Browsing by Author "Animesh Tripathi"

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Antimicrobial resistance in plant endophytes associated with poultry-manure application revealed by selective culture and whole genome sequencing
(Elsevier B.V., 2024) Animesh Tripathi; Anjali Jaiswal; Dinesh Kumar; Priyank Chavda; Ramesh Pandit; Madhvi Joshi; Damer P. Blake; Fiona M. Tomley; Chaitanya G. Joshi; Suresh Kumar Dubey
Poultry manure is widely used as organic fertilizer in agriculture during the cultivation of crops, but the persistent high-level use of antibiotics in poultry production has raised concerns about the selection for reservoirs of antimicrobial resistance genes (ARGs). Previous studies have shown that the addition of poultry manure can increase the abundance of genes associated with resistance to tetracyclines, aminoglycosides, fluoroquinolones, sulfonamides, bacitracin, chloramphenicol, and macrolide-lincosamide-streptogramin in soil and plants. Understanding the microbial populations that harbor these ARGs is important to identify microorganisms that could enter the human food chain. Here, we test the hypothesis that environmental exposure to poultry manure increases the occurrence of antimicrobial resistance (AMR) in plant endophytes using selective culture, phenotypic Antibiotic Susceptibility Testing (AST), phylogenetic analysis, and whole genome sequencing (WGS). Endophytes from poultry manure treated Sorghum bicolor (L.) Moench plant root and stem samples showed increased phenotypic and genotypic resistance against multiple antibiotics compared to untreated controls. Comparison of AMR phenotype-to-genotype relationships highlighted the detection of multi-drug resistant (MDR) plant endophytes, demonstrating the value of genomic surveillance for emerging drug-resistant pathogens. The increased occurrence of ARGs in poultry manure-exposed endophytes highlights the need for responsible antibiotic use in poultry and animal farming to reduce contamination of ecological niches and transgression into endophytic plant microbiome compartments. It also emphasizes the requirement for proper manure management practices and vigilance in monitoring and surveillance efforts to tackle the growing problem of antibiotic resistance and preserve the efficacy of antibiotics for human and veterinary medicine. © 2024 Elsevier B.V.
Biodegradation of fipronil: molecular characterization, degradation kinetics, and metabolites
(Springer Science and Business Media Deutschland GmbH, 2023) Anjali Jaiswal; Animesh Tripathi; Suresh Kumar Dubey
Fipronil (C12H4Cl2F6N4OS) is a commonly used insecticide effective against numerous insects and pests. Its immense application poses harmful effects on various non-target organisms as well. Therefore, searching the effective methods for the degradation of fipronil is imperative and logical. In this study, fipronil-degrading bacterial species are isolated and characterized from diverse environments using a culture-dependent method followed by 16S rRNA gene sequencing. Phylogenetic analysis showed the homology of organisms with Acinetobacter sp., Streptomyces sp., Pseudomonas sp., Agrobacterium sp., Rhodococcus sp., Kocuria sp., Priestia sp., Bacillus sp., Aeromonas sp., and Pantoea sp. The bacterial degradation potential for fipronil was analyzed through high-performance liquid chromatography (HPLC). Incubation-based degradation studies revealed that Pseudomonas sp. and Rhodococcus sp. were found to be the most potent isolates that degraded fipronil at 100 mg L−1 concentration, with removal efficiencies of 85.9 and 83.6%, respectively. Kinetic parameter studies, following the Michaelis-Menten model, also revealed the high degradation efficiency of these isolates. Gas chromatography-mass spectrometry (GC-MS) analysis revealed fipronil sulfide, benzaldehyde, (phenyl methylene) hydrazone, isomenthone, etc., as major metabolites of fipronil degradation. Overall investigation suggests that native bacterial species isolated from the contaminated environments could be efficiently utilized for the biodegradation of fipronil. The outcome derived from this study has immense significance in formulating an approach for bioremediation of fipronil-contaminated surroundings. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Exploring Fate of Fipronil in Different Agricultural Soils Using Adsorption–Desorption and Degradation Processes
