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Abriouel H, Manetsberger J, Lavilla Lerma L, Pestaña Blanco MD, Martínez Nogueras R, Caballero Gómez N, Benomar N. Metagenomic insights into microbial contamination in critical healthcare environments and the efficacy of a novel "HLE" disinfectant. Infect Dis Health 2023; 28:282-289. [PMID: 37558566 DOI: 10.1016/j.idh.2023.07.002] [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: 05/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Bacterial contamination on inanimate clinical surfaces is directly linked to severe health problems, especially those caused by multidrug resistant (MDR) pathogens. Here, we evaluated the microbial burden in these environments and tested the efficacy of a novel HLE disinfectant solution. METHODS Microbial contamination of healthcare surfaces [Intensive Care Unit (ICU), Long Period Hospitalization Room (LPHR) and Otolaryngology Consultation (OC)] and the efficacy of HLE disinfectant solution were determined analyzing the viable counts on general and selective media, and also by molecular studies focused on metagenomic and specific qPCR. RESULTS Different contamination loads were detected with LPHR showing the highest contamination. Treatment with the HLE disinfectant solution curbed the spread of well-adapted pathogens on touched surfaces (ICU, LPHR and OC). Metagenomic analysis of microbial diversity of the Patient Table (most contaminated surface in LPHR) revealed the presence of mainly A. johnsonii and P. putida. Furthermore, functional annotation of toxin, virulence and antibiotic resistance sequences showed a high diversity of Acinetobacter spp. and Pseudomonas spp. In this context, specific qPCR analysis confirmed the efficacy of HLE disinfectant solution against the most prevalent and critical pathogens Pseudomonas sp. and Acinetobacter sp. achieving their complete eradication. CONCLUSION Given the persistence of detrimental resistant pathogens, the application of HLE disinfection solution could be a highly beneficial and effective option -used either alone or in combination-for infection prevention and control with the aim to eliminate microbial pathogens and their genes from contaminated contact-surfaces and thus limit the spread to humans and other ecological niches.
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Affiliation(s)
- Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain.
| | - Julia Manetsberger
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | | | | | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentals, Universidad de Jaén, 23071, Jaén, Spain
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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Faucher SP, Matthews S, Nickzad A, Vounba P, Shetty D, Bédard É, Prévost M, Déziel E, Paranjape K. Toxoflavin secreted by Pseudomonas alcaliphila inhibits the growth of Legionella pneumophila and Vermamoeba vermiformis. WATER RESEARCH 2022; 216:118328. [PMID: 35364354 DOI: 10.1016/j.watres.2022.118328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/07/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Legionella pneumophila is a natural inhabitant of water systems. From there, it can be transmitted to humans by aerosolization resulting in severe pneumonia. Most large outbreaks are caused by cooling towers colonized with L. pneumophila. The resident microbiota of the cooling tower is a key determinant for the colonization and growth of L. pneumophila. In our preceding study, the genus Pseudomonas correlated negatively with the presence of L. pneumophila in cooling towers, but it was not clear which species was responsible. Therefore, we identified the Pseudomonas species inhabiting 14 cooling towers using a Pseudomonas-specific 16S rRNA amplicon sequencing strategy. We found that cooling towers that are free of L. pneumophila contained a high relative abundance of members from the Pseudomonas alcaliphila/oleovorans phylogenetic cluster. P. alcaliphila JCM 10630 inhibited the growth of L. pneumophila on agar plates. Analysis of the P. alcaliphila genome revealed the presence of a gene cluster predicted to produce toxoflavin. L. pneumophila growth was inhibited by pure toxoflavin and by extracts from P. alcaliphila culture found to contain toxoflavin by liquid chromatography coupled with mass spectrometry. In addition, toxoflavin inhibits the growth of Vermameoba vermiformis, a host cell of L. pneumophila. Our study indicates that P. alcaliphila may be important to restrict growth of L. pneumophila in water systems through the production of toxoflavin. A sufficiently high concentration of toxoflavin is likely not achieved in the bulk water but might have a local inhibitory effect such as near or in biofilms.
