bla CTX-M-152, a Novel Variant of CTX-M-group-25, Identified in a Study Performed on the Prevalence of Multidrug Resistance among Natural Inhabitants of River Yamuna, India

Prevalence of antibiotic resistance genes in bacteria from Gomti and Ganga rivers: implications for water quality and public health

Rivers serve as a significant habitat and water sources for diverse organisms, including humans. An important environmental and public health concern is the increase in antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquatic ecosystems brought about by excessive pollutant flow. The research highlighted that river water, which is receiving discharge from wastewater treatment plants, is harbouring multidrug-resistant bacteria. River water samples were collected in January, April, July and October 2022 from three separate locations of each Gomti and Ganga river. A total of 114 bacteria were isolated from Gomti as well as the Ganga River. All the isolates were tested for their resistance to various antibiotics by disc diffusion method. The isolated bacteria were tested for the antibiotic resistance genes using PCR and were identified by 16s rRNA sequencing. The ARBs percentages for each antibiotic were as follows: ampicillin (100%); cefotaxime (96.4, 63.1%); erythromycin (52.6, 57.8%); amikacin (68.4, 50.8%); tetracycline (47.3, 54.3%); nalidixic acid (47.3, 45.6%); streptomycin (68.4, 49.1%); gentamycin (43.8, 35%); chloramphenicol (26.3, 33.3%); neomycin (49.1, 29.8%) and ciprofloxacin (24.5, 7.01%). Further, antibiotic resistance genes in Gomti and Ganga water samples disclose distinctive patterns, including resistance to ermB (25, 40%); tetM (25, 33.3%); ampC (44.4, 40%) and cmlA1 (16.6%). Notably cmlA1 resistant genes were absent in all bacterial strains of the Gomti River. Additionally, gyrA gene was not found in both the river water samples. The presence of ARGs in the bacteria from river water shows threat of transferring these genes to native environmental bacteria. To protect the environment and public health, constant research is necessary to fully understand the extent and consequences of antibiotic resistance in these aquatic habitats.

An overview on the prevalence and potential impact of antimicrobials and antimicrobial resistance in the aquatic environment of India

India at present is one of the leading countries in antimicrobial drug production and use, leading to increasing antimicrobial resistance (AMR) and public health problems. Attention has mainly been focused on the human and food animals' contribution to AMR neglecting the potential contribution of the perceptibly degraded aquatic environment in India. The paper reviews the available published literature in India on the prevalence of antimicrobial residues and their dissemination pathways in wastewater of pharmaceutical industries, sewage treatment plants, hospitals, riverine, community pond water, and groundwater. The prevalence of antimicrobial residue concentration, pathogenic and non-pathogenic bacteria antimicrobial resistant bacteria (ARB), their drug resistance levels, and their specific antimicrobial resistant genes (ARGs) occurring in various water matrices of India have been comprehensively depicted from existing literature. The concentration of some widely used antimicrobials recorded from the sewage treatment plants and hospital wastewater and rivers in India has been compared with other countries. The ecotoxicological risk posed by these antimicrobials in the various water matrices in India indicated high hazard quotient (HQ) values for pharmaceutical effluents, hospital effluents, and river water. The degraded aquatic environment exhibited the selection of a wide array of co-existent resistant genes for antibiotics and metals. The review revealed improper use of antibiotics and inadequate wastewater treatment as major drivers of AMR contaminating water bodies in India and suggestion for containing the challenges posed by AMR in India has been proposed.

The Impact of Chlorine Disinfection of Hospital Wastewater on Clonal Similarity and ESBL-Production in Selected Bacteria of the Family Enterobacteriaceae

Hospitals are regarded as ecological niches of antibiotic-resistant bacteria (ARB). ARB can spread outside the hospital environment via hospital wastewater (HWW). Therefore, HWW is often disinfected in local stations to minimize that risk. Chlorine-based treatment is the most popular method of HWW disinfection around the world, however, recent research has suggested that it can contribute to the spread of antimicrobial resistance (AMR). The aim of this study is to determine the impact of HWW disinfection on the clonal similarity of Enterobacteriaceae species and their ability to produce extended-spectrum beta-lactamases (ESBLs). The study was conducted in a hospital with a local chlorine-based disinfection station. Samples of wastewater before disinfection and samples of disinfected wastewater, collected in four research seasons, were analyzed. Bacteria potentially belonging to the Enterobacteriaceae family were isolated from HWW. The Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method was used to generate DNA fingerprints of all bacterial isolates. The isolates were phenotypically tested for the production of ESBLs. Antibiotic resistance genes (bla_SHV, bla_TEM, and bla_OXA, bla_{CTX-M-1-group}, bla_{CTX-M-2-group}, bla_CTX-9-group and bla_{CTX-M-8/25-group}) were detected by PCR in strains with confirmed phenotypic ability to produce ESBLs. The ESBL+ isolates were identified by the sequencing of 16S rDNA. In the present study, the same bacterial clones were isolated from HWW before and after disinfection and HWW was sampled in different seasons. Genetic and phenotypic variations were observed in bacterial clones. ESBL+ strains were isolated significantly more often from disinfected than from non-disinfected HWW. The bla_OXA gene was significantly more prevalent in isolates from disinfected than non-disinfected HWW. Enterobacter hormaechei and Klebsiella pneumoniae were the dominant species in ESBL+ strains isolated from both sampling sites. The results of this study indicate that chlorine-based disinfection promotes the survival of ESBL-producing bacteria and/or the transmission of genetic determinants of antimicrobial resistance. As a result, chlorination increases the proportion of ESBL-producing Enterobacteriaceae in disinfected wastewater. Consequently, chlorine-based disinfection practices may pose a risk to the environment and public health by accelerating the spread of antimicrobial resistance.

Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control

Antimicrobial resistant (AMR) bacteria present one of the biggest threats to public health; this must not be forgotten while global attention is focussed on the COVID-19 pandemic. Resistant bacteria have been demonstrated to be transmittable to humans in many different environments, including public settings in urban built environments where high-density human activity can be found, including public transport, sports arenas and schools. However, in comparison to healthcare settings and agriculture, there is very little surveillance of AMR in the built environment outside of healthcare settings and wastewater. In this review, we analyse the existing literature to aid our understanding of what surveillance has been conducted within different public settings and identify what this tells us about the prevalence of AMR. We highlight the challenges that have been reported; and make recommendations for future studies that will help to fill knowledge gaps present in the literature.

Predominance of genetically diverse ESBL Escherichia coli identified in resistance mapping of Vembanad Lake, the largest fresh-cum-brackishwater lake of India

Antimicrobial resistance (AMR) burden in Escherichia coli along the 90 km stretch of Vembanad Lake, Kerala, India, was assessed. Seventy-seven percent of water samples drawn from 35 different stations of the lake harbored E. coli. Antibiotic susceptibility test performed on 116 E. coli isolates revealed resistance to ≥ one antibiotic with 39 AMR profiles in 81%, multidrug resistance in 30%, and extended spectrum β-lactamase (ESBL) producers in 32%. Of all the 15 antibiotics tested, the probability of isolating cefotaxime-resistant E. coli was the highest (P ≤ 0.05) in the lake. Genetically diverse ESBL types, namely bla_TEM-116, bla_{CTX-M -152}, bla_{CTX-M -27}, bla_{CTX-M -55}, bla_CTX-M-205, and bla_SHV-27, were identified in the lake. This is probably the first report in India for the presence of bla_CTX-M-205 (bla_{CTX-M-group 2}) in the Vembanad Lake. ST11439 and single and double loci variants of ST443 and ST4533 were identified in multilocus sequence typing (MLST). Inc plasmids (B/O, F, W, I1, FIIA, HI1, P-1α, K/B, and N) identified in the lake evidences the resistance transmission potential of the E. coli isolated from the lake. Molecular typing (ERIC-PCR, MLST, and PBRT) delineated diverse E. coli, both between and within the sampling stations. Low multiple antibiotic resistance index (average MAR< 0.2) indicates a lower risk of the lake to the human population, but the occurrence of genetically diverse ESBL E. coli in the Vembanad Lake signals health hazards and necessitates pragmatic control measures.

Easy Access to Antibiotics; Spread of Antimicrobial Resistance and Implementation of One Health Approach in India

Antimicrobial resistance (AMR) is a global public health concern because of its fast spread. India, one of the world's top consumer of antibiotics and second most populated country has its unique constraints of social, cultural and economic strata. The continual self-medication, use of antibiotics for the growth promotion in animals, and accumulation of residual antibiotics in the environment challenge the implementation of AMR containment policy. Hence, the present review attempts to delineate the influence of antibiotics abuse on the human, animal and environmental health under the realm of one health. It was based on the literature search using public databases to highlight the rapid surge in the burden of AMR in India affecting various sectors and/or ecosystems in India. It was found that the irrational and overuse of antibiotics in different sectors have led to the emergence of extended antimicrobial resistance wherein the environment acts as a reservoir of antibiotic resistance genes (ARGs); completing the cycle of contamination and recontamination. There are efforts by government policy makers to reduce the burden of AMR in the country to reduce the health risks, through the One Health approach. Parallel efforts in educating healthcare professionals, strict legislation for pharmacies and pharmaceutical companies should be prioritize. At the same time surveillance of newly emerged AMR pathogens, prioritising research focusing on AMR, and awareness camps or programs among the local population is critical while addressing the consequences of spared of AMR in India.

Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study

Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.

