption can be attributed to the increasing quantity of animals being raised for food production. Thus, veterinary medicine demands a greater and wider share of the sectoral antibiotic consumption globally. The real problem in this area is that, antibiotics were administered not only to treat the animals but for growth promotion, and significantly in disease-prevention, making the animal houses a hotspot of antibiotic resistance dissemination. Despite a large number of bans in the United States (quinolones in poultry industry), some important antibiotics continue to be routinely used for prophylactic measures among crowded animals. 4.1. Transfer from poultry farm environment Poultry litter constitutes one of the key sources of ARBs. In commercial poultry farms, antibiotics are administered from a day-old chick to an adult bird for a period of 6 weeks. Usually, poultry farm floors are covered with bedding materials. The bedding is made of materials such as softwood, and during the growing period, this gets mixed with chicken feces, skin, feather and insects. This mix is called the poultry litter and it gets replaced with fresh wood shavings between different 4


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one of the most prevalent marine pathogens responsible for coral disease in aquaculture farms was isolated from samples collected from ten different sites in Cochin and Kumarakom and four different shrimp farm hatcheries. Thirty different strains of V. coralliilyticus were analyzed for antibiotic resistance towards 20 antibiotics using disk diffusion method. Resistance was observed against beta lactams (amoxicillin, ampicillin and carbenicillin), tetracycline (oxytetracycline), pyrimidine (trimethoprim), ntirofurans (nitrofurantoin and furazolidone), sulphonamides (sulphamethoxasole), quinolones (enrofloxacin) and macrolides (erythromycin) [72]. [47] reported that the water and sediment samples obtained at the eco-regions of Chennai coast were detected with ARB. Most of the bacterial strains of a total of 960 isolates belong to the four major genera. Highest resistances were shown for vancomycin and penicillin with the frequency of 53.6% and 52.6% respectively. Chloramphenicol, ciprofloxacin, gentamicin and tetracycline were observed to be most effective on the bacteria with the frequency range of less than 7%.

time intervals. This litter is usually rich in mineral content, and can be used as a fertilizer. Antibiotics are used in poultry for growth promotion and for disease prevention. As previously mentioned, the metabolic rate of antibiotics is low and hence 90% of the administered dose is excreted in feces. Avian intestines are one of the potential reservoirs of E. coli. These bacteria have a huge potential for zoonotics, so there is a higher chance for AMR spread from birds to humans [41]. Feeding greatly influences the microbial ecosystem of broiler litter. The population of beneficial bacteria can be increased, and pathogenic E. coli populations can be decreased in the litter by the addition of mannan and purified lignin to broiler feed [42]. Resistant E. coli from contaminated litter are transferred to the environment which in turn contaminate the surface water and groundwater through run-off happening while storing litter for long time periods in an open source. 4.2. Possible link between livestock/poultry and aquaculture Van Boeckel et al. [70] has predicted that antibiotic consumption by chickens in India in chicken is rapidly increasing and area of high consumption is expected to grow by 312% by 2030. The major concern is that India has not come up with regulatory guidelines to limit the usage of antibiotics in livestock or poultry. There is a common practice existing in integrated farming in Asia, where the organic waste from livestock and poultry which is rich in ARB, are fed to farm fish. Thus, transfer of resistance happens in the aquaculture farms [43]. This link can be established with different perspectives. Companion animals like dogs and cats are being more or less treated as family members by pet lovers. Thus, these pets receive the most advanced medical treatment with newer antibiotics. There is always a risk of zoonotic infections. Due to over-usage of antibiotics, increasing resistant strains are produced which impact human health. In recent times, there are reports of increasing resistance in animals. For example, carbapenemase-positive Enterobacteriaceae, pig farm associated MRSA ST398, quinolone resistance in food products (plasmid mediated) have been reported recently [9].

