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Siboni N, Balaraju V, Carney R, Labbate M, Seymour JR. Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary. Front Microbiol 2016; 7:460. [PMID: 27148171 PMCID: PMC4829023 DOI: 10.3389/fmicb.2016.00460] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/21/2016] [Indexed: 01/22/2023] Open
Abstract
Vibrio are a genus of marine bacteria that have substantial environmental and human health importance, and there is evidence that their impact may be increasing as a consequence of changing environmental conditions. We investigated the abundance and composition of the Vibrio community within the Sydney Harbour estuary, one of the most densely populated coastal areas in Australia, and a region currently experiencing rapidly changing environmental conditions. Using quantitative PCR (qPCR) and Vibrio-specific 16S rRNA amplicon sequencing approaches we observed significant spatial and seasonal variation in the abundance and composition of the Vibrio community. Total Vibrio spp. abundance, derived from qPCR analysis, was higher during the late summer than winter and within locations with mid-range salinity (5-26 ppt). In addition we targeted three clinically important pathogens: Vibrio cholerae, V. Vulnificus, and V. parahaemolyticus. While toxigenic strains of V. cholerae were not detected in any samples, non-toxigenic strains were detected in 71% of samples, spanning a salinity range of 0-37 ppt and were observed during both late summer and winter. In contrast, pathogenic V. vulnificus was only detected in 14% of samples, with its occurrence restricted to the late summer and a salinity range of 5-26 ppt. V. parahaemolyticus was not observed at any site or time point. A Vibrio-specific 16S rRNA amplicon sequencing approach revealed clear shifts in Vibrio community composition across sites and between seasons, with several Vibrio operational taxonomic units (OTUs) displaying marked spatial patterns and seasonal trends. Shifts in the composition of the Vibrio community between seasons were primarily driven by changes in temperature, salinity and NO2, while a range of factors including pH, salinity, dissolved oxygen (DO) and NOx (Nitrogen Oxides) explained the observed spatial variation. Our evidence for the presence of a spatiotemporally dynamic Vibrio community within Sydney Harbour is notable given the high levels of human use of this waterway, and the significant increases in seawater temperature predicted for this region.
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Affiliation(s)
- Nachshon Siboni
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Varunan Balaraju
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Richard Carney
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
| | - Maurizio Labbate
- School of Life Sciences, The ithree institute, University of Technology Sydney, UltimoNSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, UltimoNSW, Australia
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Luo Y, Octavia S, Jin D, Ye J, Miao Z, Jiang T, Xia S, Lan R. US Gulf-like toxigenic O1 Vibrio cholerae causing sporadic cholera outbreaks in China. J Infect 2016; 72:564-72. [PMID: 26920786 DOI: 10.1016/j.jinf.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/15/2016] [Accepted: 02/12/2016] [Indexed: 02/01/2023]
Abstract
OBJECTIVES Cholera is potentially a life threatening disease caused by toxigenic Vibrio cholerae. Here we report the identification and characterisation of 76 non-7th pandemic clone O1 V. cholerae isolates including 65 clinical isolates from diarrhoeal patients from 2005 to 2014 in Zhejiang Province, China. METHODS We used multilocus sequence typing (MLST) to characterise 65 V. cholerae isolates. Pulse-Field Gel Electrophoresis (PFGE) was performed on a subset of the isolates and whole-genome sequencing was done on 13 isolates. RESULTS MLST separated 65 isolates into 19 sequence types (STs). Thirty three isolates belonged to ST75 which also contains the US Gulf Coast clone. PFGE separated the 33 isolates into 16 pulsotypes. Whole genome sequencing of 10 ST75 isolates showed that the US Gulf Coast clone and the Chinese ST75 isolates can be separated into two distinct lineages, ST75a and ST75b. All Zhejiang ST75 isolates were ST75b. CONCLUSION PFGE and genome sequencing confirmed the linked cases and identified small outbreaks caused by ST75b. The emergence and potential spread of ST75b may pose significant threat to public health. Epidemiological surveillance is required to further understand its epidemic potential.
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Affiliation(s)
- Yun Luo
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dazhi Jin
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Julian Ye
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Ziping Miao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Tao Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Shichang Xia
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Rahaman MH, Islam T, Colwell RR, Alam M. Molecular tools in understanding the evolution of Vibrio cholerae. Front Microbiol 2015; 6:1040. [PMID: 26500613 PMCID: PMC4594017 DOI: 10.3389/fmicb.2015.01040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/13/2015] [Indexed: 12/25/2022] Open
Abstract
Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.
