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Foxall RL, Xu F, Sebra RP, Cooper VS, Jones SH, Whistler CA. Complete genome sequence of Vibrio parahaemolyticus ST36 strain MAVP-26, a clinical isolate from an oyster-borne human gastric infection. Microbiol Resour Announc 2024; 13:e0035224. [PMID: 38864604 PMCID: PMC11256824 DOI: 10.1128/mra.00352-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
A Pacific native lineage of Vibrio parahaemolyticus ST36 serotype O4:K12 was introduced into the Atlantic, which increased local source illnesses. To identify genetic determinants of virulence and ecological resiliency and track their transfer into endemic populations, we constructed a complete genome of a 2013 Atlantic-traced clinical isolate by hybrid assembly.
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Affiliation(s)
- Randi L. Foxall
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feng Xu
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
| | - Robert P. Sebra
- Ichan School of Medicine at Mt Sinai, New York, New York, USA
| | - Vaughn S. Cooper
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Thi Truc Linh N, Thi Hai Ha P, Van Day P, Thi Thuy Hai L, Huyen Vu S, Trong Nghia N, Thanh Dung T, Quoc Phu T, Mong Huyen H, Do-Hyung K, Thanh Luan N. Efficacy of Annona glabra extract against acute hepatopancreatic necrosis disease in white-leg shrimp (Penaeus vannamei). J Invertebr Pathol 2024; 205:108142. [PMID: 38788921 DOI: 10.1016/j.jip.2024.108142] [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: 02/29/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
This study aims to investigate the use of pond apple (Annona glabra) compounds as a novel strategy to prevent and treat acute hepatopancreatic necrosis disease (AHPND) as well as to better understand the mechanism of health improvement in shrimp. The A. glabra leaf extracts were extracted using various solvents and examined for in vitro and in vivo activity against Vibrio parahaemolyticus strains. In comparison with ethanol and water extracts, methanol extract showed the strongest bactericidal effect (MBC/MIC ratio of 2.50 ± 1.00), with minimal inhibitory concentration (MIC) of 0.023 ± 0.012 mg ml-1 and minimum bactericidal concentration (MBC) of 0.065 ± 0.062 mg ml-1. White leg shrimp (P. vannamei, body weight 10.37 ± 0.27 g) fed A. glabra methanol extracts-containing diets (AMEDs) at 1 %, 1.5 %, and 2.0 % demonstrated no deleterious effects on survival and were significantly increased in length and weight after 30 days of feeding. The level of total haemocyte, hyaline haemocyte on day 15 and granulocyte on day 30 remarkably increased (p < 0.05) in shrimps fed AMEDs groups compared to those in the control group. The finding demonstrates that granulocyte was induced time dependently. In particular, the survival rate of V. parahaemolyticus challenged shrimps under medication with AMEDs at 1.5 % and 2.0 % was significantly higher (p < 0.05) than that of the control group. The decrease in bacterial load of Vibrio spp. and V. parahaemolyticus was obviously recorded in hepatopancreas shrimp given AMEDs 1.5 % and 2.0 % and may be linked to herb characteristics such as antibacterial activity, enhancing innate immunity, and its potential to maintain the integrity of hepatopancreatic tissue. Our findings suggest that A. glabra extract might be used as a health enhancer in commercial farmed shrimp.
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Affiliation(s)
- Nguyen Thi Truc Linh
- School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh province, Vietnam
| | - Pham Thi Hai Ha
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City 700000, Viet Nam
| | - Pham Van Day
- School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh province, Vietnam
| | - Luu Thi Thuy Hai
- School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh province, Vietnam
| | - Son Huyen Vu
- School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh province, Vietnam
| | - Nguyen Trong Nghia
- Faculty of Aquatic Pathology, College of Aquaculture and Fisheries, Can Tho University, Viet Nam
| | - Tu Thanh Dung
- Faculty of Aquatic Pathology, College of Aquaculture and Fisheries, Can Tho University, Viet Nam
| | - Truong Quoc Phu
- Faculty of Aquatic Pathology, College of Aquaculture and Fisheries, Can Tho University, Viet Nam
| | - Hong Mong Huyen
- Faculty of Agriculture and Rural Development, Kien Giang University, Viet Nam
| | - Kim Do-Hyung
- Department of Aquatic Life Medicine, College of Fisheries Sciences, PukyongNational University, Busan, South Korea
| | - Nguyen Thanh Luan
- Department of Science and Technology, HUTECH University, 475A Dien Bien Phu Street, Ward 25, Binh Thanh District, Ho Chi Minh City 700000, Viet Nam.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Baker‐Austin C, Hervio‐Heath D, Martinez‐Urtaza J, Caro ES, Strauch E, Thébault A, Guerra B, Messens W, Simon AC, Barcia‐Cruz R, Suffredini E. Public health aspects of Vibrio spp. related to the consumption of seafood in the EU. EFSA J 2024; 22:e8896. [PMID: 39045511 PMCID: PMC11263920 DOI: 10.2903/j.efsa.2024.8896] [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] [Indexed: 07/25/2024] Open
Abstract
Vibrio parahaemolyticus, Vibrio vulnificus and non-O1/non-O139 Vibrio cholerae are the Vibrio spp. of highest relevance for public health in the EU through seafood consumption. Infection with V. parahaemolyticus is associated with the haemolysins thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH) and mainly leads to acute gastroenteritis. V. vulnificus infections can lead to sepsis and death in susceptible individuals. V. cholerae non-O1/non-O139 can cause mild gastroenteritis or lead to severe infections, including sepsis, in susceptible individuals. The pooled prevalence estimate in seafood is 19.6% (95% CI 13.7-27.4), 6.1% (95% CI 3.0-11.8) and 4.1% (95% CI 2.4-6.9) for V. parahaemolyticus, V. vulnificus and non-choleragenic V. cholerae, respectively. Approximately one out of five V. parahaemolyticus-positive samples contain pathogenic strains. A large spectrum of antimicrobial resistances, some of which are intrinsic, has been found in vibrios isolated from seafood or food-borne infections in Europe. Genes conferring resistance to medically important antimicrobials and associated with mobile genetic elements are increasingly detected in vibrios. Temperature and salinity are the most relevant drivers for Vibrio abundance in the aquatic environment. It is anticipated that the occurrence and levels of the relevant Vibrio spp. in seafood will increase in response to coastal warming and extreme weather events, especially in low-salinity/brackish waters. While some measures, like high-pressure processing, irradiation or depuration reduce the levels of Vibrio spp. in seafood, maintaining the cold chain is important to prevent their growth. Available risk assessments addressed V. parahaemolyticus in various types of seafood and V. vulnificus in raw oysters and octopus. A quantitative microbiological risk assessment relevant in an EU context would be V. parahaemolyticus in bivalve molluscs (oysters), evaluating the effect of mitigations, especially in a climate change scenario. Knowledge gaps related to Vibrio spp. in seafood and aquatic environments are identified and future research needs are prioritised.