Lentic and effluent water of Delhi-NCR: a reservoir of multidrug-resistant bacteria harbouring blaCTX-M, blaTEM and blaSHV type ESBL genes

Antimicrobial resistance is not restricted to clinics but also spreading fast in the aquatic environment. This study focused on the prevalence and diversity of extended-spectrum β-lactamase (ESBL) genes among bacteria from lentic and effluent water in Delhi-NCR, India. Phenotypic screening of 436 morphologically distinct bacterial isolates collected from diverse sites revealed that 106 (∼24%) isolates were ESBL positive. Antibiotic profiling showed that 42, 60, 78 and 59% ESBL producing isolates collected from Ghazipur slaughterhouse, Lodhi garden pond, Hauz Khas lake and Jasola wastewater treatment plant, respectively, were multidrug-resistant (MDR). The multiple antibiotic resistance (MAR) index varied from 0.20 to 0.32 among selected locations. The prevalence of ESBL gene variants blaSHV, blaTEM and blaCTX-M were found to be 17.64, 35.29 and 64%, respectively. Furthermore, the analysis of obtained gene sequences showed three variants of blaCTX-M (15, 152 and 205) and two variants of blaTEM (TEM-1 and TEM-116) among ESBL producers. The co-existence of 2-3 gene variants was recorded among 48% ESBL positive isolates. New reports from this study include the blaCTX-M gene in Acinetobacter lwoffii, Enterobacter ludwigii, Exiguobacterium mexicanum and Aeromonas caviae. Furthermore, the identification of blaTEM and blaSHV in an environmental isolate of A. caviae is a new report from India.

Molecular detection of virulence markers to identify diarrhoeagenic Escherichia coli isolated from Mula-Mutha river, Pune District, India

In this study presence of virulence genes in multidrug resistant Escherichia coli isolated from Mula-Mutha river, Pune, India was undertaken. The objective was to understand whether the isolates were of diarrhoeagenic or of environmental origin. This was essential since the river flows through urban and rural parts of Pune and its water is used not only for industrial and agricultural purposes but also for domestic usage. One hundred and two multidrug E. coli isolates were selected from our previous study which detected genes coding for antibiotic resistance as well as identified integrons associated with multidrug resistance. Isolates were subjected to multiplex PCR to detect presence of virulence genes, set1A, set1B, sen astA, aggA, aafA, pet, stx1 and stx. Sequencing was performed to confirm the amplified PCR product. Seven of the 102 E. coli isolates showed gene set1A alone identifying them as Enteroaggregative E. coli. Thus, the findings revealed that majority of drug resistant E. coli were environmental in origin. The presence of antibiotic resistant genes, integrons in the environment as well as diarrhoeagenic E. coli isolates is a warning and calls for efficient public health measures to ensure that untreated sewage and industrial waste does not enter the Mula-Mutha river.

Genetic characterization of extended-spectrum β-lactamase-producing Enterobacteriaceae from a biological industrial wastewater treatment plant in Tunisia with detection of the colistin-resistance mcr-1 gene

This study evaluated the occurrence of extended-spectrum β-lactamases (ESBL) and associated resistance genes, integrons, and plasmid types, as well as the genetic relatedness of enterobacterial isolates in the wastewater treatment plant (WWTP) of La Charguia, Tunis City (Tunisia). A total of 100 water samples were collected at different points of the sewage treatment process during 2017-2019. Antimicrobial susceptibility was conducted by the disc-diffusion method. blaCTX-M, blaTEM and blaSHV genes as well as those encoding non-β-lactam resistance, the plasmid types, occurrence of class1 integrons and phylogenetic groups of Escherichia coli isolates were determined by PCR/sequencing. Genomic relatedness was determined by multi-locus sequence typing (MLST) for selected isolates. In total, 57 ESBL-producer isolates were recovered (47 E. coli, eight Klebsiella pneumoniae, 1 of the Citrobacter freundii complex and 1 of the Enterobacter cloacae complex). The CTX-M-15 enzyme was the most frequently detected ESBL, followed by CTX-M-27, CTX-M-55 and SHV-12. One E. coli isolate harboured the mcr-1 gene. The following phylogroups/sequence types (STs) were identified among ESBL-producing E. coli isolates: B2/ST131 (subclade-C1), A/ST3221, A/ST8900, D/ST69, D/ST2142, D/ST38, B1/ST2460 and B1/ST6448. High numbers of isolates harboured the class 1 integrons with various gene cassette arrays as well as IncP-1 and IncFIB plasmids. Our findings confirm the importance of WWTPs as hotspot collectors of ESBL-producing Enterobacteriaceae with a high likelihood of spread to human and natural environments.

Colistin Resistance Among Multiple Sequence Types of Klebsiella pneumoniae Is Associated With Diverse Resistance Mechanisms: A Report From India

Background: The resistance to colistin and carbapenems in Klebsiella pneumoniae infections have been associated with increased morbidity and mortality worldwide. A retrospective observational study was conducted to determine the prevalence and molecular events contributing to colistin resistance.

Methods: Clinical samples were screened for colistin resistance and underlying mechanisms were studied by PCR-based amplification and sequence analysis of genes of two-component regulatory system (phoPQ and pmrAB), regulatory transmembrane protein-coding mgrB, and mobilized colistin resistance genes (mcr-1-8). Gene expression of pmrC and pmrK was analyzed by qRT-PCR, and the genetic relationship was assessed by MLST. The putative effect of amino-acid substitutions was predicted by a combination of bioinformatics tools.