5. Risks and benefits of using antibiotics The market value of antimicrobial drugs used to treat animal diseases stood at $20.1 billion in 2010. It has been steadily increasing as $8.65 billion in 1992 and predicted to rise to $42.9 billion in 2018 [48]. Best quality meat with high protein content and low fat is being produced from animals fed with antibiotics [73]. Tetracycline and penicillin usage in poultry have considerably improved egg production and hatchability [49]. Besides poultry, antibiotic-supplemented feed had a marked improvement in the health of livestock. Sulfamethazine and chlortetracycline supplements, significantly reduced the rate of relapse and respiratory disease morbidity [50]. Apart from their antimicrobial effects, antibiotics (particularly macrolides) have an anti-inflammatory potential which rationalizes their beneficial effects [51]. Livestock, poultry and aquaculture industries thus rely on the crucial role of antibiotics for efficient animal food production strategies. It has been well documented that the diarrhoeagenic E. coli has been the underlying cause of acute diarrhea in Indian children. A study reported that rural child population living near poultry farms in Tamil Nadu are at high risk for E. coli resistance to fluoroquinolones, tetracycline, and gentamicin [52]. Emergence of global resistance of avian influenza strain H5N1 is due to unrestricted usage of amantadine in China. Amantadine, a potential life-saving drug rendered ineffective during the H5N1 outbreak. In India, amantadine drug resistant H5N1 avian influenza was reported in West Bengal in 2011. One of the major diseases affecting poultry industry is Salmonellosis which has posed a severe threat resulting in substantial morbidity. High stocking density, high dust levels, low ventilation and stress in poultry farms have the potential to exacerbate the problem. Center for Disease Dynamics, Economics & Policy (CDDEP) and Centre for Science and Environment [15] have reported increaextremesed levels of ARB in chickens in Punjab [53]. These studies have proven that more than 66% of the farms use antibiotics for growth promotion, out of which, farm animals have 3 times more likeliness to develop antibiotic resistance. Huge demand for good quality meat has increased the antibiotic usage in animal food industry which results in wider selection of pathogens. The result of expansion of this sector is mainly due to the demand for the poultry. The growth in consumption is expected to grow further by 312% by 2030 [74]. However, a major grey area in this field is that, even though several research works are conducted across the world on identifying the antibiotics spread and the resistance gene associated with it in various compartments of the environment such as water and wastewater, studies with respect to Indian scenario is minimal and needs to be explored to a great extent. Further, despite several research explorations happening globally to understand and fight this critical issue, other means such as vaccines and bacteriophages may turn out to be an alternate method to treat resistant bacterial infections [54]. At the same time,

4.3. Spread of AMR in the environment from wastewater There is also a common practice in countries like India where animal manure is widely used in agriculture. Animal waste represents one of critical links in spreading AMR because they harbor AMR bacteria. Antimicrobials are never completely metabolized and finally find their way into sewage treatment plants. In countries like India, pharmaceuticals and personal care products are abundant in WWTP and thus the selection pressure for AMR is high in these environments [44]. It is a pity that our WWTP are not equipped for detecting or treating pharmaceutical or personal care products and this is a massive source of antimicrobial exposure to the environment. Even some personal care products like hand wash soaps which contain triclosan, serve as a potent antimicrobial selection source in the domestic wastewater [45]. 4.4. Spread of AMR from environmental sources like rivers/lakes to humans/animals/plants In India, many rivers and streams are polluted with industrial and domestic wastewater. Many occasions when wastewater is let into the rivers without treatment lead to massive inputs of AMR-laden bacteria into the natural unpolluted environments. This water is being used to feed the livestock, and is also used for irrigation and thus, transfer is obvious in these aquatic environments. A recent research article in 2017 investigated water samples collected from the Musi River near a WWTP of a pharmaceutical industry in Hyderabad [46]. Samples were analyzed for 25 antibiotics with liquid chromatography–tandem mass spectrometry. High concentrations of moxifloxacin, voriconazole, and fluconazole were detected in the sewers in an industrial area in Patancheru–Bollaram area. In a recent research study, Vibrio coralliilyticus, 5


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7. Conclusions

experimentation of such alternate methods must be assessed of their pros and cons before commercializing them.