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Orel N, Fadeev E, Herndl GJ, Turk V, Tinta T. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics 2024; 25:146. [PMID: 38321410 PMCID: PMC10845552 DOI: 10.1186/s12864-024-10062-2] [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: 01/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. RESULTS We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. CONCLUSIONS Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
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Foxall RL, Means J, Marcinkiewicz AL, Schillaci C, DeRosia-Banick K, Xu F, Hall JA, Jones SH, Cooper VS, Whistler CA. Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus. mBio 2024; 15:e0285123. [PMID: 38112441 PMCID: PMC10790759 DOI: 10.1128/mbio.02851-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.
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Affiliation(s)
- Randi L. Foxall
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jillian Means
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Graduate Program in Microbiology, University of New Hampshire, Durham, New Hampshire, USA
| | - Ashely L. Marcinkiewicz
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Graduate Program in Microbiology, University of New Hampshire, Durham, New Hampshire, USA
| | - Christopher Schillaci
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Kristin DeRosia-Banick
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
| | - Feng Xu
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jeffrey A. Hall
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Vaughn S. Cooper
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Souhail B, Danjean M, Mercier-Darty M, Amaddeo G, Sessa A, Fihman V, Galy A, Woerther PL, Lepeule R. First report of Acinetobacter pittii acute community-acquired pneumonia in an immunocompetent patient in France following a heat wave. BMC Infect Dis 2024; 24:35. [PMID: 38166743 PMCID: PMC10763415 DOI: 10.1186/s12879-023-08945-y] [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: 08/23/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND In recent years, Acinetobacter baumannii-calcoaceticus complex (ABC) infections have attracted attention, mainly because of the impact of carbapenem-resistant isolates in hospital-acquired infections. However, acute community-acquired ABC infections are not uncommon in warm and humid countries, where they are responsible for community-acquired infections with specific clinical features. To date, such infection has not been reported in France. CASE PRESENTATION We report the case of a 55-year-old non-immunocompromised patient living in France with no known risk factors for community-acquired ABC infections who presented pneumonia with bloodstream infection due to wild-type A. pittii. The outcome was favorable after 7 days of antibiotic treatment with cefepime. We confirmed bacterial identification with whole-genome sequencing, and we examined the A. pitii core-genome phylogeny for genomic clusters. CONCLUSIONS This situation is uncommon in Europe and occurred after a heat wave in France with temperatures above 38 °C. Herein, we discuss the possibility that this pneumonia may be emerging in the current context of global warming.
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Affiliation(s)
- Bérénice Souhail
- Antimicrobial Stewardship Team, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, 1, rue Gustave Eiffel, 94000, Créteil, France.
| | - Maxime Danjean
- Bacteriology and Infection Control Unit, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, Créteil, France
- EnvA, DYNAMYC, UPEC, Paris-Est Créteil University, EA 7380, Créteil, France
| | - Mélanie Mercier-Darty
- Next Generation Sequencing Platform, Henri Mondor University Hospital, AP-HP, Créteil, France
| | - Giuliana Amaddeo
- Hepatology Department, Henri Mondor University Hospital, AP-HP, Créteil, France
| | - Anna Sessa
- Hepatology Department, Henri Mondor University Hospital, AP-HP, Créteil, France
| | - Vincent Fihman
- Bacteriology and Infection Control Unit, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, Créteil, France
- EnvA, DYNAMYC, UPEC, Paris-Est Créteil University, EA 7380, Créteil, France
| | - Adrien Galy
- Antimicrobial Stewardship Team, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, 1, rue Gustave Eiffel, 94000, Créteil, France
- EnvA, DYNAMYC, UPEC, Paris-Est Créteil University, EA 7380, Créteil, France
| | - Paul Louis Woerther
- Bacteriology and Infection Control Unit, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, Créteil, France
- EnvA, DYNAMYC, UPEC, Paris-Est Créteil University, EA 7380, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Team, Department of Prevention, Diagnosis, and Treatment of Infections, Henri Mondor University Hospital, AP-HP, 1, rue Gustave Eiffel, 94000, Créteil, France
- EnvA, DYNAMYC, UPEC, Paris-Est Créteil University, EA 7380, Créteil, France
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Billaud M, Larbret F, Czerucka D. Impact of rising seawater temperature on a phagocytic cell population during V. parahaemolyticus infection in the sea anemone E. pallida. Front Immunol 2023; 14:1292410. [PMID: 38077367 PMCID: PMC10703433 DOI: 10.3389/fimmu.2023.1292410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Climate change is increasing ocean temperatures and consequently impacts marine life (e.g., bacterial communities). In this context, studying host-pathogen interactions in marine organisms is becoming increasingly important, not only for ecological conservation, but also to reduce economic loss due to mass mortalities in cultured species. In this study, we used Exaiptasia pallida (E. pallida), an anemone, as an emerging marine model to better understand the effect of rising temperatures on the infection induced by the pathogenic marine bacterium Vibrio parahaemolyticus. The effect of temperature on E. pallida was examined at 6, 24, or 30 h after bath inoculation with 108 CFU of V. parahaemolyticus expressing GFP (Vp-GFP) at 27°C (husbandry temperature) or 31°C (heat stress). Morphological observations of E. pallida and their Hsps expression demonstrated heat stress induced increasing damage to anemones. The kinetics of the infections revealed that Vp-GFP were localized on the surface of the ectoderm and in the mucus during the first hours of infection and in the mesenterial filaments thereafter. To better identify the E. pallida cells targeted by Vp-GFP infection, we used spectral flow cytometry. E. pallida cell types were identified based on their autofluorescent properties. corresponding to different cell types (algae and cnidocytes). We identified an AF10 population whose autofluorescent spectrum was identical to that of human monocytes/macrophage, suggesting that this spectral print could be the hallmark of phagocytic cells called "amebocytes''. AF10 autofluorescent cells had a high capacity to phagocytize Vp-GFP, suggesting their possible role in fighting infection. This was confirmed by microscopy using sorted AF10 and GFP-positive cells (AF10+/GFP+). The number of AF10+/GFP+ cells were reduced at 31°C, demonstrating that increased temperature not only damages tissue but also affects the immune response of E. pallida. In conclusion, our study provides a springboard for more comprehensive studies of immune defense in marine organisms and paves the way for future studies of the dynamics, activation patterns, and functional responses of immune cells when encountering pathogens.