Results: Of 335 Klebsiella spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). K. pneumoniae isolates belonged to clonal complex-11 (CC11) with sequence types (STs): 14, 16, 43, 54, 147 and 395, whereby four isolates conferred three novel STs (3986, 3987 and 3988) profiles. Sequence analysis revealed non-synonymous potentially deleterious mutations in phoP (T151A), phoQ (del87–90, del263–264, L30Q, and A351D), pmrA (G53S), pmrB (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and mgrB (C28G) genes. The mgrB gene in three strains was disrupted by insertion sequences encoding IS1-like and IS5/IS1182 family-like transposase genes. All 11 isolates showed an elevation in the transcription level of pmrC gene. Mobilized colistin-resistance (mcr) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes bla_NDM-1-like, bla_OXA-48-like, and bla_CTX-M-like were detected in eight, five, and nine isolates, respectively.

Conclusion: All the studied colistin- and carbapenem-resistant K. pneumoniae isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.

Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study

Multidrug resistance due to the expression of extended spectrum β-lactamases (ESBLs) by bacterial pathogens is an alarming health concern with huge socio-economic burden. Here, 102 bacterial isolates from Wastewater treatment plants (WTPs) were screened for resistance to different antibiotics. Kirby-Bauer method and phenotypic disc confirmatory test confirmed the prevalence of 20 ESBLs. Polymerase chain reaction-based detection confirmed 11 bla_CTX-M positive bacterial isolates. Genotyping of bacterial isolates by 16S rRNA gene sequencing showed the dissemination of bla_CTX-M in Escherichia fergusonii, Escherichia coli, Shigella sp., Kluyvera georgiana and Enterobacter sp. Amongst Kluyvera georgiana isolates, two were harboring bla_CTX-M-152. The 3D model of CTX-M-152 protein was generated using SwissProt and characterized by Ramachandran plot and SAVES. A library of natural compounds was screened to identify novel CTX-M-152 inhibitor(s). High-throughput virtual screening (HTVS), standard precision (SP) and extra precision (XP) docking led to the identification of five natural compounds (Naringin dihydrochalcone, Salvianolic acid B, Inositol, Guanosine and Ellagic acid) capable of binding to active site of CTX-M-152. Futher, characterization by MM-GBSA (Molecular Mechanism General Born Surface Area), and ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) showed that Ellagic acid was the most potent inhibitor of CTX-M-152. Molecular dynamics simulation also confirmed that Ellagic acid form a stable complex with CTX-M-152. The ability of Ellagic acid to inhibit growth of bacteria harboring CTX-M-152 was confirmed by MIC (Minimum Inhibitory Concentration; broth dilution method) and Zone of Inhibition (ZOI) studies with respect to Cefotaxime. The identification of a novel inhibitor of CTX-M-152 from a natural source holds promise for employment in the control of bacterial infections.

Genetic characterization of ESBL-producing Escherichia coli and Klebsiella pneumoniae isolated from wastewater and river water in Tunisia: predominance of CTX-M-15 and high genetic diversity

Aquatic environments are crucial hotspots for the dissemination of antibiotic resistant microorganisms and resistance genes. Thus, the purpose of this study was to investigate the occurrence and the genetic characterization of cefotaxime-resistant (CTX^R) Enterobacteriaceae at a Tunisian semi-industrial pilot plant with biological treatment (WWPP) and its receiving river (Rouriche River, downstream from WWPP) located in Tunis City, during 2017-2018. We collected 105 and 15 water samples from the WWPP and the Rouriche River, respectively. Samples were screened to recover ESBL-producing Enterobacteriaceae (ESBL-E) and isolates were characterized for phenotype/genotype of antimicrobial resistance, integrons, plasmid types and molecular typing (multilocus sequence typing, MLST). Among 120 water samples, 33 and 4 contained ESBL-producing E. coli and K. pneumoniae isolates, respectively. Most isolates were multidrug resistant and produced CTX-M-15 (28 isolates), CTX-M-1 (4 isolates), CTX-M-55 (2 isolates), CTX-M-27 (one isolate), SHV-12 (one isolate) and VEB beta-lactamases (one isolate). All K. pneumoniae were CTX-M-15-positive. Four colistin-resistant isolates were found (MIC 4-8 μg/ml), but they were negative for the mcr genes tested. Class 1 integrons were detected in 21/25 trimethoprim/sulfamethoxazole-resistant isolates, and nine of them carried the gene cassette arrays: aadA2 + dfrA12 (n = 4), aadA1 + dfrA15 (n = 2), aadA5 + dfrA17 (n = 2) and aadA1/2 (n = 1). The IncP and IncFIB plasmids were found in 30 and 16 isolates, respectively. Genetic lineages detected were as follows: E. coli (ST48-ST10 Cplx, ST2499, ST906, ST2973 and ST2142); K. pneumoniae: (ST1540 and ST661). Our findings show a high rate of CTX-M-15 and high genetic diversity of ESBL-E isolates from WWPP and receiving river water.

Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India

Antibiotic resistance is one of the major current global health crises. Because of increasing contamination with antimicrobials, pesticides, and heavy metals, the aquatic environment has become a hotspot for emergence, maintenance, and dissemination of antibiotic and heavy metal resistance genes among bacteria. The aim of the present study was to determine the co-resistance to quinolones, ampicillin, and heavy metals among the bacterial isolates harboring extended-spectrum β-lactamases (ESBLs) genes. Among 73 bacterial strains isolated from a highly polluted stretch of the Yamuna River in Delhi, those carrying blaCTX-M, blaTEM, or blaSHV genes were analyzed to detect the genetic determinants of resistance to quinolones, ampicillin, mercury, and arsenic. The plasmid-mediated quinolone resistance (PMQR) gene qnrS was found in 22 isolates; however, the qnrA, B, C, and qnrD genes could not be detected in any of the bacteria. Two variants of CMY, blaCMY-2 and blaCMY-42, were identified among eight and seven strains, respectively. Furthermore, merB, merP, merT, and arsC genes were detected in 40, 40, 44, and 24 bacterial strains, respectively. Co-transfer of different resistance genes was also investigated in a transconjugation experiment. Successful transconjugants had antibiotic and heavy metal resistance genes with similar tolerance toward antibiotics and heavy metals as did their donors. This study indicates that the aquatic environment is a major reservoir of bacteria harboring resistance genes to antibiotics and heavy metals and emphasizes the need to study the genetic basis of resistant microorganisms and their public health implications.

Harmonized One Health Trans-Species and Community Surveillance for Tackling Antibacterial Resistance in India: Protocol for a Mixed Methods Study

Background

India has the largest burden of drug‑resistant organisms compared with other countries around the world, including multiresistant and extremely drug‑resistant tuberculosis and resistant Gram‑negative and Gram‑positive bacteria. Antibiotic resistant bacteria are found in all living hosts and in the environment and move between hosts and ecosystems. An intricate interplay of infections, exposure to antibiotics, and disinfectants at individual and community levels among humans, animals, birds, and fishes triggers evolution and spread of resistance. The One Health framework proposes addressing antibiotic resistance as a complex multidisciplinary problem. However, the evidence base in the Indian context is limited.

Objective

This multisectoral, trans-species surveillance project aims to document the infection and resistance patterns of 7 resistant-priority bacteria and the risk factors for resistance following the One Health framework and geospatial epidemiology.

Methods

This hospital- and community-based surveillance adopts a cross-sectional design with mixed methodology (quantitative, qualitative, and spatial) data collection. This study is being conducted at 6 microbiology laboratories and communities in Khurda district, Odisha, India. The laboratory surveillance collects data on bacteria isolates from different hosts and their resistance patterns. The hosts for infection surveillance include humans, animals (livestock, food chain, and pet animals), birds (poultry), and freshwater fishes (not crustaceans). For eligible patients, animals, birds and fishes, detailed data from their households or farms on health care seeking (for animals, birds and fishes, the illness, and care seeking of the caretakers), antibiotic use, disinfection practices, and neighborhood exposure to infection risks will be collected. Antibiotic prescription and use patterns at hospitals and clinics, and therapeutic and nontherapeutic antibiotic and disinfectant use in farms will also be collected. Interviews with key informants from animal breeding, agriculture, and food processing will explore the perceptions, attitudes, and practices related to antibiotic use. The data analysis will follow quantitative (descriptive and analytical), qualitative, and geospatial epidemiology principles.

Results

The study was funded in May 2019 and approved by Institute Ethics Committees in March 2019. The data collection started in September 2019 and shall continue till March 2021. As of June 2020, data for 56 humans, 30 animals and birds, and fishes from 10 ponds have been collected. Data analysis is yet to be done.

Conclusions

This study will inform about the bacterial infection and resistance epidemiology among different hosts, the risk factors for infection, and resistance transmission. In addition, it will identify the potential triggers and levers for further exploration and action.

International Registered Report Identifier (IRRID)

DERR1-10.2196/23241

Pharmaceutical disposal facilitates the mobilization of resistance determinants among microbiota of polluted environment