This review mainly focuses on (i) the usage and prevalence of antibiotics in the environment, (ii) presence of antibiotic resistance in animals and (iii) dissemination of antibiotic resistance through various mechanisms in Indian scenario. Due to excessive and inappropriate human consumption of antibiotics, and administration of antibiotics to animals (not just for treatment of infections, but also for prophylactic purposes and as a form of growth promoters), it has resulted in the presence of antibiotics in the environment,in turn leading to dissemination of antibiotic resistance. The best way to control the spread of antibiotic resistance is to raise awareness to the general public by print and social media to increase the demand for antibiotic-free food products. Veterinarians, agricultural experts and legal authorities in India should address the issue of antibiotic resistance by regulating policies which can monitor or track the antibiotic usage, limiting its dosage, etc. Apart from these, people involved in waste management and municipal authorities should be educated about proper disposal of expired medications, poultry and aquaculture wastewater. Non-therapeutic use of antibiotics should be tracked and phased out. A systematic nationwide rigorous surveillance system to monitor the antibiotic residues in veterinary, poultry and aquaculture environments is very much essential. Vertical surveillance cannot identify all the major drivers of AMR whereas a cross-sectional surveillance can ensure better understanding of underlying factors in spread of AMR to best identify the sectoral contribution. The other effective method is to control or prevent infection in humans and animal sources, which can be done by healthcare professionals. Wastewater treatment facilities built near the pharmaceutical manufacturing facilities must treat the effluents and remove the antibiotics and their metabolites before their release into the environment.

6. Implications on human health A research study published in the Lancet in 2010 by Karthikeyan Kumarasamy et al. about the NDM1 superbug created a storm in the healthcare sector of India. Politicians and physicians felt exposed after this publication about multidrug resistance in India and medical tourism in the country was severely criticized [55]. In 2016, Indian researchers have identified mcr-1, which has resistance to the last mile antibiotic (colistin) that humans have access to. Environmental reservoirs of AMR have demonstrated the potential to serve as the source of antibiotic resistance genes for clinically relevant microbes [56,57]. Further, antimicrobial compounds which end up in aquatic systems have the potential to interrupt native microbial species which is essential to maintaining the ecosystem (nitrification/denitrification), soil fertility and biological cycles [58–60]. As such, antimicrobials are widely recognized as emerging environmental contaminants [30] and, given their alarming levels were classified as a priority risk group in recent years. Besides, several human pathogens have started gaining resistance. Among enteric pathogens, Vibrio cholera seems to have attained resistance towards nalidixic acid, furazolidone and cotrimoxazole and is susceptible to tetracycline (near Delhi region, India). However, in some areas of Bangladesh, tetracycline seems to be ineffective. This shows that resistance spectrum varies between regions and antibiotic consumption practices [61,62]. Typhoid and paratyphoid causing microorganisms had higher susceptibility to antibiotics, back in late 1980s, which made them treatable using chloramphenicol, ampicillin and cotrimaxazole. However, soon after acquirement of resistance to these drugs to a great extent, the usage of fluoroquinolones has been in the fore-front. Later, chloramphenicol lost sensitivity for a short period, following which due to the popularization of fluoroquinolone, sensitivity to chloramphenicol was restored [63,64]. Ray et al. [65] and Khaki et al. [66] have studied the resistance of Neisseria gonorrhoeae (pathogen causing sexually transmitted diseases) towards penicillin and fluoroquinolone. This has resulted in a situation where third generation antibiotics need to be used. Furthermore, it is becoming more difficult to treat deadly diseases like tuberculosis by using basic level drugs. Mycobacterium tuberculosis has acquired multi-drug resistance (simultaneous resistance to rifampicin and isoniazid). In addition, it has lost sensitivity to fluoroquinoline and a few second line drugs which has made it an extensively drug resistant bacteria [64,67]. Further, Mycobacteria genus also causes leprosy, (the causative pathogen being Mycobacteria leprae). However, this pathogen has started acquiring resistance to rifampicin, clofazimine and dapsone. This is not a healthy sign for curing such dangerous diseases. On the other hand, urinary infections are less dangerous and common among out-patient infection complaints, they have acquired resistance to antibiotics as well. Based on the research work conducted by Kumar et al. [68] in Aligarh, India, 100 samples out of 920 exhibited loss of susceptibility to the antibiotics tested. Out of 100 samples, 61% was E. coli and 22% was Klebsiella spp. that were resistant. In addition, ampicillin and co-trimoxazole were found to be ineffective against Gram negative bacilli. Kumar et al. [69] have investigated AMR patterns of 654 enteric pathogens in India. They have conducted a detailed study on AMR traits on multi-drug enteric pathogens. The study included microbial species namely, P. stuartii, K. pneumoniae, E. coli, S. typhimurium, S. flexneri and P. aeruginosa. Their study indicates that these pathogens are resistant against 22 antibiotics which belong to 9 distinct classes of antibiotics. The major findings of their study are as follows. (i) About 97% of strains have lost susceptibility towards at least 2 antibiotics, (ii) 24% against at least 10 antibiotics and (iii) 3% of the isolates seem to exhibit resistance against at least 15 antibiotics.

