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Denissen J, Reyneke B, Waso-Reyneke M, Havenga B, Barnard T, Khan S, Khan W. Prevalence of ESKAPE pathogens in the environment: Antibiotic resistance status, community-acquired infection and risk to human health. Int J Hyg Environ Health 2022; 244:114006. [PMID: 35841823 DOI: 10.1016/j.ijheh.2022.114006] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 01/10/2023]
Abstract
The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens are characterised by increased levels of resistance towards multiple classes of first line and last-resort antibiotics. Although these pathogens are frequently isolated from clinical environments and are implicated in a variety of life-threatening, hospital-associated infections; antibiotic resistant ESKAPE strains have been isolated from environmental reservoirs such as surface water, wastewater, food, and soil. Literature on the persistence and subsequent health risks posed by the ESKAPE isolates in extra-hospital settings is however, limited and the current review aims to elucidate the primary reservoirs of these pathogens in the environment, their antibiotic resistance profiles, and the link to community-acquired infections. Additionally, information on the current state of research regarding health-risk assessments linked to exposure of the ESKAPE pathogens in the natural environment, is outlined.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Monique Waso-Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Tobias Barnard
- Water and Health Research Centre, University of Johannesburg, PO Box 17011, Doornfontein, 7305, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Geng N, Sun G, Liu WJ, Gao BC, Sun C, Xu C, Hua E, Xu L. Distribution, Phylogeny and Evolution of Clinical and Environmental Vibrio vulnificus Antibiotic-Resistant Genes. Evol Bioinform Online 2022; 18:11769343221134400. [PMID: 36404992 PMCID: PMC9669696 DOI: 10.1177/11769343221134400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Vibrio vulnificus is an emergent marine pathogen and is the
cause of a deadly septicemia. However, the evolution mechanism of
antibiotic-resistant genes (ARGs) is still unclear. Twenty-two high-quality
complete genomes of V. vulnificus were obtained and grouped
into 16 clinical isolates and 6 environmental isolates. Genomic annotations
found 23 ARG orthologous genes, among which 14 ARGs were shared by V.
vulnificus and other Vibrio members. Furthermore,
those ARGs were located in their chromosomes, rather than in the plasmids.
Phylogenomic reconstruction based on single-copy orthologous protein sequences
and ARG protein sequences revealed that clinical and environmental V.
vulnificus isolates were in a scattered distribution. The
calculation of non-synonymous and synonymous substitutions indicated that most
of ARGs evolved under purifying selection with the
Ka/Ks ratios lower than one, while
h-ns, rsmA, and soxR in several clinical
isolates evolved under the positive selection with
Ka/Ks ratios >1. Our result indicated
that V. vulnificus antibiotic-resistant armory was not only
confined to clinical isolates, but to environmental ones as well and clinical
isolates inclined to accumulate beneficial non-synonymous substitutions that
could be retained to improve competitiveness.
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Affiliation(s)
- Nan Geng
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Guojin Sun
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Wen-Jia Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Bin-Cheng Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
| | - Cundong Xu
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Ertian Hua
- Key Laboratory for Technology in Rural Water Management of Zhejiang Province, Zhejiang University of Water Resources and Electric Power, Hangzhou, People’s Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd, Shaoxing, People’s Republic of China
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Zubkov IN, Nepomnyshchiy AP, Kondratyev VD, Sorokoumov PN, Sivak KV, Ramsay ES, Shishlyannikov SM. Adaptation of Pseudomonas helmanticensis to fat hydrolysates and SDS: fatty acid response and aggregate formation. J Microbiol 2021; 59:1104-1111. [PMID: 34697784 DOI: 10.1007/s12275-021-1214-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/15/2023]
Abstract
An essential part of designing any biotechnological process is examination of the physiological state of producer cells in different phases of cultivation. The main marker of a bacterial cell's state is its fatty acid (FA) profile, reflecting membrane lipid composition. Consideration of FA composition enables assessment of bacterial responses to cultivation conditions and helps biotechnologists understand the most significant factors impacting cellular metabolism. In this work, soil SDS-degrading Pseudomonas helmanticensis was studied at the fatty acid profile level, including analysis of rearrangement between planktonic and aggregated forms. The set of substrates included fat hydrolysates, SDS, and their mixtures with glucose. Such media are useful in bioplastic production since they can help incrementally lower overall costs. Conventional gas chromatography-mass spectrometry was used for FA analysis. Acridine orange-stained aggregates were observed by epifluorescence microscopy. The bacterium was shown to change fatty acid composition in the presence of hydrolyzed fats or SDS. These changes seem to be driven by the depletion of metabolizable substrates in the culture medium. Cell aggregation has also been found to be a defense strategy, particularly with anionic surfactant (SDS) exposure. It was shown that simple fluidity indices (such as saturated/unsaturated FA ratios) do not always sufficiently characterize a cell's physiological state, and morphological examination is essential in cases where complex carbon sources are used.