The emergence of resistance on exposure to pharmaceuticals among microorganisms has raised serious concern in the therapeutic approach against infectious diseases. Effluents discharge from hospitals, industries, and urban settlements containing pharmaceuticals and other toxic compounds into the aquatic ecosystem selects bacterial population against them; thereby promotes acquisition and dissemination of resistant traits among the inhabitant microbiota. The present study was aimed to determine the prevalence and multidrug resistance pattern of Extended Spectrum β-lactamase (ESBL) producing and non-producing bacterial isolates from the heavily polluted Delhi stretch of river Yamuna, India. Additionally, the role of abiotic factors in the dissemination of conjugative plasmids harbouring resistance genes was also studied using E. coli J53 as recipient and resistant E. coli isolates as donor strains. Of the 227 non-duplicate bacterial isolates, 60% (136) were identified as ESBL⁺ and 40% (91) as ESBL. ESBL⁺ isolates were found highly resistant to β-lactam and non-β-lactam classes of antibiotics compared with the ESBL^- isolates. 68% of ESBL⁺ and 24% of ESBL^- isolates showed an MAR index of ≥0.5. Surprisingly, multidrug resistance (MDR), extensively drug resistance (XDR), and pandrug resistance (PDR) phenotype were observed for 78.6%, 16.9%, and 0.7% of ESBL⁺ and 90%, 3%, and none for PDR among ESBL^- isolates. Conjugation under different conditions showed a higher mobilization rate at neutral pH (7-7.5) for ESBL⁺ isolates. Conjugation frequency was maximum at 40 °C for the isolate E. coli MRB6 (4.1 × 10^-5) and E. coli MRE32 (4.89 × 10^-4) and at 35 °C for E. coli MRA11 (4.89 × 10^-5). The transconjugants obtained were found tolerating different concentrations of mercuric chloride (0.0002-0.2 mg/L). Increased biofilm formation for ESBL⁺ isolates was observed on supplementing media with HgCl₂ (2 μg/mL) either singly or in combination with CTX (10 μg/mL). The present study demonstrates that anthropogenically influenced aquatic environments act as a reservoir of MDR, XDR, and even PDR strains; thereby posing a potent public health risk.

Antimicrobial resistance: Call for rational antibiotics practice in India

It is a well-known fact that microorganisms are developing resistance to antimicrobial drugs present in the market that is known as antimicrobial resistance (AMR). This resistance in microbes is a great matter of concern among the scientific fraternity. This review article focuses on antibiotics and their respective resistant microbes, factors that cause resistance among microbes, and consequences of AMR at global as well as Indian scenario. This article would be a helpful resource in nutshell for making the ground for discovery of new antibiotics that will be more effective toward microbes.

Bacterial isolates harboring antibiotics and heavy-metal resistance genes co-existing with mobile genetic elements in natural aquatic water bodies

The rise in antibiotic-resistant bacteria and contamination of water bodies is a serious issue that demands immense attention of scientific acumen. Here, we examined the pervasiveness of ESBL producing bacteria in Dal Lake and Wular Lake of Kashmir valley, India. Isolates were screened for antibiotic, heavy metal resistant elements, and their coexistence with mobile genetic elements. Out of two hundred one isolates screened, thirty-eight were found positive for ESBL production. Antibiotic profiling of ESBL positive isolates with 16 different drugs representing β-lactam or -non-β-lactam, exhibited multidrug resistance phenotype among 55% isolates. Molecular characterization revealed the occurrence of drug resistance determinants blaTEM, AmpC, qnrS, and heavy metal resistance genes (MRGs) merB, merP, merT, silE, silP, silS, and arsC. Furthermore, mobile genetic elements IntI, SulI, ISecp1, TN3, TN21 were also detected. Conjugation assay confirmed the transfer of different ARGs, HMRGs, and mobile elements in recipient Escherichia coli J53 AZ^R strain. Plasmid incompatibility studies showed blaTEM to be associated with Inc groups B/O, HI1, HI2, I1, N, FIA, and FIB. Co-occurrence of blaTEM, HMRGs, and mobile elements from the aquatic milieu of Kashmir, India has not been reported so far. From this study, the detection of the blaTEM gene in the bacteria Bacillus simplex and Brevibacterium frigoritolerans are found for the first time. Considering all the facts it becomes crucial to conduct studies in natural aquatic environments that could help depict the epidemiological situations in which the resistance mechanism might have clinical relevance.

Mass bathing events in River Kshipra, Central India- influence on the water quality and the antibiotic susceptibility pattern of commensal E.coli

BACKGROUND

Antibiotic resistance is one of the major global health emergencies. One potential source of dissemination of resistant bacteria is mass gatherings, e.g. mass bathing events. We evaluated the physicochemical parameters of water quality and the antibiotic resistance pattern in commensal Escherichia coli from river-water and river-sediment in pre-, during- and post-mass bathing events in river Kshipra, Central India.

METHOD/DESIGN

Water and sediment samples were collected from three selected points during eight mass bathing events during 2014-2016. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. In river water and sediment samples, antibiotic susceptibility patterns of isolated E. coli to 17 antibiotics were tested.

RESULTS

pH, turbidity and dissolved oxygen were significantly lower and total dissolved solid, free carbon dioxide were higher during mass bathing, whilst TSS, BOD and COD were lowest in pre-bathing and highest in post-bathing period. E.coli with multi drug resistance (MDR) or extended spectrum beta-lactamase (ESBL) production were between 9-44% and 6-24%, respectively in river-water as well as river-sediment. Total coliform count/ml and E. coli count were higher during-and post-bathing in river water than in pre-bathing period. Thus, the percentage of resistance was significantly higher during and post-bathing period (p<.05) than in pre-bathing. Colony forming unit (CFU)/ml in river-sediment was much higher than in river-water. Percentage of resistance was significantly higher in river-water (p<.05) than in river-sediment.