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Affiliation(s)
- Mélanie Billaud
- Biomedical Department, Scientific Center of Monaco, Monaco, Monaco
- LIA ROPSE, Laboratoire International Associé, Centre Scientifique de Monaco, Université Côte d’Azur, Nice, France
| | - Frédéric Larbret
- LIA ROPSE, Laboratoire International Associé, Centre Scientifique de Monaco, Université Côte d’Azur, Nice, France
- Université Côte d’Azur, L’Institut national de la santé et de la recherche médicale (INSERM), Centre Méditerranéen de Médecine Moléculaire (C3M), Nice, France
| | - Dorota Czerucka
- Biomedical Department, Scientific Center of Monaco, Monaco, Monaco
- LIA ROPSE, Laboratoire International Associé, Centre Scientifique de Monaco, Université Côte d’Azur, Nice, France
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Xue M, Gao Q, Yan R, Liu L, Wang L, Wen B, Wen C. Comparative Genomic Analysis of Shrimp-Pathogenic Vibrio parahaemolyticus LC and Intraspecific Strains with Emphasis on Virulent Factors of Mobile Genetic Elements. Microorganisms 2023; 11:2752. [PMID: 38004763 PMCID: PMC10672994 DOI: 10.3390/microorganisms11112752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Vibrio parahaemolyticus exhibits severe pathogenicity in humans and animals worldwide. In this study, genome sequencing and comparative analyses were conducted for in-depth characterization of the virulence factor (VF) repertoire of V. parahaemolyticus strain LC, which presented significant virulence to shrimp Litopenaeus vannamei. Strain LC, harboring two circular chromosomes and three linear plasmids, demonstrated ≥98.14% average nucleotide identities with 31 publicly available V. parahaemolyticus genomes, including 13, 11, and 7 shrimp-, human-, and non-pathogenic strains, respectively. Phylogeny analysis based on dispensable genes of pan-genome clustered 11 out of 14 shrimp-pathogenic strains and 7 out of 11 clinical strains into two distinct clades, indicating the close association between host-specific pathogenicity and accessory genes. The VFDB database revealed that 150 VFs of LC were mainly associated with the secretion system, adherence, antiphagocytosis, chemotaxis, motility, and iron uptake, whereas no homologs of the typical pathogenic genes pirA, pirB, tdh, and trh were detected. Four genes, mshB, wbfT, wbfU, and wbtI, were identified in both types of pathogenic strains but were absent in non-pathogens. Notably, a unique cluster similar to Yen-Tc, which encodes an insecticidal toxin complex, and diverse toxin-antitoxin (TA) systems, were identified on the mobile genetic elements (MGEs) of LC. Conclusively, in addition to the common VFs, various unique MGE-borne VFs, including the Yen-Tc cluster, TA components, and multiple chromosome-encoded chitinase genes, may contribute to the full spectrum of LC virulence. Moreover, V. parahaemolyticus demonstrates host-specific virulence, which potentially drives the origin and spread of pathogenic factors.
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Affiliation(s)
| | | | | | | | | | | | - Chongqing Wen
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (M.X.)
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9
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Richards GP, Watson MA, Williams HN, Jones JL. Predator-Prey Interactions between Halobacteriovorax and Pathogenic Vibrio parahaemolyticus Strains: Geographical Considerations and Influence of Vibrio Hemolysins. Microbiol Spectr 2023; 11:e0235323. [PMID: 37409976 PMCID: PMC10434201 DOI: 10.1128/spectrum.02353-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Halobacteriovorax is a genus of naturally occurring marine predatory bacteria that attack, replicate within, and lyse vibrios and other bacteria. This study evaluated the specificity of four Halobacteriovorax strains against important sequence types (STs) of clinically relevant Vibrio parahaemolyticus, including pandemic strains ST3 and ST36. The Halobacteriovorax bacteria were previously isolated from seawater from the Mid-Atlantic, Gulf of Mexico, and Hawaiian coasts of the United States. Specificity screening was performed using a double agar plaque assay technique on 23 well-characterized and genomically sequenced V. parahaemolyticus strains isolated from infected individuals from widely varying geographic locations within the United States. With few exceptions, results showed that Halobacteriovorax bacteria were excellent predators of the V. parahaemolyticus strains regardless of the origins of the predator or prey. Sequence types and serotypes of V. parahaemolyticus did not influence host specificity, nor did the presence or absence of genes for the thermostable direct hemolysin (TDH) or the TDH-related hemolysin, although faint (cloudy) plaques were present when one or both hemolysins were absent in three of the Vibrio strains. Plaque sizes varied depending on both the Halobacteriovorax and Vibrio strains evaluated, suggesting differences in Halobacteriovorax replication and/or growth rates. The very broad infectivity of Halobacteriovorax toward pathogenic strains of V. parahaemolyticus makes Halobacteriovorax a strong candidate for use in commercial processing applications to enhance the safety of seafoods. IMPORTANCE Vibrio parahaemolyticus is a formidable obstacle to seafood safety. Strains pathogenic to humans are numerous and difficult to control, especially within molluscan shellfish. The pandemic spread of ST3 and ST36 has caused considerable concern, but many other STs are also problematic. The present study demonstrates broad predatory activity of Halobacteriovorax strains obtained along U.S. coastal waters from the Mid-Atlantic, Gulf Coast, and Hawaii toward strains of pathogenic V. parahaemolyticus. This broad activity against clinically relevant V. parahaemolyticus strains suggests a role for Halobacteriovorax in mediating pathogenic V. parahaemolyticus levels in seafoods and their environment as well as the potential application of these predators in the development of new disinfection technologies to reduce pathogenic vibrios in molluscan shellfish and other seafoods.