References [1] CDDEP, Antibiotic Use and Resistance in Food Animals: Current Policy and Recommendations, The Centre for Diseases Dynamics, Economics and Policy (CDDEP), (2017) https://www.cddep.org/publications/antibiotic_use_and_ resistance_food_animals_current_policy_and_recommendations/. [2] T.P. Van Boeckel, C. Brower, M. Gilbert, B.T. Grenfell, S.A. Levin, T.P. Robinson, et al., Global trends in antimicrobial use in food animals, Proc. Nat. Acad. Sci. U.S.A. 112 (18) (2015) 5649–5654. [3] S. Ramesh, Antibiotic Usage Patterns in Animal Husbandry and Food Safety: Regulations and Practice CIBA Report, (2016). [4] P. Washer, H. Joffe, The hospital superbug: social representations of MRSA, Social Sci. Med. 63 (8) (2006) 2141–2152. [5] S.M. Aly, A. Albutti, Antimicrobials use in aquaculture and their public health impact, J. Aquacult. Res. Dev. 5 (4) (2014) 1. [6] CIBA, CIBA Special Publication No. 83, Responsible Use of Antimicrobials in Indian Aquaculture, Opportunities and Challenges, 7th December 2016, ICAR – CIBA, Chennai, 2016. [7] A.J. Hernández, S. Satoh, V. Kiron, Supplementation of citric acid and amino acid chelated trace elements in low-fish meal diet for rainbow trout affect growth and phosphorus utilization, J. World Aquacult. Soc. 43 (5) (2012) 688–696. [8] J. Bérdy, Thoughts and facts about antibiotics: where we are now and where we are heading, J. Antibiot. 65 (8) (2012) 385–395. [9] M.A. Argudín, A. Deplano, A. Meghraoui, M. Dodémont, A. Heinrichs, O. Denis, C. Nonhoff, S. Roisin, Bacteria from animals as a pool of antimicrobial resistance genes, Antibiotics 6 (2) (2017) 12. [10] V.M. D’Costa, K.M. McGrann, D.W. Hughes, G.D. Wright, Sampling the antibiotic resistome, Science 311 (5759) (2006) 374–377. [11] H.K. Allen, J. Donato, H.H. Wang, K.A. Cloud-Hansen, J. Davies, J. Handelsman, Call of the wild: antibiotic resistance genes in natural environments, Nat. Rev. Microbiol. 8 (4) (2010) 251–259. [12] H.W. Stokes, M.R. Gillings, Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens, FEMS Microbiol. Rev. 35 (5) (2011) 790–819. [13] T.F. Landers, B. Cohen, T.E. Wittum, E.L. Larson, A review of antibiotic use in food animals: perspective, policy, and potential, Public Health Rep. 127 (1) (2012) 4–22. [14] Expert Consultation on Antimicrobial Use in Aquaculture and Antimicrobial Resistance Seoul, WHO/OIE/FDA, Republic of Korea, 2006. [15] David Burch, Antimicrobial Resistance −Veterinary and Public Health Concerns in Europe, (2012). [16] S.K. Manna, M.P. Brahmane, C. Manna, K. Batabyal, R. Das, Occurrence virulence characteristics and antimicrobial resistance of Escherichia coli O157 in slaughtered