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Affiliation(s)
- Sebastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Sara Matthews
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Arvin Nickzad
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada
| | - Passoret Vounba
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Deeksha Shetty
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Émilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Québec, Canada
| | - Michele Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Québec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, QC, Canada
| | - Kiran Paranjape
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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4
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Kang D, Liu W, Kakahi FB, Delvigne F. Combined utilization of metabolic inhibitors to prevent synergistic multi-species biofilm formation. AMB Express 2022; 12:32. [PMID: 35244796 PMCID: PMC8897544 DOI: 10.1186/s13568-022-01363-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/12/2022] [Indexed: 12/04/2022] Open
Abstract
Biofilm is ubiquitous in industrial water systems, causing biofouling and leading to heat transfer efficiency decreases. In particular, multi-species living in biofilms could boost biomass production and enhance treatment resistance. In this study, a total of 37 bacterial strains were isolated from a cooling tower biofilm where acetic acid and propionic acid were detected as the main carbon sources. These isolates mainly belonged to Proteobacteria and Firmicutes, which occupied more than 80% of the total strains according to the 16S rRNA gene amplicon sequencing. Four species (Acinetobacter sp. CTS3, Corynebacterium sp. CTS5, Providencia sp. CTS12, and Pseudomonas sp. CTS17) were observed co-existing in the synthetic medium. Quantitative comparison of biofilm biomass from mono- and multi-species showed a synergistic effect towards biofilm formation among these four species. Three metabolic inhibitors (sulfathiazole, 3-bromopyruvic acid, and 3-nitropropionic acid) were employed to prevent biofilm formation based on their inhibitory effect on corresponding metabolic pathways. All of them displayed evident inhibition profiles to biofilm formation. Notably, combining these three inhibitors possessed a remarkable ability to block the multi-species biofilm development with lower concentrations, suggesting an enhanced effect appeared in simultaneous use. This study demonstrates that combined utilization of metabolic inhibitors is an alternative strategy to prevent multi-species biofilm formation. 37 bacterial strains were isolated and identified from a cooling tower biofilm. Synergistic effect of biofilm formation was observed among four species. Three metabolic inhibitors showed effective inhibition against biofilm formation. Targeting cellular metabolism is an effective way to inhibit biofilm formation.
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5
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He B, Chen X, Yang H, Cernava T. Microbiome Structure of the Aphid Myzus persicae (Sulzer) Is Shaped by Different Solanaceae Plant Diets. Front Microbiol 2021; 12:667257. [PMID: 34290679 PMCID: PMC8287905 DOI: 10.3389/fmicb.2021.667257] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
Myzus persicae (Sulzer) is an important insect pest in agriculture that has a very broad host range. Previous research has shown that the microbiota of insects has implications for their growth, development, and environmental adaptation. So far, there is little detailed knowledge about the factors that influence and shape the microbiota of aphids. In the present study, we aimed to investigate diet-induced changes in the microbiome of M. persicae using high-throughput sequencing of bacterial 16S ribosomal RNA gene fragments in combination with molecular and microbiological experiments. The transfer of aphids to different plants from the Solanaceae family resulted in a substantial decrease in the abundance of the primary symbiont Buchnera. In parallel, a substantial increase in the abundance of Pseudomonas was observed; it accounted for up to 69.4% of the bacterial community in M. persicae guts and the attached bacteriocytes. In addition, we observed negative effects on aphid population dynamics when they were transferred to pepper plants (Capsicum annuum L.). The microbiome of this treatment group showed a significantly lower increase in the abundance of Pseudomonas when compared with the other Solanaceae plant diets, which might be related to the adaptability of the host to this diet. Molecular quantifications of bacterial genera that were substantially affected by the different diets were implemented as an additional verification of the microbiome-based observations. Complementary experiments with bacteria isolated from aphids that were fed with different plants indicated that nicotine-tolerant strains occur in Solanaceae-fed specimens, but they were not restricted to them. Overall, our mechanistic approach conducted under controlled conditions provided strong indications that the aphid microbiome shows responses to different plant diets. This knowledge could be used in the future to develop environmentally friendly methods for the control of insect pests in agriculture.