(Springer Nature, 2025) Anjali Jaiswal; Animesh Tripathi; Suresh Kumar Dubey
The adsorption–desorption characteristics of fipronil vary widely among soil types and are intricate and complex. These interactions greatly influence its environmental behaviour, impacting its mobility, bioavailability, persistence, and possible risks. To properly anticipate the behaviour of fipronil in different soil ecosystems, in-depth studies focusing on particular soil features and local environmental variables are required. Adsorption–desorption characteristics of fipronil on three different soils in Eastern Uttar Pradesh were studied. Distribution coefficient (Kd) values ranged from 2.90—0.686 L kg−1, found maximum for soil S3 and minimum for soil S2 and had a close relationship with the soil's organic carbon content. The adsorption capacities of different soils were as follows: vertisol (S3) > inceptisol (S1) > alfisol (S2). Freundlich model is a better fit for the adsorption isotherms, and Freundlich adsorption coefficients (Kf) values increased as the soils' organic carbon content increased. Maximum hysteresis effect (minimum Hysteresis-Index) was observed for soil S3. The calculated Gibbs energy change (ΔG) value for each soil was ~ 13 kJ mol−1, indicating that van der Waals force is predominant in adsorption of fipronil in the soil. The degradation rate was found to be maximum for soil S3 and minimum for soil S2. It is imperative to comprehend and manage these processes with the intent of ensuring the safe use of fipronil in industry, agriculture, and other sectors for the maintenance of environmental health. Designing soil and water remediation-techniques requires understanding these features since adding materials that improve adsorption can help immobilise pollutants like pesticides including fipronil. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.
Immune Responses to Filarial Nematodes: A Mechanistic Evaluation of Evasion and Modulation Strategies
(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Tripti Singh; Shivani Sharma; Animesh Tripathi; Sunil Kumar; Anchal Pratap Singh
Filarial parasites are long-lived organisms that cause extreme morbidity due to pathological manifestations, including lymphedema, hydrocele, and elephantiasis. Understanding the hosts’ immune responses to filarial parasites is crucial to developing new and effective anti-filarial treatments. The review thoroughly examines and summarises immunological modulation, evasion strategies, and filarial–host immune interactions to provide an updated knowledge of the immune evasion manoeuvres used by filarial parasites. An extensive literature search was conducted using databases such as PubMed, Google Scholar, ScienceDirect, Web of Science, and Scopus to identify articles published mostly between 2000 and 2025 that focus on the crucial molecular, cellular, and immunomodulatory strategies of filarial parasites. The immune evasion mechanisms include the modulation of effector T cells, induction of apoptosis in immune cells, the release of immunomodulatory proteins, and the induction of regulatory immune cell populations, thereby ensuring the mutual survival of both the parasite and the host. An antigen-specific T helper 2 (Th2) response and an increase in Interleukin-10 (IL-10) producing CD4+ T cells, along with a suppressed T helper 1 (Th1) response, are the key immunological characteristics of filarial pathogenesis. This antigen-specific T-cell hyporesponsiveness seems necessary for keeping the long-term infection going, which often involves large parasite densities. This review summarises filarial parasites’ mechanisms and strategies in regulating host immune responses and will facilitate future studies on the filarial pathogenesis, leading to the development of novel anti-filarial therapeutics. © 2025 by the authors.