6


K. Sivagami et al.

[17]

[18]

[19]

[20]

[21]

[22]

[23]

[24]

[25] [26]

[27]

[28]

[29]

[30]

[31]

[32]

[33]

[34]

[35]

[36]

[37]

[38]

[39]

[40]

[41] C. Ewers, S. Guenther, L.H. Wieler, P. Schierack, Mallard ducks–a waterfowl species with high risk of distributing Escherichia coli pathogenic for humans, Environ. Microbiol. Rep. 1 (6) (2009) 510–517. [42] B. Baurhoo, L. Phillip, C.A. Ruiz-Feria, Effects of purified lignin and mannan oligosaccharides on intestinal integrity and microbial populations in the ceca and litter of broiler chickens? Poult. Sci. 86 (6) (2007) 1070–1078. [43] K. Jayathilakan, K. Sultana, K. Radhakrishna, A.S. Bawa, Utilization of byproducts and waste materials from meat, poultry and fish processing industries: a review, J. Food Sci. Technol. 49 (3) (2012) 278–293. [44] N.P. Marathe, V.R. Regina, S.A. Walujkar, S.S. Charan, E.R. Moore, D.J. Larsson, Y.S. Shouche, A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria, PLoS One 8 (10) (2013) e77310. [45] J. Jutkina, N.P. Marathe, C.F. Flach, D.G.J. Larsson, Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations, Sci. Total Environ. 616 (2017) 172. [46] C. Lübbert, C. Baars, A. Dayakar, N. Lippmann, A.C. Rodloff, M. Kinzig, F. Sörgel, Environmental pollution with antimicrobial agents from bulk drug manufacturing industries in Hyderabad, South India, is associated with dissemination of extendedspectrum beta-lactamase and carbapenemase-producing pathogens, Infection (2017) 1–13. [47] S. Vignesh, H.U. Dahms, K. Muthukumar, G. Vignesh, R.A. James, Biomonitoring along the tropical southern Indian coast with multiple biomarkers, PLoS One 11 (12) (2016) e0154105. [48] GIA, Animal Health Market to Hit $43 Billion in Five Years, (2012) http:// westernfarmpress.com/management/animal-health-market-hit- 43-billion-fiveyears. [49] R.H. Gustafson, R.E. Bowen, Antibiotic use in animal agriculture, J. Appl. Microbiol. 83 (5) (1997) 531–541. [50] G.F. Gallo, J.L. Berg, Efficacy of a feed-additive antibacterial combination for improving feedlot cattle performance and health, Can. Vet. J. 36 (4) (1995) 223. [51] A.G. Buret, Immuno-modulation and anti-inflammatory benefits of antibiotics: the example of tilmicosin, Can. J. Vet. Res. 74 (1) (2010) 1–10. [52] T.R.G.K. Murthy, N. Dorairajan, G.A. Balasubramanium, A.M. Dinakaran, K. Saravanabava, Pathogenic bacteria related to respiratory diseases in poultry with reference to Ornithobacterium rhinotracheale isolated in India, Veterinarski Arhiv 78 (2) (2008) 131. [53] CSE, CSE Report, (2014) http://www.cseindia.org/userfiles/NG_Jayasimha.pdf. [54] D. Raghunathan, P.R. Narayanan, Antibiotic therapy of salmolellosis, Med. J. Armed Forces India 45 (1989) 3–4. [55] K.K. Kumarasamy, M.A. Toleman, T.R. Walsh, J. Bagaria, F. Butt, R. Balakrishnan, P. Krishnan, Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study, Lancet Infect. Dis. 10 (9) (2010) 597–602. [56] S. Ghosh, T.M. LaPara, The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria, ISME J. 1 (3) (2007) 191–203. [57] J.A. Perry, G.D. Wright, The antibiotic resistance mobilome: searching for the link between environment and clinic, Front. Microbiol. 4 (2013). [58] S.D. Costanzo, J. Murby, J. Bates, Ecosystem response to antibiotics entering the aquatic environment, Mar. Pollut. Bull. 51 (1) (2005) 218–223. [59] C.A. Kinney, E.T. Furlong, S.L. Werner, J.D. Cahill, Presence and distribution of wastewater derived pharmaceuticals in soil irrigated with reclaimed water, Environ. Toxicol. Chem. 25 (2) (2006) 317–326. [60] K. Kümmerer, Resistance in the environment, J. Antimicrob. Chemother. 54 (2) (2004) 311–320. [61] N.C. Sharma, P.K. Mandal, R. Dhillon, M. Jain, Changing profile of vibrio cholerae O1, O139 in delhi & its periphery (2003–2005), Indian J. Med. Res. 125 (5) (2007) 633. [62] D. Saha, M.M. Karim, W.A. Khan, S. Ahmed, M.A. Salam, M.L. Bennish, Single-dose azithromycin for the treatment of cholera in adults, New Engl. J. Med. 354 (23) (2006) 2452–2462. [63] A.C. Anand, V.K. Kataria, W. Singh, S.K. Chatterjee, Epidemic multiresistant enteric fever in eastern India, Lancet 335 (8685) (1990) 352. [64] D. Raghunath, Emerging antibiotic resistance in bacteria with special reference to India, J. Biosci. 33 (4) (2008) 593–603. [65] K. Ray, M. Bala, S.M. Gupta, N. Khunger, Changing trends in sexually transmitted infections at a Regional STD Centre in north India, Indian J. Med. Res. 124 (5) (2006) 559. [66] P. Khaki, P. Bhalla, A. Sharma, V. Kumar, Correlation between in vitro susceptibility and treatment outcome with azithromycin in gonorrhoea: a prospective study, Indian J. Med. Microbiol. 25 (4) (2007) 354. [67] M.V. Jesudason, U. Mukundan, R. Saaya, K. Vanitha, M.K. Lalitha, Resistance of mycobacterium tuberculosis to the first line anti tubercular drugs − a twenty-year review, Indian J. Med. Microbiol. 21 (2) (2003) 127. [68] M. Akram, M. Shahid, A.U. Khan, Etiology and antibiotic resistance patterns of community-acquired urinary tract infections in JNMC Hospital Aligarh, India, Ann. Clin. Microbiol. Antimicrob. 6 (1) (2007) 4. [69] P. Kumar, S. Bag, T.S. Ghosh, P. Dey, M. Dayal, B. Saha, J. Verma, A. Pant, S. Saxena, A. Desigamani, P. Rama, D. Kumar, N. Sharma, C. Hanpude, P. Maiti, A.K. Mukhopadhyay, Molecular insights into antimicrobial resistance traits of multidrug resistant enteric pathogens isolated from India, Sci. Rep. 7 (1) (2017) 14468. [70] T. Suresh, A.A.M. Hatha, D. Sreenivasan, N. Sangeetha, P. Lashmanaperumalsamy, Prevalence and antimicrobial resistance of Salmonella enteritidis and other salmonellas in the eggs and egg-storing trays from retails markets of Coimbatore,