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Affiliation(s)
- Md Habibur Rahaman
- Department of Biology and Chemistry, North South University, Dhaka Bangladesh
| | - Tarequl Islam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA ; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Munirul Alam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
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Lutz C, Erken M, Noorian P, Sun S, McDougald D. Environmental reservoirs and mechanisms of persistence of Vibrio cholerae. Front Microbiol 2013; 4:375. [PMID: 24379807 PMCID: PMC3863721 DOI: 10.3389/fmicb.2013.00375] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/21/2013] [Indexed: 12/23/2022] Open
Abstract
It is now well accepted that Vibrio cholerae, the causative agent of the water-borne disease cholera, is acquired from environmental sources where it persists between outbreaks of the disease. Recent advances in molecular technology have demonstrated that this bacterium can be detected in areas where it has not previously been isolated, indicating a much broader, global distribution of this bacterium outside of endemic regions. The environmental persistence of V. cholerae in the aquatic environment can be attributed to multiple intra- and interspecific strategies such as responsive gene regulation and biofilm formation on biotic and abiotic surfaces, as well as interactions with a multitude of other organisms. This review will discuss some of the mechanisms that enable the persistence of this bacterium in the environment. In particular, we will discuss how V. cholerae can survive stressors such as starvation, temperature, and salinity fluctuations as well as how the organism persists under constant predation by heterotrophic protists.
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Affiliation(s)
- Carla Lutz
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia
| | - Martina Erken
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia ; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| | - Parisa Noorian
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia
| | - Shuyang Sun
- The Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore
| | - Diane McDougald
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales Sydney, NSW, Australia ; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
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Hsu CY, Pollett S, Ferguson P, McMullan BJ, Sheppeard V, Mahady SE. Locally acquired severe non-O1 and non-O139 Vibrio cholerae infection associated with ingestion of imported seafood. Med J Aust 2013; 199:26-7. [PMID: 23829253 DOI: 10.5694/mja13.10087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 04/07/2013] [Indexed: 11/17/2022]
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Bhowmick TS, Das M, Sarkar BL. Genotypic characterization of Vibrio cholerae isolates using several DNA fingerprint techniques. Future Microbiol 2011; 6:29-42. [PMID: 21162634 DOI: 10.2217/fmb.10.159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Serious pandemics of cholera have occurred throughout the known history of mankind, especially in India, which is a motherland for cholera disease. For the last 20 years several DNA-based typing methods have been employed to study the clonal relatedness between Vibrio cholerae isolates irrespective of their geographical locations. Traditional typing methods, such as biochemical tests, phage typing, serotyping, biotyping and antimicrobial susceptibility tests, have produced reliable and informative data regarding V. cholerae for a long time. Gradually molecular typing techniques have taken the place of traditional typing methods because they produce the same results upon repeat testing of V. cholerae strain. In this article we focus on the discriminatory power of different DNA fingerprint techniques that are generally used to know the homogeneity and heterogeneity among different V. cholerae isolates.
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Affiliation(s)
- Tushar Suvra Bhowmick
- Vibrio Phage Reference Laboratory, National Institute of Cholera and Enteric Diseases, Kolkata, India
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Zhou HJ, Diao BW, Cui ZG, Pang B, Zhang LJ, Kan B. Comparison of automated ribotyping and pulsed-field gel electrophoresis for subtyping of Vibrio cholerae. Lett Appl Microbiol 2009; 48:726-31. [PMID: 19344358 DOI: 10.1111/j.1472-765x.2009.02606.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To compare the discriminatory power of an automated ribotyping method for Vibrio cholerae subtyping with the pulsed-field gel electrophoresis (PFGE), to evaluate the possibility of automated ribotyping in use of outbreak investigations and surveillance of cholera. METHODS AND RESULTS Eight-one epidemiologically unrelated isolates of V. cholerae, and 19 isolates from seven cholera outbreaks were used as the panels. When comparing the two methods using the epidemiologically unrelated isolates, automated ribotyping using PvuII distinguished 38 different ribotypes with a D-value of 0.8956. When combined with serotyping, the D-value is 0.9466. However, PFGE with NotI and SfiI digestions had higher D-values of 0.9951 and 0.9948, respectively. PFGE could cluster the isolates from each outbreak into the same pattern, and distinguish different patterns from different outbreaks, whereas automated ribotyping had lower discriminatory ability. CONCLUSIONS The automated ribotyping has lower discriminatory ability compared to PFGE, and is limited to application in V. cholerae subtyping and outbreak investigation. SIGNIFICANCE AND IMPACT OF THE STUDY The study evaluated the limitation in subtyping of automated ribotyping for V. cholerae, and raise the question of improvement for the automated ribotyping in subtyping.