CONCLUSIONS

Antibiotic resistance in E.coli isolated from the Kshipra River showed significant variation during mass bathing events. Guidelines and regulatory standards are needed to control environmental dissemination of resistant bacteria.

Antimicrobial resistance in the environment: The Indian scenario

Antimicrobial resistance (AMR) continues to pose a significant public health problem in terms of mortality and economic loss. Health authorities of several countries including India have formulated action plans for its containment. In this fight against AMR, it is important to realize the contribution by all the following four spheres: humans, animals, food and environment. This review incorporates all the spheres of One Health concept from the Indian perspective. India has one of the highest rates of resistance to antimicrobial agents used both in humans and food animals. The environment, especially the water bodies, have also reported the presence of resistant organisms or their genes. Specific socio-economic and cultural factors prevalent in India make the containment of resistance more challenging. Injudicious use of antimicrobials and inadequate treatment of waste waters are important drivers of AMR in India. Use of sludge in agriculture, improper discard of livestock animals and aquaculture industry are considered AMR contributors in other countries but Indian data regarding these are lacking. Efforts to combat AMR have been initiated by the Indian health authorities but are still at preliminary stages. Keeping in view the challenges unique to India, future directions are proposed.

Prevalence and diversity of blaTEM, blaSHV and blaCTX-M variants among multidrug resistant Klebsiella spp. from an urban riverine environment in India

In the present study, we have investigated prevalence and diversity of ESBL genes among Klebsiella isolates obtained from highly polluted stretch of river Yamuna, India. Phenotypic screenings of 116 Klebsiella isolates revealed ~30% were positive for ESBL production. Antibiotic profiling showed multidrug resistance phenotype among 90% isolates. Prevalence of blaTEM, blaSHV and blaCTX-M genes were found to be 57, 54 and 48% respectively. Furthermore, we identified eight variants of blaSHV (SHV-1, SHV-11, SHV-27, SHV-28, SHV-38, SHV-61, SHV-144, SHV-148), three each of blaTEM (TEM-1, TEM-116, TEM-206) and blaCTX-M (CTX-M-15, CTX-M-55, CTX-M-188) among Klebsiella spp. Co-occurrence of blaTEM, blaSHV and blaCTX-M (any two or all three) was observed among 45% Klebsiella isolates. Occurrence of blaCTX-M-188 and blaTEM-206 in environmental isolates of K. pneumoniae has not been reported earlier. Identification of blaTEM-206, blaSHV-27 and blaSHV-144 from Klebsiella spp. and blaTEM-116 from K. quasipneumoniae and K. variicola is the first report from India.

River Ganges water as reservoir of microbes with antibiotic and metal ion resistance genes: High throughput metagenomic approach

The large scale usage of antibiotics and trace elements leads to their progressive release in the environment, and ultimately the spread of antibiotic resistance genes (ARGs) and metal ion resistance genes (MRGs) in bacteria. A high-throughput metagenomic sequencing of the microbial community in water and sediments in the river Ganges harboring resistance genes was performed. The results revealed that the river harbors a broad spectrum of resistance genes with high abundance in sediments. The highly dominant ARGs type was beta-lactam, multidrug/efflux and elfamycin. The ARGs such as (tuf, parY, ileS, mfd) were highly abundant in water and sediments. The MRGs subtype acn was the most abundant metal resistance gene in water and sediments. Majority of ARGs types showed significant (p ≤ 0.05) positive correlation with the MRGs types in the river environment suggesting their distribution and transfer to be possibly linked. Taxonomic classification revealed that Proteobacteria and Actinobacteria were the two most abundant phyla in water and sediments. Arcobacter, Terrimicrobium, Acidibacter and Pseudomonas were the most abundant genera. This study suggests that antibiotics and metals are the driving force for the emergence of resistance genes, and their subsequent propagation and accumulation in the environmental bacteria. The present metagenomic investigation highlights significance of such study, and attracts attention for the mitigation of pollutants associated with the propagation of ARGs and MRGs in the river environment.

Antibiotic Resistance Characterization of Environmental E. coli Isolated from River Mula-Mutha, Pune District, India

In the current study, ceftazidime- and ciprofloxacin-resistant—or dual drug-resistant (DDR)—E. coli were isolated from river Mula-Mutha, which flows through rural Pune district and Pune city. The DDR E. coli were further examined for antibiotic resistance to six additional antibiotics. The study also included detection of genes responsible for ceftazidime and ciprofloxacin resistance and vectors for horizontal gene transfer. Twenty-eight percent of the identified DDR E. coli were resistant to more than six antibiotics, with 12% being resistant to all eight antibiotics tested. Quinolone resistance was determined through the detection of qnrA, qnrB, qnrS and oqxA genes, whereas cephalosporin resistance was confirmed through detection of TEM, CTX-M-15, CTX-M-27 and SHV genes. Out of 219 DDR E. coli, 8.2% were qnrS positive and 0.4% were qnrB positive. Percentage of isolates positive for the TEM, CTX-M-15 and CTX-M-27 genes were 32%, 46% and 0.9%, respectively. None of the DDR E. coli tested carried the qnrA, SHV and oqxA genes. Percentage of DDR E. coli carrying Class 1 and 2 integrons (mobile genetic elements) were 47% and 8%, respectively. The results showed that antibiotic resistance genes (ARGs) and integrons were present in the E. coli isolated from the river at points adjoining and downstream of Pune city.