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Affiliation(s)
- Baoyu He
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, China
| | - Xiaoyulong Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, China.,College of Tobacco Science, Guizhou University, Guiyang, China
| | - Hong Yang
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, China.,College of Tobacco Science, Guizhou University, Guiyang, China
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, Guiyang, China.,Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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6
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Hahn MW, Huemer A, Pitt A, Hoetzinger M. Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit. Mol Ecol Resour 2021; 21:2471-2485. [PMID: 34101998 DOI: 10.1111/1755-0998.13444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca2+ -rich and Ca2+ -poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Andrea Huemer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Matthias Hoetzinger
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
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7
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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Vega FE, Emche S, Shao J, Simpkins A, Summers RM, Mock MB, Ebert D, Infante F, Aoki S, Maul JE. Cultivation and Genome Sequencing of Bacteria Isolated From the Coffee Berry Borer ( Hypothenemus hampei), With Emphasis on the Role of Caffeine Degradation. Front Microbiol 2021; 12:644768. [PMID: 33889142 PMCID: PMC8055839 DOI: 10.3389/fmicb.2021.644768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
The coffee berry borer, the most economically important insect pest of coffee worldwide, is the only insect capable of feeding and reproducing solely on the coffee seed, a food source containing the purine alkaloid caffeine. Twenty-one bacterial species associated with coffee berry borers from Hawai’i, Mexico, or a laboratory colony in Maryland (Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai, Delftia lacustris, Erwinia sp. S38, S43, S63, Klebsiella oxytoca, Ochrobactrum sp. S45, S46, Pantoea sp. S61, Pseudomonas aeruginosa, P. parafulva, and Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75) were found to have at least one of five caffeine N-demethylation genes (ndmA, ndmB, ndmC, ndmD, ndmE), with Pseudomonas spp. S31, S32, S37, S60 and P. parafulva having the full complement of these genes. Some of the bacteria carrying the ndm genes were detected in eggs, suggesting possible vertical transmission, while presence of caffeine-degrading bacteria in frass, e.g., P. parafulva (ndmABCDE) and Bacillus aryabhattai (ndmA) could result in horizontal transmission to all insect life stages. Thirty-five bacterial species associated with the insect (Acinetobacter sp. S40, S54, S55, B. aryabhattai, B. cereus group, Bacillus sp. S29, S70, S71, S72, S73, D. lacustris, Erwinia sp. S38, S43, S59, S63, K. oxytoca, Kosakonia cowanii, Ochrobactrum sp. S45, S46, Paenibacillus sp. S28, Pantoea sp. S61, S62, P. aeruginosa, P. parafulva, Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75, Stenotrophomonas sp. S39, S41, S48, S49) might contribute to caffeine breakdown using the C-8 oxidation pathway, based on presence of genes required for this pathway. It is possible that caffeine-degrading bacteria associated with the coffee berry borer originated as epiphytes and endophytes in the coffee plant microbiota.
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Affiliation(s)
- Fernando E Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Sarah Emche
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ann Simpkins
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Meredith B Mock
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Sayaka Aoki
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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9
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de Oliveira Luz AC, da Silva Junior WJ, do Nascimento Junior JB, da Silva JMA, de Queiroz Balbino V, Leal-Balbino TC. Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems. Curr Genet 2021; 67:663-672. [PMID: 33751147 DOI: 10.1007/s00294-021-01173-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The CRISPR-Cas are adaptive immune systems found in archaea and bacteria, responsible for providing sequence-specific resistance against foreign DNA. Strains of Pseudomonas aeruginosa may carry CRISPR/Cas system types I-F, I-E and/or I-C; however, several aspects related to the epidemiology and functionality of these systems have not yet been revealed. Here, we report 13 genomes of clinical strains of P. aeruginosa from Brazil that were positive for CRISPR/Cas system types I-F and I-E, a rare feature in this species. The phylogenetic tree, which was constructed with 161 other publicly available genomes, suggested no direct relationship between positive strains, and the various types of CRISPR/Cas systems were spread throughout the tree. Comparative analysis of the genetic locations of type I-F and a specific orphan CRISPR array (without cas genes), named the LES locus, showed sequence similarities between this orphan locus and type I-F, but these LES loci were inserted in a different genomic location. We also report the presence of prophages, the presence of anti-CRISPR genes, and possibly the presence of self-targeting spacers. Here, we conclude that CRISPR/Cas is highly associated with certain lineages and is spread throughout the phylogenetic tree, showing no clear pattern of evolutionary distribution. Moreover, the LES locus might be a CRISPR1 locus related to type I-F that may have been misplaced and maintained over time. Furthermore, strains carrying I-F and I-E are rare, and not all of them are closely related. Further functional work is needed to better comprehend if aspects reported in this study are functional, including the LES locus, self-targeting spacers, anti-CRISPR protection, and I-F/I-E-carrying lineages.
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Affiliation(s)
| | - Wilson José da Silva Junior
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - José Bandeira do Nascimento Junior
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valdir de Queiroz Balbino
- Laboratory of Bioinformatics and Evolutionary Biology, Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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10
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Mao G, Liang J, Wang Q, Zhao C, Bai Y, Liu R, Liu H, Qu J. Epilithic biofilm as a reservoir for functional virulence factors in wastewater-dominant rivers after WWTP upgrade. J Environ Sci (China) 2021; 101:27-35. [PMID: 33334522 DOI: 10.1016/j.jes.2020.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 06/12/2023]
Abstract
Virulence factors (VFs) confer upon pathogens the ability to cause various types of damage or diseases. Wastewater treatment plants (WWTPs) are important point sources for the emission of pathogens and VFs into receiving rivers. Conventional WWTP upgrades are often implemented to improve the water quality of receiving ecosystems. However, knowledge on the pathogens, VFs, and health risks to receiving aquatic ecosystems after upgrade remains limited. In this study, we investigated detailed pathogenic information, including taxa, pathogenicity, and health risk, in two wastewater-dominant rivers after WWTP upgrade. Using 16S rRNA gene sequencing, we screened 14 potential pathogens in water and epilithic biofilm samples, though they were significantly more enriched in the biofilms. Combining 16S rRNA and metagenomic sequencing data, we identified Pseudomonas and Aeromonas as the dominant pathogenic taxa carrying functional VFs (e.g., mobility and offensive) in the epilithic biofilm. Moreover, strong pathogen-specific VF-host co-occurrence events were observed in the epilithic biofilm samples, indicating the importance of biofilms as reservoirs and vehicles for VFs. Further, we demonstrated that mobility VF is crucial for biofilm formation and pathogens in biofilm carrying offensive VF may be highly invasive. Quantification and health risk assessment suggested that the skin contact risk of P. aeruginosa carrying VFs was higher than the acceptable probability of 10-4 in both water and epilithic biofilm samples, which may threaten ecological and human health.