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Affiliation(s)
- Gary P. Richards
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Michael A. Watson
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Henry N. Williams
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Jessica L. Jones
- U.S. Food and Drug Administration, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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10
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Li M, Xu H, Tian Y, Zhang Y, Jiao X, Gu D. Comparative genomic analysis reveals the potential transmission of Vibrio parahaemolyticus from freshwater food to humans. Food Microbiol 2023; 113:104277. [PMID: 37098434 DOI: 10.1016/j.fm.2023.104277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/15/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Vibrio parahaemolyticus is an increasingly important foodborne pathogen that cause acute gastroenteritis in humans. However, the prevalence and transmission of this pathogen in freshwater food remains unclear. This study aimed to determine the molecular characteristics and genetic relatedness of V. parahaemolyticus isolates obtained from freshwater food, seafood, environmental, and clinical samples. A total of 138 (46.6%) isolates were detected from 296 food and environmental samples, and 68 clinical isolates from patients. Notably, V. parahaemolyticus was more prevalent in freshwater food (56.7%, 85/150) than in seafood (38.8%, 49/137). Virulence phenotype analyses revealed that the high motility of isolates from freshwater food (40.0%) and clinical isolates (42.0%) was higher than that of isolates from seafood (12.2%), whereas the biofilm-forming capacity of freshwater food isolates (9.4%) was lower than that of seafood (22.4%) and clinical isolates (15.9%). Virulence genes analysis showed that 46.4% of the clinical isolates contained the tdh gene encoding thermostable direct hemolysin (TDH) and only two freshwater food isolates contained the trh gene encoding TDH-related hemolysin (TRH). Multilocus sequence typing (MLST) analysis divided the 206 isolates into 105 sequence types (STs), including 56 (53.3%) novel STs. ST2583, ST469, and ST453 have been isolated from freshwater food and clinical samples. Whole-genome sequence (WGS) analyses revealed that the 206 isolates were divided into five clusters. Cluster II contained isolates from freshwater food and clinical samples, whereas the other clusters contained isolates from seafood, freshwater food, and clinical samples. In addition, we observed that ST2516 had the same virulence pattern, with a close phylogenetic relationship to ST3. The increased prevalence and adaption of V. parahaemolyticus in freshwater food is a potential cause of clinical cases closely related to the consumption of V. parahaemolyticus contaminated freshwater food.
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11
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Campbell AM, Hauton C, Baker-Austin C, van Aerle R, Martinez-Urtaza J. An integrated eco-evolutionary framework to predict population-level responses of climate-sensitive pathogens. Curr Opin Biotechnol 2023; 80:102898. [PMID: 36739640 DOI: 10.1016/j.copbio.2023.102898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 02/05/2023]
Abstract
It is critical to gain insight into how climate change impacts evolutionary responses within climate-sensitive pathogen populations, such as increased resilience, opportunistic responses and the emergence of dominant variants from highly variable genomic backgrounds and subsequent global dispersal. This review proposes a framework to support such analysis, by combining genomic evolutionary analysis with climate time-series data in a novel spatiotemporal dataframe for use within machine learning applications, to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. Such workflows will inform accessible public health tools and early-warning systems, to aid decision-making and mitigate future human health threats.
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Affiliation(s)
- Amy M Campbell
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK; Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Chris Hauton
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, UK
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, UK; Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain.
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12
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Lau DYL, Aguirre Sánchez JR, Baker-Austin C, Martinez-Urtaza J. What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:337-352. [PMID: 36792883 DOI: 10.1007/978-3-031-22997-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.
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Affiliation(s)
- Dawn Yan Lam Lau
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK
| | - Jose Roberto Aguirre Sánchez
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK.,Centro de Investigación en Alimentación y Desarrollo (CIAD), Culiacán, Sinaloa, Mexico
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK
| | - Jaime Martinez-Urtaza
- Centre for Environment, Fisheries and Aquaculture (CEFAS), Weymouth, Dorset, UK. .,Department of Genetics and Microbiology, Facultat de Biociències, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain.
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13
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Gavilan RG, Caro-Castro J, Blondel CJ, Martinez-Urtaza J. Vibrio parahaemolyticus Epidemiology and Pathogenesis: Novel Insights on an Emerging Foodborne Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:233-251. [PMID: 36792879 DOI: 10.1007/978-3-031-22997-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The epidemiological dynamics of V. parahaemolyticus´ infections have been characterized by the abrupt appearance of outbreaks in remote areas where these diseases had not been previously detected, without knowing the routes of entry of the pathogens in the new area. However, there are recent studies that show the link between the appearance of epidemic outbreaks of Vibrio and environmental factors such as oceanic transport of warm waters, which has provided a possible mechanism for the dispersion of Vibrio diseases globally. Despite this evidence, there is little information on the possible routes of entry and transport of infectious agents from endemic countries to the entire world. In this sense, the recent advances in genomic sequencing tools are making it possible to infer possible biogeographical patterns of diverse pathogens with relevance in public health like V. parahaemolyticus. In this chapter, we will address several general aspects about V. parahaemolyticus, including their microbiological and genetic detection, main virulence factors, and the epidemiology of genotypes involved in foodborne outbreaks globally.
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Affiliation(s)
- Ronnie G Gavilan
- Instituto Nacional de Salud, Lima, Peru. .,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru.
| | | | - Carlos J Blondel
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jaime Martinez-Urtaza
- Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Barcelona, Spain
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14
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Ellett AN, Rosales D, Jacobs JM, Paranjpye R, Parveen S. Growth Rates of Vibrio parahaemolyticus Sequence Type 36 Strains in Live Oysters and in Culture Medium. Microbiol Spectr 2022; 10:e0211222. [PMID: 36445142 PMCID: PMC9769909 DOI: 10.1128/spectrum.02112-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
The pathogenic marine bacterium Vibrio parahaemolyticus can cause seafood-related gastroenteritis via the consumption of raw or undercooked seafood. Infections originating from relatively cool waters in the northeast United States are typically rare, but recently, this region has shown an increase in infections attributed to the ecological introduction of pathogenic sequence type 36 (ST36) strains, which are endemic to the cool waters of the Pacific Northwest. A 2005 risk assessment performed by the Food and Drug Administration (FDA) modeled the postharvest growth of V. parahaemolyticus in oysters as a function of air temperature and the length of time the oysters remained unrefrigerated. This model, while useful, has raised questions about strain growth differences in oyster tissue and whether invasive pathogenic strains exhibit different growth rates than nonclinical strains, particularly at lower temperatures. To investigate this question, live eastern oysters were injected with ST36 clinical strains and non-ST36 nonclinical strains, and growth rates were measured using the most probable number (MPN) enumeration. The presence of V. parahaemolyticus was confirmed using PCR by targeting the thermolabile hemolysin gene (tlh), thermostable direct hemolysin (tdh), tdh-related hemolysin (trh), and a pathogenesis-related protein (prp). The growth rates of the ST36 strains were compared to the FDA model and several other data sets of V. parahaemolyticus growth in naturally inoculated oysters harvested from the Chesapeake Bay. Our data indicate that the growth rates from most studies fall within the mean of the FDA model, but with slightly higher growth at lower temperatures for ST36 strains injected into live oysters. These data suggest that further investigations of ST36 growth capability in oysters at temperatures previously thought unsuitably low for Vibrio growth are warranted. IMPORTANCE Vibrio parahaemolyticus is the leading cause of seafood-related gastroenteritis in the United States, with an estimated 45,000 cases per year. Most individuals who suffer from vibriosis consume raw or undercooked seafood, including oysters. While gastroenteritis vibriosis is usually self-limiting and treatable, V. parahaemolyticus infections are a stressor on the growing aquaculture industry. Much effort has been placed on modeling the growth of Vibrio cells in oysters in order to aid oyster growers in designing harvesting best practices and ultimately, to protect the consumer. However, ecological invasions of nonnative bacterial strains make modeling their growth complicated, as these strains are not accounted for in current models. The National Shellfish Sanitation Program (NSSP) considers 10°C (50°F) a temperature too low to enable Vibrio growth, where 15°C is considered a cutoff temperature for optimal Vibrio growth, with temperatures approaching 20°C supporting higher growth rates. However, invasive strains may be native to cooler waters. This research aimed to understand strain growth in live oysters by measuring growth rates when oysters containing ST36 strains, which may be endemic to the U.S. Pacific Northwest, were exposed to multiple temperatures postharvest. Our results will be used to aid future model development and harvesting best practices for the aquaculture industry.