cattle and diarrhoeic calves in West Bengal, India, Lett. Appl. Microbiol. 43 (4) (2006) 405–409. I. Samanta, S.N. Joardar, P.K. Das, T.K. Sar, S. Bandyopadhyay, T.K. Dutta, U. Sarkar, Prevalence and antibiotic resistance profiles of Salmonella serotypes isolated from backyard poultry flocks in West Bengal, India, J. Appl. Poult. Res. 23 (3) (2014) 536–545. R. Kumar, B.R. Yadav, R.S. Singh, Antibiotic resistance and pathogenicity factors in Staphylococcus aureus isolated from mastitic Sahiwal cattle, J. Biosci. 36 (1) (2011) 175–188. R. Kumar, B.R. Yadav, S.K. Anand, R.S. Singh, Molecular surveillance of putative virulence factors and antibiotic resistance in Staphylococcus aureus isolates recovered from intra-mammary infections of river buffaloes, Microb. Pathog. 51 (1) (2011) 31–38. G. Arya, A. Roy, V. Choudhary, M.M. Yadav, C.G. Joshi, Serogroups, atypical biochemical characters, colicinogeny and antibiotic resistance pattern of shiga toxinproducing escherichia coli isolated from diarrhoeic calves in gujarat, India, Zoonoses Public Health 55 (2) (2008) 89–98. P.K. Saikia, G.N. Dutta, L.A. Devriese, C.C. Kalita, Characterisation and antimicrobial susceptibility of Enterococcus species from the intestines of ducks in Assam, Res. Vet. Sci. 58 (3) (1995) 288–289. S. Saravanan, V. Purushothaman, T.R.G.K. Murthy, K. Sukumar, P. Srinivasan, V. Gowthaman, M. Balusamy, R. Atterbury, S.V. Kuchipudi, Molecular epidemiology of Nontyphoidal Salmonella in poultry and poultry products in India: implications for human health, Indian J. Microbiol. 55 (3) (2015) 319–326. M. Singh, S.C. Sanyal, J.N. Yadav, Enterotoxigenic drug resistant plasmids in animal isolates of Escherichia coli and their zoonotic importance, J. Trop. Med. Hyg. 95 (5) (1992) 316–321. T.K. Dutta, P. Roychoudhury, S. Bandyopadhyay, C. Rajesh, Detection and characterization of shiga toxigenic Escherichia coli from piglets with or without diarrhoea in Mizoram, Indian J. Anim. Sci. (India) (2011). S.K. Sethi, S. Anand, A. Singh, D.V. Vadehra, Resistance of Salmonella serotypes to chloramphenicol, Bull. World Health Organ. 54 (3) (1976) 353. V.K. Deekshit, B.K. Kumar, P. Rai, S. Srikumar, I. Karunasagar, Detection of class 1 integrons in Salmonella Weltevreden and silent antibiotic resistance genes in some seafood associated nontyphoidal isolates of Salmonella in south west coast of India, J. Appl. Microbiol. 112 (6) (2012) 1113–1122. K. Sathiyamurthy, A. Purushothaman, V. Ramaiyan, Antibiotic-resistant Vibrio cholerae in Parangipettai coastal environs, south east India, Microb. Drug Resist. 3 (3) (1997) 267–270. S. Sudha, P.S. Divya, B. Francis, A.A. Hatha, Prevalence and distribution of Vibrio parahaemolyticus in finfish from Cochin (south India), Vet. Ital. 48 (269) (2012) e81. A.P. Magiorakos, A. Srinivasan, R.B. Carey, Y. Carmeli, M.E. Falagas, C.G. Giske, D.L. Paterson, Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance, Clin. Microbiol. Infect. 