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Gupta SS, Hamza Kh M, Sones CL, Zhang X, Sivaraman GK. The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems. Funct Integr Genomics 2024; 24:110. [PMID: 38806846 DOI: 10.1007/s10142-024-01362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/30/2024]
Abstract
With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.
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Affiliation(s)
- Sobin Sonu Gupta
- Founder & CEO at Times of Biotech, Navelim Bicholim, Goa-403505, India
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Muneeb Hamza Kh
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Collin L Sones
- Founder and CTO of Highfield Diagnostics, Zepler Institute of Photonics and Nanoelectronics, University of Southampton, SO17 1BJ, Southampton, UK
| | - Xunli Zhang
- School of Engineering & Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India.
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Kumar A, Sharma S, Dindhoria K, Thakur A, Kumar R. Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production. Int Microbiol 2024:10.1007/s10123-024-00530-w. [PMID: 38760649 DOI: 10.1007/s10123-024-00530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.
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Affiliation(s)
- Aman Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sonia Sharma
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kiran Dindhoria
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Aman Thakur
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakshak Kumar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Department of Molecular Biology & Bioinformatics, Tripura University (A Central University), Suryamaninagar, Tripura, 799022, India.
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Lee J, Cha I, Lee K, Son YK, Cho S, Seol D. Complete genome sequence and potential pathogenic assessment of Flavobacterium plurextorum RSG-18 isolated from the gut of Schlegel's black rockfish, Sebastes schlegelii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13226. [PMID: 38298071 PMCID: PMC10878011 DOI: 10.1111/1758-2229.13226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/04/2023] [Indexed: 02/02/2024]
Abstract
Flavobacterium plurextorum is a potential fish pathogen of interest, previously isolated from diseased rainbow trout (Oncorhynchus mykiss) and oomycete-infected chum salmon (Oncorhynchus keta) eggs. We report here the first complete genome sequence of F. plurextorum RSG-18 isolated from the gut of Schlegel's black rockfish (Sebastes schlegelii). The genome of RSG-18 consists of a circular chromosome of 5,610,911 bp with a 33.57% GC content, containing 4858 protein-coding genes, 18 rRNAs, 63 tRNAs and 1 tmRNA. A comparative analysis was conducted on 11 Flavobacterium species previously reported as pathogens or isolated from diseased fish to confirm the potential pathogenicity of RSG-18. In the SEED classification, RSG-18 was found to have 36 genes categorized in 'Virulence, Disease and Defense'. Across all Flavobacterium species, a total of 16 antibiotic resistance genes and 61 putative virulence factors were identified. All species had at least one phage region and type I, III and IX secretion systems. In pan-genomic analysis, core genes consist of genes linked to phages, integrases and matrix-tolerated elements associated with pathology. The complete genome sequence of F. plurextorum RSG-18 will serve as a foundation for future research, enhancing our understanding of Flavobacterium pathogenicity in fish and contributing to the development of effective prevention strategies.
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Affiliation(s)
- Jisol Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
| | - In‐Tae Cha
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | - Ki‐Eun Lee
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | - Youn Kyoung Son
- Microorganism Resources DivisionNational Institute of Biological ResourcesIncheonSouth Korea
| | | | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulSouth Korea
- Department of SurgerySeoul National University Bundang HospitalSeongnamSouth Korea
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Srivastava A, Verma D. Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India. World J Microbiol Biotechnol 2023; 39:294. [PMID: 37656255 DOI: 10.1007/s11274-023-03730-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/13/2023] [Indexed: 09/02/2023]
Abstract
A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environemntal Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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Gieseker CM, Gaunt PS, Hawke JP, Crosby TC, Hasbrouck NR, Gao DX, Declercq AM. Epidemiological Cutoff Values for Standard Broth Microdilution Susceptibility Testing of Flavobacterium columnare Isolated from Fishes. Microb Drug Resist 2022; 28:948-955. [PMID: 35972354 DOI: 10.1089/mdr.2022.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Flavobacterium columnare, the causative agent of columnaris disease in a large variety of freshwater fish, is a major problem in commercial aquaculture. A limited number of antimicrobial therapies are available to control this disease; therefore, these agents must be used judiciously. To facilitate effective monitoring for changes in susceptibility, the Clinical Laboratory Standards Institute (CLSI) has a standard broth microdilution test method specific for F. columnare. However, there are no CLSI-approved criteria (termed epidemiological cutoff values [ECVs]) to interpret results. Nevertheless, researchers have developed provisional ECVs based on testing by one laboratory. To satisfy CLSI data requirements, three laboratories used the standard method to generate additional antimicrobial susceptibility data against ampicillin, enrofloxacin, erythromycin, florfenicol, flumequine, gentamicin, oxolinic acid, oxytetracycline, sulfadimethoxine/ormetoprim, and sulfamethoxazole-trimethoprim using 109 F. columnare isolates. The new data combined with previously published data from 120 F. columnare isolates were analyzed and ECVs proposed to CLSI. Of the 10 antimicrobials, ECVs were approved for ampicillin, enrofloxacin, erythromycin, florfenicol, flumequine, oxolinic acid, and oxytetracycline, which were published in the 2020 edition of the CLSI document VET04 performance standards. These ECVs will help microbiologists categorize decreased antimicrobial susceptibility among F. columnare and will help in surveillance efforts to ensure judicious antimicrobial use.
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Affiliation(s)
- Charles M Gieseker
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Patricia S Gaunt
- Thad Cochran National Warmwater Aquaculture Center, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, USA
| | - John P Hawke
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Tina C Crosby
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Nicholas R Hasbrouck
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Dana X Gao
- Thad Cochran National Warmwater Aquaculture Center, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi, USA
| | - Annelies M Declercq
- Department of Animal Sciences and Aquatic Ecology, Laboratory of Aquaculture and Artemia Reference Center, Ghent University, Ghent, Belgium.,Department of Pathology, Bacteriology, and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Rahmatelahi H, El-Matbouli M, Menanteau-Ledouble S. Delivering the pain: an overview of the type III secretion system with special consideration for aquatic pathogens. Vet Res 2021; 52:146. [PMID: 34924019 PMCID: PMC8684695 DOI: 10.1186/s13567-021-01015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are known to subvert eukaryotic cell physiological mechanisms using a wide array of virulence factors, among which the type three-secretion system (T3SS) is often one of the most important. The T3SS constitutes a needle-like apparatus that the bacterium uses to inject a diverse set of effector proteins directly into the cytoplasm of the host cells where they can hamper the host cellular machinery for a variety of purposes. While the structure of the T3SS is somewhat conserved and well described, effector proteins are much more diverse and specific for each pathogen. The T3SS can remodel the cytoskeleton integrity to promote intracellular invasion, as well as silence specific eukaryotic cell signals, notably to hinder or elude the immune response and cause apoptosis. This is also the case in aquatic bacterial pathogens where the T3SS can often play a central role in the establishment of disease, although it remains understudied in several species of important fish pathogens, notably in Yersinia ruckeri. In the present review, we summarise what is known of the T3SS, with a special focus on aquatic pathogens and suggest some possible avenues for research including the potential to target the T3SS for the development of new anti-virulence drugs.
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Affiliation(s)
- Hadis Rahmatelahi
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Simon Menanteau-Ledouble
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria.
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Ø, Denmark.
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