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Affiliation(s)
- Ava N. Ellett
- University of Maryland Eastern Shore, Princess Anne, Maryland, USA
- National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic and Atmospheric Administration, Oxford, Maryland, USA
| | - Detbra Rosales
- University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - John M. Jacobs
- National Centers for Coastal Ocean Science, National Ocean Service, National Oceanic and Atmospheric Administration, Oxford, Maryland, USA
| | - Rohinee Paranjpye
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Salina Parveen
- University of Maryland Eastern Shore, Princess Anne, Maryland, USA
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Stanojković A, Skoupý S, Škaloud P, Dvořák P. High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genus Laspinema (cyanobacteria). Front Microbiol 2022; 13:977454. [PMID: 36160208 PMCID: PMC9500459 DOI: 10.3389/fmicb.2022.977454] [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: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
The sympatric occurrence of closely related lineages displaying conserved morphological and ecological traits is often characteristic of free-living microbes. Gene flow, recombination, selection, and mutations govern the genetic variability between these cryptic lineages and drive their differentiation. However, sequencing conservative molecular markers (e.g., 16S rRNA) coupled with insufficient population-level sampling hindered the study of intra-species genetic diversity and speciation in cyanobacteria. We used phylogenomics and a population genomic approach to investigate the extent of local genomic diversity and the mechanisms underlying sympatric speciation of Laspinema thermale. We found two cryptic lineages of Laspinema. The lineages were highly genetically diverse, with recombination occurring more frequently within than between them. That suggests the existence of a barrier to gene flow, which further maintains divergence. Genomic regions of high population differentiation harbored genes associated with possible adaptations to high/low light conditions and stress stimuli, although with a weak diversifying selection. Overall, the diversification of Laspinema species might have been affected by both genomic and ecological processes.
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Affiliation(s)
| | - Svatopluk Skoupý
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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16
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Abstract
The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.
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17
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Paria P, Behera BK, Mohapatra PKD, Parida PK. Virulence factor genes and comparative pathogenicity study of tdh, trh and tlh positive Vibrio parahaemolyticus strains isolated from Whiteleg shrimp, Litopenaeus vannamei (Boone, 1931) in India. INFECTION GENETICS AND EVOLUTION 2021; 95:105083. [PMID: 34536578 DOI: 10.1016/j.meegid.2021.105083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 01/20/2023]
Abstract
Vibrio parahaemolyticus is a gram-negative halophilic bacterium responsible for gastrointestinal infection in human and vibriosis in aquatic animals. The thermostable direct hemolysin (tdh), tdh-related hemolysin (trh) and thermolabile hemolysin (tlh) positive strains of V. parahaemolyticus were identified from brackishwater aquaculture farms of West Bengal and Andhra Pradesh, India. Moreover, the presence of other virulent genes like vcrD1, vopD, vp1680 under type three secretion system 1 (T3SS1) and vcrD2 vopD2, vopB2, vopC2 under type three secretion system 2 (T3SS2) were detected in tdh positive strain of V. parahaemolyticus. Furthermore, the study revealed that the tdh and trh positive isolates were resistant to β-lactam antibiotics and were able to lyse more than 95% of human Red Blood Cells (RBCs). In addition, both the isolates showed high cytotoxicity in Human Embryonic Kidney (HEK) cell line compared to tlh positive strain. Additionally, intraperitoneal and oral administration of tdh and trh positive strain of V. parahaemolyticus in Indian Major Carp, Labeo rohita caused 100% mortality at the level of 2.0 × 108 CFU ml-1 and 1.6 × 108 CFU ml-1, respectively. In contrast, only 10% mortality was observed in the case of tlh positive strain at the level of 2.5× 108 CFU ml-1. The histopathological changes like infiltration of blood cells and degenerated hepatic tissue in the liver of L. rohita were observed after the experimental challenge. The changes like degeneration of glomeruli, necrosis of renal tubules and Bowman's capsule were observed in the kidney section. Ragged, irregular shaped villi and necrosis of the villus were observed in the intestinal lumen. Overall, the study demonstrates that isolated V. parahaemolyticus is a potent aquatic microbial pathogen. Additionally, as V. parahaemolyticus is also a human pathogen and might pose a threat to the human population, proper management strategies are required to prevent the possible occurrence of disease.
