{"title":"Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences.","authors":"Mrinmoy Patra, Anand Kumar Pandey, Suresh Kumar Dubey","doi":"10.1007/s11274-025-04323-9","DOIUrl":null,"url":null,"abstract":"<p><p>The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 4","pages":"114"},"PeriodicalIF":4.0000,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"World journal of microbiology & biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1007/s11274-025-04323-9","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.
期刊介绍：
World Journal of Microbiology and Biotechnology publishes research papers and review articles on all aspects of Microbiology and Microbial Biotechnology.
Since its foundation, the Journal has provided a forum for research work directed toward finding microbiological and biotechnological solutions to global problems. As many of these problems, including crop productivity, public health and waste management, have major impacts in the developing world, the Journal especially reports on advances for and from developing regions.
Some topics are not within the scope of the Journal. Please do not submit your manuscript if it falls into one of the following categories:
· Virology
· Simple isolation of microbes from local sources
· Simple descriptions of an environment or reports on a procedure
· Veterinary, agricultural and clinical topics in which the main focus is not on a microorganism
· Data reporting on host response to microbes
· Optimization of a procedure
· Description of the biological effects of not fully identified compounds or undefined extracts of natural origin
· Data on not fully purified enzymes or procedures in which they are applied
All articles published in the Journal are independently refereed.
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