18 (3) (2012) 268–281. A. Pruden, R. Pei, H. Storteboom, K.H. Carlson, Antibiotic resistance genes as emerging contaminants: studies in northern Colorado, Environ. Sci. Technol. 40 (23) (2006) 7445–7450. S.S. Kawoosa, I. Samanta, S.A. Wani, In vitro drug sensitivity profile of positive Escherichia Coli from diarrhoeic calves in kashmir valley, Indian J. Anim. Sci. 77 (7) (2007). S. Ghatak, A. Singha, A. Sen, C. Guha, A. Ahuja, U. Bhattacharjee, T.K. Dey, Detection of New Delhi metallo-beta-lactamase and extended-spectrum beta-lactamase genes in Escherichia coli isolated from mastitic milk samples, Transbound. Emerg. Dis. 60 (5) (2013) 385–389. S. Sharma, A. Khan, D. Dahiya, J. Jain, V. Sharma, Prevalence: identification and drug resistance pattern of Staphylococcus aureus and Escherichia coli isolated from raw milk samples of Jaipur city of Rajasthan, J. Pure Appl. Microbiol. 9 (2015) 341–348. J.G. Tiwari, S.P. Chaudhary, H. Kumar Tiwari, T. Kumar Dutta, P. Saikia, P. Hazarika, Microbial evaluation of market milk and milk-products of Mizoram, India with special reference to Staphylococcus aureus, Indian J. Anim. Sci. 81 (4) (2011) 429. V. Kumar, S.C. Das, S. Guin, S.V.S. Malik, Virulence, enterotoxigenicity and antibiotic profile of Staphylococcus aureus from buffalo clinical mastitis, Indian J. Anim. Sci. (India) (2012). P.L. Preethirani, S. Isloor, S. Sundareshan, V. Nuthanalakshmi, K. Deepthikiran, A.Y. Sinha, D. Rathnamma, K.N. Prabhu, R. Sharada, T.K. Mukkur, N.R. Hegde, Isolation, biochemical and molecular identification, and in-vitro antimicrobial resistance patterns of bacteria isolated from bubaline subclinical mastitis in South India, PLoS One 10 (11) (2015). S.B. Shivachandra, A.A. Kumar, A. Biswas, M.A. Ramakrishnan, V.P. Singh, S.K. Srivastava, Antibiotic sensitivity patterns among Indian strains of avian Pasteurella multocida, Trop. Anim. Health Prod. 36 (8) (2004) 743–750. I.A. Mir, S.K. Kashyap, S. Maherchandani, Isolation, serotype diversity and antibiogram of Salmonella Enterica isolated from different species of poultry in India, Asian Pac. J. Trop. Biomed. 5 (7) (2015) 561–567. D. Kar, S. Bandyopadhyay, D. Bhattacharyya, I. Samanta, A. Mahanti, P.K. Nanda, B. Mondal, P. Dandapat, A.K. Das, T.K. Dutta, S. Bandyopadhyay, R.K. Singh, Molecular and phylogenetic characterization of multidrug resistant extended spectrum beta-lactamase producing Escherichia coli isolated from poultry and cattle in Odisha, India, Infect. Genet. Evol. 29 (82–90) (2015) 385–389. M.U. Rasheed, N. Thajuddin, P. Ahamed, Z. Teklemariam, K. Jamil, Antimicrobial drug resistance in strains of Escherichia coli isolated from food sources, Rev. Inst. Med. Trop. São Paulo 56 (4) (2014) 341–346.