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Affiliation(s)
- Prasenjit Paria
- Biotechnology Laboratory, Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India; Department of Microbiology, Vidyasagar University, Midnapure 721102, West Bengal, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India.
| | | | - Pranaya Kumar Parida
- Biotechnology Laboratory, Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
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18
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Brumfield KD, Usmani M, Chen KM, Gangwar M, Jutla AS, Huq A, Colwell RR. Environmental parameters associated with incidence and transmission of pathogenic Vibrio spp. Environ Microbiol 2021; 23:7314-7340. [PMID: 34390611 DOI: 10.1111/1462-2920.15716] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022]
Abstract
Vibrio spp. thrive in warm water and moderate salinity, and they are associated with aquatic invertebrates, notably crustaceans and zooplankton. At least 12 Vibrio spp. are known to cause infection in humans, and Vibrio cholerae is well documented as the etiological agent of pandemic cholera. Pathogenic non-cholera Vibrio spp., e.g., Vibrio parahaemolyticus and Vibrio vulnificus, cause gastroenteritis, septicemia, and other extra-intestinal infections. Incidence of vibriosis is rising globally, with evidence that anthropogenic factors, primarily emissions of carbon dioxide associated with atmospheric warming and more frequent and intense heatwaves, significantly influence environmental parameters, e.g., temperature, salinity, and nutrients, all of which can enhance growth of Vibrio spp. in aquatic ecosystems. It is not possible to eliminate Vibrio spp., as they are autochthonous to the aquatic environment and many play a critical role in carbon and nitrogen cycling. Risk prediction models provide an early warning that is essential for safeguarding public health. This is especially important for regions of the world vulnerable to infrastructure instability, including lack of 'water, sanitation, and hygiene' (WASH), and a less resilient infrastructure that is vulnerable to natural calamity, e.g., hurricanes, floods, and earthquakes, and/or social disruption and civil unrest, arising from war, coups, political crisis, and economic recession. Incorporating environmental, social, and behavioural parameters into such models allows improved prediction, particularly of cholera epidemics. We have reported that damage to WASH infrastructure, coupled with elevated air temperatures and followed by above average rainfall, promotes exposure of a population to contaminated water and increases the risk of an outbreak of cholera. Interestingly, global predictive risk models successful for cholera have the potential, with modification, to predict diseases caused by other clinically relevant Vibrio spp. In the research reported here, the focus was on environmental parameters associated with incidence and distribution of clinically relevant Vibrio spp. and their role in disease transmission. In addition, molecular methods designed for detection and enumeration proved useful for predictive modelling and are described, namely in the context of prediction of environmental conditions favourable to Vibrio spp., hence human health risk.
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Affiliation(s)
- Kyle D Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
| | - Moiz Usmani
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Kristine M Chen
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Mayank Gangwar
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Antarpreet S Jutla
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA.,University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
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Liu J, Qin K, Wu C, Fu K, Yu X, Zhou L. De Novo Sequencing Provides Insights Into the Pathogenicity of Foodborne Vibrio parahaemolyticus. Front Cell Infect Microbiol 2021; 11:652957. [PMID: 34055666 PMCID: PMC8162212 DOI: 10.3389/fcimb.2021.652957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
Vibrio parahaemolyticus is a common pathogenic marine bacterium that causes gastrointestinal infections and other health complications, which could be life-threatening to immunocompromised patients. For the past two decades, the pathogenicity of environmental V. parahaemolyticus has increased greatly, and the genomic change behind this phenomenon still needs an in-depth exploration. To investigate the difference in pathogenicity at the genomic level, three strains with different hemolysin expression and biofilm formation capacity were screened out of 69 environmental V. parahaemolyticus strains. Subsequently, 16S rDNA analysis, de novo sequencing, pathogenicity test, and antibiotic resistance assays were performed. Comparative genome-scale interpretation showed that various functional region differences in pathogenicity of the selected V. parahaemolyticus strains were due to dissimilarities in the distribution of key genetic elements and in the secretory system compositions. Furthermore, the genomic analysis-based hypothesis of distinct pathogenic effects was verified by the survival rate of mouse models infected with different V. parahaemolyticus strains. Antibiotic resistance results also presented the multi-directional evolutionary potential in environmental V. parahaemolyticus, in agreement with the phylogenetic analysis results. Our study provides a theoretical basis for better understanding of the increasing pathogenicity of environmental V. parahaemolyticus at the genome level. Further, it has a key referential value for the exploration of pathogenicity and prevention of environmental V. parahaemolyticus in the future.
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Affiliation(s)
- Jianfei Liu
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Kewei Qin
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Chenglin Wu
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Kaifei Fu
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Xiaojie Yu
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
| | - Lijun Zhou
- Central Laboratory, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China.,College of Otolaryngology Head and Neck Surgery, The Sixth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, China
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20
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Research on the role of LuxS/AI-2 quorum sensing in biofilm of Leuconostoc citreum 37 based on complete genome sequencing. 3 Biotech 2021; 11:189. [PMID: 33927980 DOI: 10.1007/s13205-021-02747-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Leuconostoc citreum, a type of food-grade probiotic bacteria, plays an important role in food fermentation and intestinal probiotics. Biofilms help bacteria survive under adverse conditions, and LuxS/AI-2-dependent quorum sensing (QS) plays an important role in the regulation of their biofilm-forming activities. L. citreum 37 was a biofilm-forming strain isolated from dairy products. The aim of this study was to analyze genes involved in the LuxS/AI-2 system based on genome sequencing and biofilm formation of L. citreum 37. Genome assembly yielded two contigs (one chromosome and one plasmid), and the complete genome contained 1,946,279 base pairs (bps) with a G + C content of 38.91%. The genome sequence analysis showed that there were several pathways such as the two-component system, QS, and seven other signal pathways, and 26 genes (including luxS, pfs, and 24 other genes) may participate in QS related to biofilm formation. All these results showed that the LuxS/AI-2 system is complete in the genome of L. citreum 37. The quantitative polymerase chain reaction (qPCR) of pfs, luxS genes, and AI-2 production of L. citreum 37 in planktonic state and biofilm state showed that the expression of pfs and luxS genes was consistent with the production of AI-2 and was positively correlated with biofilm formation. After luxS of L. citreum 37 expressed in Escherichia coli BL21, AI-2 production was detected, suggesting that the luxS gene played an important role in AI-2 synthesis, Therefore, luxS may regulate the biofilm formation of L. citreum 37 by participating in AI-2 synthesis. It is projected that results of this study could help facilitate further understanding and application of L. citreum 37. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02747-2.