Study of pandrug and heavy metal resistance among E. coli from anthropogenically influenced Delhi stretch of river Yamuna

Escalating burden of antibiotic resistance that has reached new heights present a grave concern to mankind. As the problem is no longer confined to clinics, we hereby report identification of a pandrug resistant Escherichia coli isolate from heavily polluted Delhi stretch of river Yamuna, India. E. coli MRC11 was found sensitive only to tobramycin against 21 antibiotics tested, with minimum inhibitory concentration values >256μg/mL for amoxicillin, carbenicillin, aztreonam, ceftazidime and cefotaxime. Addition of certain heavy metals at higher concentrations were ineffective in increasing susceptibility of E. coli MRC11 to antibiotics. Withstanding sub-optimal concentration of cefotaxime (10μg/mL) and mercuric chloride (2μg/mL), and also resistance to their combinatorial use, indicates better adaptability in heavily polluted environment through clustering and expression of resistance genes. Interestingly, E. coli MRC11 harbours two different variants of blaTEM (blaTEM-116 and blaTEM-1 with and without extended-spectrum activity, respectively), in addition to mer operon (merB, merP and merT) genes. Studies employing conjugation, confirmed localization of blaTEM-116, merP and merT genes on the conjugative plasmid. Understanding potentialities of such isolates will help in determining risk factors attributing pandrug resistance and strengthening strategic development of new and effective antimicrobial agents.

Unexpected common occurrence of transferable extended spectrum cephalosporinase-producing Escherichia coli in Swedish surface waters used for drinking water supply

The presence of Enterobacteriaceae producing extended spectrum beta-lactamases (ESBL) or transferable AmpC beta-lactamases (pAmpC) is increasingly being reported in humans, food-producing animals and food world-wide. However, the occurrence and impact of these so-called extended spectrum cephalosporinase (ESC)-producing Enterobacteriaceae in aquatic environments are poorly documented. This study investigated the occurrence, concentrations and characteristics of ESC-producing E. coli (ESC-Ec) in samples of surface water collected at five Swedish water treatment plants that normally have relatively high prevalence and concentration of E. coli in surface water. ESC-Ec was found in 27 of 98 surface water samples analysed. All but two positive samples were collected at two of the water treatment plants studied. The ESC-Ec concentration, 1-3cfu/100mL, represented approximately 4% of the total amount of E. coli in the respective surface water sample. In total, 74% of the isolates were multi-resistant, but no isolate was resistant to carbapenems. Six types of ESBL/pAmpC genes were found in the 27 E. coli isolates obtained from the positive samples, of which four (bla_CTX-M-15, bla_CMY-2, bla_CTX-M-1 and bla_CTX-M-14) were found during the whole sampling period, in samples taken at more than one water treatment plant. In addition, the genes were situated on various types of plasmids and most E. coli isolates were not closely related with regard to MLST types. The combinations of ESBL/pAmpC genes, plasmids and E. coli isolates were generally similar to those found previously in healthy and sick individuals in Sweden. In conclusion, the occurrence of ESC-Ec in Swedish surface water shows that resistant bacteria of clinical concern are present in aquatic environments even in a low-prevalence country such as Sweden.

A Three-Year Follow-Up Study of Antibiotic and Metal Residues, Antibiotic Resistance and Resistance Genes, Focusing on Kshipra-A River Associated with Holy Religious Mass-Bathing in India: Protocol Paper

BACKGROUND

Antibiotic resistance (ABR) is one of the major health emergencies for global society. Little is known about the ABR of environmental bacteria and therefore it is important to understand ABR reservoirs in the environment and their potential impact on health.

METHOD/DESIGN

Quantitative and qualitative data will be collected during a 3-year follow-up study of a river associated with religious mass-bathing in Central India. Surface-water and sediment samples will be collected from seven locations at regular intervals for 3 years during religious mass-bathing and in absence of it to monitor water-quality, antibiotic residues, resistant bacteria, antibiotic resistance genes and metals. Approval has been obtained from the Ethics Committee of R.D. Gardi Medical College, Ujjain, India (No. 2013/07/17-311).

RESULTS

The results will address the issue of antibiotic residues and antibiotic resistance with a focus on a river environment in India within a typical socio-behavioural context of religious mass-bathing. It will enhance our understanding about the relationship between antibiotic residue levels, water-quality, heavy metals and antibiotic resistance patterns in Escherichia coli isolated from river-water and sediment, and seasonal differences that are associated with religious mass-bathing. We will also document, identify and clarify the genetic differences/similarities relating to phenotypic antibiotic resistance in bacteria in rivers during religious mass-bathing or during periods when there is no mass-bathing.