1
|
Lydon KA, Grim C, Robertson MJ, Lipp EK. Draft genome sequence of multidrug-resistant Vibrio navarrensis strain DA9 isolated from a coastal canal in the Florida Keys (USA). Microbiol Resour Announc 2024; 13:e0078923. [PMID: 38095430 DOI: 10.1128/mra.00789-23] [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: 08/23/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
A presumptive Vibrio isolate with a multidrug resistance profile was isolated from surface seawater collected from a coastal canal in 2014 and identified as Vibrio navarrensis, designated as strain DA9. Here, we report a 5.1-Mb draft genome sequence of strain DA9 with a G + C content of 47.5%.
Collapse
Affiliation(s)
- Keri Ann Lydon
- Department of Environmental Health Sciences, College of Public Health, University of Georgia , Athens, Georgia, USA
| | - Christopher Grim
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland, USA
| | - Megan J Robertson
- Department of Environmental Health Sciences, College of Public Health, University of Georgia , Athens, Georgia, USA
| | - Erin K Lipp
- Department of Environmental Health Sciences, College of Public Health, University of Georgia , Athens, Georgia, USA
| |
Collapse
|
2
|
Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
Collapse
Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| |
Collapse
|
3
|
Lai KP, Tsang CF, Li L, Yu RMK, Kong RYC. Microplastics act as a carrier for wastewater-borne pathogenic bacteria in sewage. CHEMOSPHERE 2022; 301:134692. [PMID: 35504476 DOI: 10.1016/j.chemosphere.2022.134692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Microplastic pollution, a pressing global environmental problem, has a severe impact on both aquatic ecosystems and public health worldwide. Due to the small size of microplastics, they are able to pass through the filtration systems of municipal wastewater treatment works (WWTWs). In recent years, studies have focused on the environmental abundance and ecotoxicological effects of microplastics, but there are limited studies investigating the colonization of microplastics by bacteria, especially those pathogenic ones. In this study, we examined the colonization and composition of the bacterial communities on polyethylene microbeads after incubation in raw sewage collected from three municipal WWTWs in Hong Kong (Sha Tin Sewage Treatment Works, Stonecutters Island Sewage Treatment Works, and Shek Wu Hui Sewage Treatment Works). Scanning electron microscopy (SEM) results indicate that bacterial cells were colonized on the surfaces of the microbeads and formed biofilms after sewage incubation. Metagenomic sequencing data demonstrated an increase in bacterial diversity after 21 days of sewage incubation when compared to shorter incubation periods of 6, 11 and 16 days. Importantly, human and fish pathogens such as Arcobacter cryaerophilus, Aeromonas salmonicida, Vibrio areninigrae and Vibrio navarrensis were found in the resident bacterial communities. Taken together, our results demonstrate that microplastics could act as a carrier for wastewater-borne pathogenic bacteria in municipal sewage.
Collapse
Affiliation(s)
- Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, PR China; Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
| | - Chau Fong Tsang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Lei Li
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China
| | - Richard Man Kit Yu
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.
| | - Richard Yuen Chong Kong
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
4
|
Huang J, Zeng B, Liu D, Wu R, Zhang J, Liao B, He H, Bian F. Classification and structural insight into vibriolysin-like proteases of Vibrio pathogenicity. Microb Pathog 2018; 117:335-340. [PMID: 29510206 DOI: 10.1016/j.micpath.2018.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/18/2018] [Accepted: 03/02/2018] [Indexed: 12/17/2022]
Abstract
Vibriolysin-like proteases (VLPs) are important virulence agents in the arsenal of Vibrio causing instant cytotoxic effects during infection. Most of Vibrio secreted VLPs show serious pathogenicity, while some species of Vibrio with VLPs are non-pathogenic, like Vibrio tasmaniensis and Vibrio pacinii. To investigate the relation between VLPs and Vibrio pathogenicity, one phylogenetic tree of VLPs was constructed and compared consensus sequences at the N-terminus of VLPs. Based on these results, VLPs were defined into nine phylogenetic clades. Pathogenicity analysis of Vibrio showed that Vibrio species with VLPs III, VI, VII or VIII are serious pathogenic bacteria, while species with VLPs I, II, IV or IX are opportunistic pathogens. Multiple sequence alignment showed that the N-terminal 5-16 nucleotides of each clade are highly conservative. Topological analysis of VLPs exhibited the structural differences in N-terminal regions of each VLP clade. These results suggest that structure of N-terminus might play a key role in the pathogenicity of VLPs. Our findings give new insights into the classification of VLPs and the relationship between VLPs and Vibrio pathogenicity.