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21
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Watts N, Amann M, Arnell N, Ayeb-Karlsson S, Beagley J, Belesova K, Boykoff M, Byass P, Cai W, Campbell-Lendrum D, Capstick S, Chambers J, Coleman S, Dalin C, Daly M, Dasandi N, Dasgupta S, Davies M, Di Napoli C, Dominguez-Salas P, Drummond P, Dubrow R, Ebi KL, Eckelman M, Ekins P, Escobar LE, Georgeson L, Golder S, Grace D, Graham H, Haggar P, Hamilton I, Hartinger S, Hess J, Hsu SC, Hughes N, Jankin Mikhaylov S, Jimenez MP, Kelman I, Kennard H, Kiesewetter G, Kinney PL, Kjellstrom T, Kniveton D, Lampard P, Lemke B, Liu Y, Liu Z, Lott M, Lowe R, Martinez-Urtaza J, Maslin M, McAllister L, McGushin A, McMichael C, Milner J, Moradi-Lakeh M, Morrissey K, Munzert S, Murray KA, Neville T, Nilsson M, Sewe MO, Oreszczyn T, Otto M, Owfi F, Pearman O, Pencheon D, Quinn R, Rabbaniha M, Robinson E, Rocklöv J, Romanello M, Semenza JC, Sherman J, Shi L, Springmann M, Tabatabaei M, Taylor J, Triñanes J, Shumake-Guillemot J, Vu B, Wilkinson P, Winning M, Gong P, Montgomery H, Costello A. The 2020 report of The Lancet Countdown on health and climate change: responding to converging crises. Lancet 2021; 397:129-170. [PMID: 33278353 DOI: 10.1016/s0140-6736(20)32290-x] [Citation(s) in RCA: 699] [Impact Index Per Article: 233.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 01/18/2023]
Abstract
For the Chinese, French, German, and Spanish translations of the abstract see Supplementary Materials section.
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Affiliation(s)
- Nick Watts
- Institute for Global Health, University College London, London, UK.
| | - Markus Amann
- Air Quality and Greenhouse Gases Program, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Nigel Arnell
- Department of Meteorology, University of Reading, Reading, UK
| | - Sonja Ayeb-Karlsson
- Institute for Environment and Human Security, United Nations University, Bonn, Germany
| | - Jessica Beagley
- Institute for Global Health, University College London, London, UK
| | - Kristine Belesova
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Maxwell Boykoff
- Environmental Studies Program, University of Colorado Boulder, Boulder, CO, USA
| | - Peter Byass
- Department of Epidemiology and Global Health, Umeå University, Umeå, Sweden
| | - Wenjia Cai
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Diarmid Campbell-Lendrum
- Environment, Climate Change and Health Department, World Health Organization, Geneva, Switzerland
| | | | - Jonathan Chambers
- Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Samantha Coleman
- Institute for Global Health, University College London, London, UK
| | - Carole Dalin
- Institute for Sustainable Resources, University College London, London, UK
| | - Meaghan Daly
- Department of Environmental Studies, University of New England, Biddeford, ME, USA
| | - Niheer Dasandi
- School of Government, University of Birmingham, Birmingham, UK
| | - Shouro Dasgupta
- Centro Euro-Mediterraneo sui Cambiamenti Climatici, Venice, Italy
| | - Michael Davies
- Institute for Environmental Design and Engineering, University College London, London, UK
| | - Claudia Di Napoli
- School of Agriculture, Policy, and Development, University of Reading, Reading, UK
| | - Paula Dominguez-Salas
- Department of Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Paul Drummond
- Institute for Sustainable Resources, University College London, London, UK
| | - Robert Dubrow
- Yale Center on Climate Change and Health, Yale University, New Haven, CT, USA
| | - Kristie L Ebi
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Matthew Eckelman
- Department of Civil & Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Paul Ekins
- Institute for Sustainable Resources, University College London, London, UK
| | - Luis E Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Su Golder
- Department of Health Sciences, University of York, York, UK
| | - Delia Grace
- CGIAR Research Program on Agriculture for Human Nutrition and Health, International Livestock Research Institute, Nairobi, Kenya
| | - Hilary Graham
- Department of Environmental Studies, University of New England, Biddeford, ME, USA
| | - Paul Haggar
- School of Psychology, Cardiff University, Cardiff, UK
| | - Ian Hamilton
- Energy Institute, University College London, London, UK
| | - Stella Hartinger
- School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeremy Hess
- Center for Health and the Global Environment, University of Washington, Seattle, WA, USA
| | - Shih-Che Hsu
- Energy Institute, University College London, London, UK
| | - Nick Hughes
- Institute for Sustainable Resources, University College London, London, UK
| | | | - Marcia P Jimenez
- Department of Epidemiology, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Ilan Kelman
- Institute for Global Health, University College London, London, UK
| | - Harry Kennard
- Energy Institute, University College London, London, UK
| | - Gregor Kiesewetter
- Air Quality and Greenhouse Gases Program, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Patrick L Kinney
- Department of Environmental Health, Boston University, Boston, MA, USA
| | - Tord Kjellstrom
- Health and Environment International Trust, Nelson, New Zealand
| | | | - Pete Lampard
- Department of Health Sciences, University of York, York, UK
| | - Bruno Lemke
- School of Health, Nelson Marlborough Institute of Technology, Nelson, New Zealand
| | - Yang Liu
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Zhao Liu
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Melissa Lott
- Center on Global Energy Policy, Columbia University, New York, NY, USA
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jaime Martinez-Urtaza
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mark Maslin
- Department of Geography, University College London, London, UK
| | - Lucy McAllister
- Center for Energy Markets, Technical University of Munich, Munich, Germany
| | - Alice McGushin
- Institute for Global Health, University College London, London, UK
| | - Celia McMichael
- School of Geography, University of Melbourne, Melbourne, VIC, Australia
| | - James Milner
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Maziar Moradi-Lakeh
- Preventive Medicine and Public Health Research Center, Psychosocial Health Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Karyn Morrissey
- European Centre for Environment and Human Health, University of Exeter, Exeter, UK
| | | | - Kris A Murray
- Medical Research Council Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Bakau, The Gambia
| | - Tara Neville
- Environment, Climate Change and Health Department, World Health Organization, Geneva, Switzerland
| | - Maria Nilsson
- Department of Epidemiology and Global Health, Umeå University, Umeå, Sweden
| | | | | | - Matthias Otto
- Department of Arts, Media and Digital Technologies, Nelson Marlborough Institute of Technology, Nelson, New Zealand
| | - Fereidoon Owfi
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Olivia Pearman
- Environmental Studies Program, University of Colorado Boulder, Boulder, CO, USA
| | - David Pencheon
- Medical and Health School, University of Exeter, Exeter, UK
| | - Ruth Quinn
- Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK
| | - Mahnaz Rabbaniha
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Elizabeth Robinson
- School of Agriculture, Policy, and Development, University of Reading, Reading, UK
| | - Joacim Rocklöv
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Marina Romanello
- Institute for Global Health, University College London, London, UK
| | - Jan C Semenza
- Scientific Assessment Section, European Centre for Disease Prevention and Control, Solna, Sweden
| | - Jodi Sherman
- Department of Anesthesiology, Yale University, New Haven, CT, USA
| | - Liuhua Shi
- Gangarosa Department of Environmental Health, Atlanta, GA, USA
| | | | - Meisam Tabatabaei
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Jonathon Taylor
- Department of Civil Engineering, Tampere University, Tampere, Finland
| | - Joaquin Triñanes
- Department of Electronics and Computer Science, CRETUS Institute, Universidade de Santiago de Compostela, Santiago, Spain
| | | | - Bryan Vu
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Paul Wilkinson
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Matthew Winning
- Institute for Sustainable Resources, University College London, London, UK
| | - Peng Gong
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Hugh Montgomery
- Institute for Human Health and Performance, University College London, London, UK
| | - Anthony Costello
- Office of the Vice Provost for Research, University College London, London, UK
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Abanto M, Gavilan RG, Baker-Austin C, Gonzalez-Escalona N, Martinez-Urtaza J. Global Expansion of Pacific Northwest Vibrio parahaemolyticus Sequence Type 36. Emerg Infect Dis 2021; 26:323-326. [PMID: 31961301 PMCID: PMC6986845 DOI: 10.3201/eid2602.190362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We report transcontinental expansion of Vibrio parahaemolyticus sequence type 36 into Lima, Peru. From national collections, we identified 7 isolates from 2 different Pacific Northwest complex lineages that surfaced during 2011–2016. Sequence type 36 is likely established in environmental reservoirs. Systematic surveillance enabled detection of these epidemic isolates.