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Affiliation(s)
- Ilya N Zubkov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia.
| | - Anatoly P Nepomnyshchiy
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Vadim D Kondratyev
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Pavel N Sorokoumov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
| | - Konstantin V Sivak
- Smorodintsev Research Institute of Influenza, 15/17 Ulitsa Professora Popova, Saint Petersburg, 4197022, Russia
| | - Edward S Ramsay
- Smorodintsev Research Institute of Influenza, 15/17 Ulitsa Professora Popova, Saint Petersburg, 4197022, Russia
| | - Sergey M Shishlyannikov
- All-Russian Research Institute for Food Additives, Branch of V. M. Gorbatov Federal Research Center for Food Systems (RAS), 55 Liteyny Prospekt, Saint Petersburg, 191014, Russia
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Nair AV, K PN, M LA, Vijayan KK. Antibacterial assay guided isolation of a novel hydroxy-substituted pentacyclo ketonic compound from Pseudomonas aeruginosa MBTDCMFRI Ps04. Braz J Microbiol 2020; 52:335-347. [PMID: 33237498 DOI: 10.1007/s42770-020-00404-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022] Open
Abstract
Antimicrobial compounds from the natural source have gained greater relevance because of their wide spectrum of possible applications, especially in the aquaculture industry where pathogenic threat and antibacterial resistance are serious concerns. In this regard, Pseudomonas aeruginosa MBTDCMFRI Ps04 (P. aeruginosa Ps04) strain isolated from the tropical estuarine habitats of Cochin was evaluated for its antibacterial potential against major aquaculture pathogens. The physiological conditions for the maximum production of the active metabolite were also optimized. An activity-guided approach was employed further to isolate and characterize the secondary metabolite responsible for the inhibitory potential. It was found that the cell free supernatant (CFS) of P. aeruginosa Ps04 exhibited strong antibacterial activity against major aquaculture pathogens belonging to the genus Vibrio and Aeromonas and retained its potential even at 30% (v/v) dilution. The highest antibacterial activity was detected from 3rd day culture, grown in glycerol alanine media (1% each) as carbon and nitrogen source, respectively, at 30 °C, pH 7.0 and at a salinity of 20 parts per thousand (ppt). The activity of the antagonistic principle was found to be stable against variations in pH (pH 2-pH 12), temperature (up to 120 °C) and enzymatic treatments. Bioassay-guided purification followed by spectroscopic characterization of active fractions of P. aeruginosa Ps04 revealed that the compound 4-Hydroxy-11-methylpentacyclo [11.8.0.02,3.011, 12.016,17]henicosa-1,3,5,8(9),17-penten-14-one is responsible for its major antibacterial activity. The results of this study indicated that P. aeruginosa Ps04 has beneficial antibacterial properties which could be used in developing novel antimicrobial therapeutics against a variety of aquaculture pathogens.
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Affiliation(s)
- Anusree V Nair
- ICAR - Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Praveen N K
- Department of Chemistry, NSS College Cherthala, Cherthala, Kerala, India
| | - Leo Antony M
- ICAR - Central Institute of Brackish Water Aquaculture, Chennai, India
| | - K K Vijayan
- ICAR - Central Institute of Brackish Water Aquaculture, Chennai, India.
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Microbial Diversity and Phage-Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing. Mar Drugs 2020; 18:md18110558. [PMID: 33202695 PMCID: PMC7697616 DOI: 10.3390/md18110558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/18/2023] Open
Abstract
Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage-host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage-host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
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Townsley L, Shank EA. Natural-Product Antibiotics: Cues for Modulating Bacterial Biofilm Formation. Trends Microbiol 2017; 25:1016-1026. [PMID: 28688575 PMCID: PMC5701842 DOI: 10.1016/j.tim.2017.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/09/2017] [Indexed: 12/15/2022]
Abstract
Cell-cell communication enables bacteria to coordinate their behavior through the production, recognition, and response to chemical signals produced by their microbial neighbors. An important example of coordinated behavior in bacteria is biofilm formation, where individual cells organize into highly complex, matrix-encased communities that differentiate into distinct cell types and divide labor among individual cells. Bacteria rely on environmental cues to influence biofilm development, including chemical cues produced by other microbes. A multitude of recent studies have demonstrated that natural-product antibiotics at subinhibitory concentrations can impact biofilm formation in neighboring microbes, supporting the hypothesis that these compounds may have evolved as signaling molecules that mediate cell-cell interactions. In this review we discuss the role of antibiotics in modulating biofilm formation and interspecies communication in bacteria.
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Affiliation(s)
- Loni Townsley
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth A Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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