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Affiliation(s)
- H-J Zhou
- Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Abstract
We resolved the relationships between 2 pandemic clones of Vibrio cholerae. Using 26 housekeeping genes, we showed that the US Gulf clone, the Australian clone, and 3 El Tor strains isolated before the seventh pandemic were related to the seventh pandemic clone. The sixth pandemic clone was well separated from them.
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Affiliation(s)
- Anna Salim
- University of Sydney, Sydney, New South Wales, Australia
| | - Ruiting Lan
- University of New South Wales, Sydney, New South Wales, Australia
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Finch CE, Stanford CB. Meat‐Adaptive Genes and the Evolution of Slower Aging in Humans. QUARTERLY REVIEW OF BIOLOGY 2004; 79:3-50. [PMID: 15101252 DOI: 10.1086/381662] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The chimpanzee life span is shorter than that of humans, which is consistent with a faster schedule of aging. We consider aspects of diet that may have selected for genes that allowed the evolution of longer human life spans with slower aging. Diet has changed remarkably during human evolution. All direct human ancestors are believed to have been largely herbivorous. Chimpanzees eat more meat than other great apes, but in captivity are sensitive to hypercholesterolemia and vascular disease. We argue that this dietary shift to increased regular consumption of fatty animal tissues in the course of hominid evolution was mediated by selection for "meat-adaptive" genes. This selection conferred resistance to disease risks associated with meat eating also increased life expectancy. One candidate gene is apolipoprotein E (apoE), with the E3 allele evolved in the genus Homo that reduces the risks for Alzheimer's and vascular disease, as well as influencing inflammation, infection, and neuronal growth. Other evolved genes mediate lipid metabolism and host defense. The timing of the evolution of apoE and other candidates for meat-adaptive genes is discussed in relation to key events in human evolution.
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Affiliation(s)
- Caleb E Finch
- Andrus Gerontology Center, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.
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Abstract
Recently, the role of the environment and climate in disease dynamics has become a subject of increasing interest to microbiologists, clinicians, epidemiologists, and ecologists. Much of the interest has been stimulated by the growing problems of antibiotic resistance among pathogens, emergence and/or reemergence of infectious diseases worldwide, the potential of bioterrorism, and the debate concerning climate change. Cholera, caused by Vibrio cholerae, lends itself to analyses of the role of climate in infectious disease, coupled to population dynamics of pathogenic microorganisms, for several reasons. First, the disease has a historical context linking it to specific seasons and biogeographical zones. In addition, the population dynamics of V. cholerae in the environment are strongly controlled by environmental factors, such as water temperature, salinity, and the presence of copepods, which are, in turn, controlled by larger-scale climate variability. In this review, the association between plankton and V. cholerae that has been documented over the last 20 years is discussed in support of the hypothesis that cholera shares properties of a vector-borne disease. In addition, a model for environmental transmission of cholera to humans in the context of climate variability is presented. The cholera model provides a template for future research on climate-sensitive diseases, allowing definition of critical parameters and offering a means of developing more sophisticated methods for prediction of disease outbreaks.
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Affiliation(s)
- Erin K Lipp
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
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Affiliation(s)
- H J Koornhof
- Department of Clinical Microbiology and Infectious Diseases, South African Institute for Medical Research, Johannesburg, South Africa
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Marshall S, Clark CG, Wang G, Mulvey M, Kelly MT, Johnson WM. Comparison of molecular methods for typing Vibrio parahaemolyticus. J Clin Microbiol 1999; 37:2473-8. [PMID: 10405387 PMCID: PMC85259 DOI: 10.1128/jcm.37.8.2473-2478.1999] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An outbreak of Vibrio parahaemolyticus gastroenteritis on Canada's west coast in 1997 emphasized the need to develop molecular methods for differentiation and typing of these organisms. Isolates were analyzed by enterobacterial repetitive intergenic consensus sequence (ERIC) PCR, detection of restriction fragment length polymorphisms (RFLP) in rRNA genes (ribotyping), pulsed-field gel electrophoresis (PFGE), and RFLP analysis of the genetic locus encoding the polar flagellum (Fla locus RFLP analysis). ERIC PCR and ribotyping were the most informative typing methods, especially when used together, while Fla locus RFLP analysis was the least discriminatory. PFGE exhibited good discrimination but suffered from a high incidence of DNA degradation. ERIC PCR and ribotyping will be useful for the evaluation of genetic and epidemiological relationships among V. parahaemolyticus strains.
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Affiliation(s)
- S Marshall
- National Laboratory for Outbreak Investigations and Antibiotic Resistance, Laboratory Centre for Disease Control, Health Canada, Ottawa, Ontario
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