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Affiliation(s)
- Guannan Mao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jinsong Liang
- Harbin Institute of Technology, School of Civil and Environmental Engineering, Shenzhen 518055, China.
| | - Qiaojuan Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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11
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Sperling J, MacDonald Z, Normandeau J, Merrill E, Sperling F, Magor K. Within-population diversity of bacterial microbiomes in winter ticks (Dermacentor albipictus). Ticks Tick Borne Dis 2020; 11:101535. [DOI: 10.1016/j.ttbdis.2020.101535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/25/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022]
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12
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Macroporous epoxy-based monoliths for rapid quantification of Pseudomonas aeruginosa by adsorption elution method optimized for qPCR. Anal Bioanal Chem 2020; 412:8185-8195. [PMID: 33011838 PMCID: PMC7584540 DOI: 10.1007/s00216-020-02956-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023]
Abstract
Pseudomonas aeruginosa contaminations in tap water systems have caused severe health problems in both hospital and household settings. To ensure fast and reliable detection, culture-independent methods are recommendable. However, the typically low cell number in water samples requires sample enrichment prior to analysis. Therefore, we developed and optimized an adsorption elution method using monolithic adsorption filtration and subsequent centrifugal ultrafiltration that can be combined with culture-independent detection methods. The principle of adsorption of Pseudomonas aeruginosa by hydrophobic and ionic interactions was studied in modified epoxy-based monoliths. Optimized conditions (5-L initial sample volume at pH 3 filtered for 30 min through hydrolyzed monoliths (MAF-OH) and eluted with beef extract glycine buffer at pH 9.5) achieved a recovery of 67.1 ± 1.2% and a concentration factor of 103. For the first time, we therefore present a culture-independent approach for rapid enrichment and subsequent molecular biological quantification of P. aeruginosa by qPCR from tap water samples by monolithic adsorption filtration. The total enrichment and quantification process takes 4 h. This work further stresses the versatility of the monolithic adsorption filtration and its possibilities as a concentration tool for culture-independent analytics of pathogenic bacteria in the environment. Graphical abstract![]()
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13
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Samson R, Shah M, Yadav R, Sarode P, Rajput V, Dastager SG, Dharne MS, Khairnar K. Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:288-299. [PMID: 31005831 DOI: 10.1016/j.scitotenv.2019.04.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy river of India with great mythological history and religious significance. The Yamuna River meets Ganges at the Prayagraj (formerly known as Allahabad), India to form a unique confluence. The influence of Yamuna River on taxonomic and functional aspects of microbiome at this confluence and its downstream, remains unexplored. To unveil this dearth, whole metagenome sequencing of the microbial (bacterial and archaeal) community from the sediment samples of December 2017 sampling expedition was executed using high throughput MinION technology. Results revealed differences in the relative abundance of bacterial and archaeal communities across the confluence. Grouped by the confluence, a higher abundance of Proteobacteria and lower abundance of Bacteroidetes and Firmicutes was observed for Yamuna River (G15Y) and at immediate downstream of confluence of Ganges (G15DS), as compared to the upstream, confluence, and farther downstream of confluence. A similar trend was observed for archaeal communities with a higher abundance of Euryarchaeota in G15Y and G15DS, indicating Yamuna River's influence. Functional gene(s) analysis revealed the influence of Yamuna River on xenobiotic degradation, resistance to toxic compounds, and antibiotic resistance interceded by the autochthonous microbes at the confluence and succeeding downstream locations. Overall, similar taxonomic and functional profiles of microbial communities before confluence (upstream of Ganges) and farther downstream of confluence, suggested a transient influence of Yamuna River. Our study is significant since it may be foundational basis to understand impact of Yamuna River and also rare event of mass bathing on the microbiome of River Ganges. Further investigation would be required to understand, the underlying cause behind the restoration of microbial profiles post-confluence farther zone, to unravel the rejuvenation aspects of this unique ecosystem.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Manan Shah
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Priyanka Sarode
- Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Syed G Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Mahesh S Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India.
| | - Krishna Khairnar
- Academy of Scientific and Industrial Research (AcSIR), New Delhi, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
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