Collapse
Affiliation(s)
- JiaFeng Huang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - BingQi Zeng
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - Dan Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - RiBang Wu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - Jiang Zhang
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - BinQiang Liao
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China
| | - HaiLun He
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha 410013, China.
| | - Fei Bian
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250000, China.
| |
Collapse
|
5
|
Schwartz K, Kukuc C, Bier N, Taureck K, Hammerl JA, Strauch E. Diversity of Vibrio navarrensis Revealed by Genomic Comparison: Veterinary Isolates Are Related to Strains Associated with Human Illness and Sewage Isolates While Seawater Strains Are More Distant. Front Microbiol 2017; 8:1717. [PMID: 28932221 PMCID: PMC5592226 DOI: 10.3389/fmicb.2017.01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/24/2017] [Indexed: 12/30/2022] Open
Abstract
Strains of Vibrio navarrensis are present in aquatic environments like seawater, rivers, and sewage. Recently, strains of this species were identified in human clinical specimens. In this study, V. navarrensis strains isolated from livestock in Germany were characterized that were found in aborted fetuses and/or placentas after miscarriages. The veterinary strains were analyzed using phenotypical and genotypical methods and compared to isolates from marine environments of the Baltic Sea and North Sea. The investigated phenotypical traits were similar in all German strains. Whole genome sequencing (WGS) was used to evaluate a phylogenetic relationship by performing a single nucleotide polymorphism (SNP) analysis. For the SNP analysis, WGS data of two American human pathogenic strains and two Spanish environmental isolates from sewage were included. A phylogenetic analysis of concatenated sequences of five protein-coding housekeeping genes (gyrB, pyrH, recA, atpA, and rpoB), was additionally performed. Both phylogenetic analyses reveal a greater distance of the environmental seawater strains to the other strains. The phylogenetic tree constructed from concatenated sequences of housekeeping genes places veterinary, human pathogenic and Spanish sewage strains into one cluster. Presence and absence of virulence-associated genes were investigated based on WGS data and confirmed by PCR. However, this analysis showed no clear pattern for the potentially pathogenic strains. The detection of V. navarrensis in human clinical specimens strongly suggests that this species should be regarded as a potential human pathogen. The identification of V. navarrensis strains in domestic animals implicates a zoonotic potential of this species. This could indicate a potential threat for humans, as according to the “One Health” concept, human, animal, and environmental health are linked. Future studies are necessary to search for reservoirs of these bacteria in the environment and/or in living organisms.
Collapse
Affiliation(s)
- Keike Schwartz
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Cindy Kukuc
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Nadja Bier
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Karin Taureck
- Landesuntersuchungsanstalt für das Gesundheits- und Veterinärwesen SachsenDresden, Germany
| | - Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| | - Eckhard Strauch
- Department of Biological Safety, German Federal Institute for Risk AssessmentBerlin, Germany
| |
Collapse
|
6
|
CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules. J Bacteriol 2017; 199:JB.00842-16. [PMID: 28264992 DOI: 10.1128/jb.00842-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/29/2022] Open
Abstract
Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs.IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and catalyze their incorporation into bacterial chromosomes, which could convert a strain into a pathogen with very different disease pathologies. Each island had the ability to excise from the chromosome as distinct, complete units for possible transfer. Evolutionary analysis of these regions indicates that they were acquired by horizontal transfer and that PAIs are the units of transfer. Similar to the case for phage evolution, PAIs have a modular structure where different functional regions are acquired by identical recombination modules.
Collapse
|
7
|
Orata FD, Xu Y, Gladney LM, Rishishwar L, Case RJ, Boucher Y, Jordan IK, Tarr CL. Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis. Int J Syst Evol Microbiol 2016; 66:4148-4155. [PMID: 27468862 DOI: 10.1099/ijsem.0.001327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus, based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis, their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA-DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4-95.8 % and 61.9-64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus. Based on these differences, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.
Collapse
Affiliation(s)
- Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yue Xu
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Lori M Gladney
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.,IHRC, Incorporated, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Santiago de Cali, Valle del Cauca, Colombia
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yan Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Santiago de Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|