Omics-centric evidences of fipronil biodegradation by Rhodococcus sp. FIP_B3
(Elsevier Ltd, 2025) Anjali Jaiswal; Anand Kumar Pandey; Animesh Tripathi; Suresh Kumar Dubey
The widespread use of the pesticide fipronil in domestic and agriculture sectors has resulted in its accumulation across the environment. Its use to assure food security has inadvertently affected soil microbiome composition, fertility and, ultimately, human health. Degradation of residual fipronil present in the environment using specific microbial species is a promising strategy for its removal. The present study delves into the omics approach for fipronil biodegradation using the native bacterium Rhodococcus sp. FIP_B3. It has been observed that within 40 days, nearly 84% of the insecticide gets degraded. The biodegradation follows a pseudo-first-order kinetics (k = 0.0197/d with a half-life of ∼11 days). Whole genome analysis revealed Cytochrome P450 monooxygenase, peroxidase-related enzyme, haloalkane dehalogenase, 2-nitropropane dioxygenase, and aconitate hydratase are involved in the degradation process. Fipronil-sulfone, 5-amino-1-(2-chloro-4-(trifluoromethyl)phenyl)-4- ((trifluoromethyl)sulfonyl)-1H-pyrazole-3-carbonitrile, (E)-5-chloro-2-oxo-3- (trifluoromethyl)pent-4-enoic acid, 4,4,4-trifluoro-2-oxobutanoic acid, and 3,3,3- trifluoropropanoic acid were identified as the major metabolites that support the bacterial degradation of fipronil. In-silico molecular docking and molecular dynamic simulation-based analyses of degradation pathway intermediates with their respective enzymes have indicated stable interactions with significant binding energies (−5.9 to −9.7 kcal/mol). These results have provided the mechanistic cause of the elevated potential of Rhodococcus sp. FIP_B3 for fipronil degradation and will be advantageous in framing appropriate strategies for the bioremediation of fipronil-contaminated environment. © 2024 Elsevier Ltd
Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant
(Elsevier Ltd, 2023) Animesh Tripathi; Dinesh Kumar; Priyank Chavda; Dalip Singh Rathore; Ramesh Pandit; Damer Blake; Fiona Tomley; Madhvi Joshi; Chaitanya G. Joshi; Suresh Kumar Dubey
Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health. © 2023 Elsevier Ltd
Whole genome sequencing revealed high occurrence of antimicrobial resistance genes in bacteria isolated from poultry manure
(Elsevier B.V., 2025) Animesh Tripathi; Anjali Jaiswal; Dinesh Vinoth Kumar; Ramesh J. Pandit; Damer P. Blake; Fiona M. Tomley; Madhvi N. Joshi; C. G. Joshi; Suresh Kumar Dubey
Background: Global demand for food has driven expansion and intensification of livestock production, particularly in developing nations where antibiotic use is often routine. Waste from poultry production, including manure, is commonly utilized as fertilizers in agroecosystems, risking environmental contamination with potentially zoonotic bacteria and antimicrobial resistance genes (ARGs). Methods: Here, 33 bacterial isolates were recovered from broiler (n = 17) and layer (n = 16) chicken manure by aerobic culture using Luria Bertani agar. Antimicrobial susceptibility testing (AST) was performed using disc diffusion method. MALDI-ToF and 16S rRNA sequencing were used to identify and compare a subset of antibiotic-resistant isolates (n = 13). Comparison of whole genome sequence assemblies and phenotypic assays were used to assess capacity for biofilm formation, heavy metal tolerance and virulence. Results: AST by disc diffusion revealed all isolates were resistant to a minimum of three antibiotics, with resistance to ampicillin, co-trimoxazole, fluoroquinolones, tetracyclines, streptomycin, rifampicin and/or chloramphenicol detected. Stutzerimonas sp. and Acinetobacter sp. were the common genera observed in this study. Genome sequencing of each selected isolate revealed carriage of multiple ARGs capable of conferring resistance to many antimicrobials commonly employed in poultry production and human medicine, including tetracyclines, quinolones, macrolides, sulfonamide and cephalosporins. Conclusions: The high occurrence of ARGs in studied bacterial isolates confirms that poultry manure could act as a source of genetic material that could be transferred to commensal microbiota and opportunistic pathogens of humans. Understanding the complex resistome interplay between humans, animals, and the environment requires a One Health approach, with implications for agricultural settings and public health. © 2025 Elsevier Ltd and International Society of Antimicrobial Chemotherapy