7


K. Sivagami et al.

[74] T.P. Van Boeckel, C. Brower, M. Gilbert, B.T. Grenfell, S.A. Levin, T.P. Robinson, et al., Global trends in antimicrobial use in food animals, Nat. Acad. Sci. U. S. A. 112 (18) (2015) 5649–5654. [75] A.A.M. Hatha, P. Lakshmanaperumalsamy, Antibiotic resistance of Salmonella strains isolated from fish and crustaceans, Lett. appl. microbiol. 21 (1) (1995) 47–49. [76] S. Kamath, S. Sinha, E. Shaari, D. Young, A.C. Campbell, Role of topical antibiotics in hip surgery: a prospective randomised study, Injury 36 (6) (2005) 783–787.

South India, Food Microbiol. 23 (3) (2006) 294–299. [71] Kumararaja, R. Saraswathi, P.K. Patil, N. Lalitha, M. Muralidhar, Fate of antibiotics in environment, Responsible Use of Antimicrobials in Indian Aquaculture : Opportunities and Challenges, (2016) CIBA Special Publication No. 83. [72] R. Silvester, D. Alexander, M. George, A.A.M. Hatha, Prevalence and multiple antibiotic resistance of Vibrio coralliilyticus, along the southwest coast of India, Current Sci. 112 (8) (2017) (00113891). [73] P. Hughes, J. Heritage, Antibiotic growth-promoters in food animals, Food Agric. Organ. (2002).

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