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Fu S, Ni P, Yang Q, Hu H, Wang Q, Ye S, Liu Y. Delineating the key virulence factors and intraspecies divergence of Vibrio harveyi via whole-genome sequencing. Can J Microbiol 2020; 67:231-248. [PMID: 32941745 DOI: 10.1139/cjm-2020-0079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrio harveyi is one of the major pathogens in aquaculture. To identify the key virulence factors affecting pathogenesis of V. harveyi towards fish, we conducted a field investigation for three representative fish farms infected with V. harveyi. Multilocus sequence typing (MLST) and whole-genome sequencing were conducted to delineate the phylogenetic relationship and genetic divergence of V. harveyi. A total of 25 V. harveyi strains were isolated from the diseased fish and groundwater and were subtyped into 12 sequence types by MLST. Five virulence genes, mshB, pilA, hutR, ureB, and ureG, were variably presented in the sequenced strains. The virulence gene profiles strongly correlated with the distinct pathogenicity of V. harveyi strains, with a strain harboring all five genes exhibiting the highest virulence towards fish. Phenotype assay confirmed that reduced virulence correlated with decreased motility and biofilm formation ability. Additionally, three types of type VI secretion system, namely T6SS1, T6SS2, and T6SS3, were identified in V. harveyi strains, which can be classified into six, four, and 12 subtypes, respectively. In conclusion, the results indicated that the virulence level of V. harveyi is mainly determined by the above virulence genes, which may play vital roles in environmental adaptation for V. harveyi.
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Affiliation(s)
- Songzhe Fu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, P.R. China.,Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, P.R. China
| | - Ping Ni
- Dalian Key Laboratory of Marine Animal Disease Control and Prevention, Dalian Ocean University, Dalian, P.R. China
| | - Qian Yang
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Huizhi Hu
- Hubei Key Laboratory of Regional Development and Environmental Response, School of Resources and Environment, Hubei University, Wuhan, P.R. China
| | - Qingyao Wang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, P.R. China.,Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, P.R. China
| | - Shigen Ye
- Dalian Key Laboratory of Marine Animal Disease Control and Prevention, Dalian Ocean University, Dalian, P.R. China
| | - Ying Liu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, P.R. China.,Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian, P.R. China
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Couchoud C, Bertrand X, Valot B, Hocquet D. Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software. Microb Genom 2020; 6:e000356. [PMID: 32213253 PMCID: PMC7371109 DOI: 10.1099/mgen.0.000356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) is now widely used in microbiology to explore genome evolution and the structure of pathogen outbreaks. Bioinformatics pipelines readily detect single-nucleotide polymorphisms or short indels. However, bacterial genomes also evolve through the action of small transposable elements called insertion sequences (ISs), which are difficult to detect due to their short length and multiple repetitions throughout the genome. We designed panISa software for the ab initio detection of IS insertions in the genomes of prokaryotes. PanISa has been released as open source software (GPL3) available from https://github.com/bvalot/panISa. In this study, we assessed the utility of this software for evolutionary studies, by reanalysing five published datasets for outbreaks of human major pathogens in which ISs had not been specifically investigated. We reanalysed the raw data from each study, by aligning the reads against reference genomes and running panISa on the alignments. Each hit was automatically curated and IS-related events were validated on the basis of nucleotide sequence similarity, by comparison with the ISFinder database. In Acinetobacter baumannii, the panISa pipeline identified ISAba1 or ISAba125 upstream from the ampC gene, which encodes a cephalosporinase in all third-generation cephalosporin-resistant isolates. In the genomes of Vibrio cholerae isolates, we found that early Haitian isolates had the same ISs as Nepalese isolates, confirming the inferred history of the contamination of this island. In Enterococcus faecalis, panISa identified regions of high plasticity, including a pathogenicity island enriched in IS-related events. The overall distribution of ISs deduced with panISa was consistent with SNP-based phylogenic trees, for all species considered. The role of ISs in pathogen evolution has probably been underestimated due to difficulties detecting these transposable elements. We show here that panISa is a useful addition to the bioinformatics toolbox for analyses of the evolution of bacterial genomes. PanISa will facilitate explorations of the functional impact of ISs and improve our understanding of prokaryote evolution.
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Affiliation(s)
- Charlotte Couchoud
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoit Valot
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
- Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- UMR CNRS 6249 Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
- Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
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25
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Galanis E, Otterstatter M, Taylor M. Measuring the impact of sea surface temperature on the human incidence of Vibrio sp. infection in British Columbia, Canada, 1992-2017. Environ Health 2020; 19:58. [PMID: 32460848 PMCID: PMC7251872 DOI: 10.1186/s12940-020-00605-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Vibrio growth in the environment is related to sea surface temperature (SST). The incidence of human Vibrio illness increased sharply in British Columbia (BC) between 2008 and 2015 for unknown reasons, culminating in the largest outbreak of shellfish-associated Vibrio parahaemolyticus (Vp) in Canadian history in 2015. Our objective was to assess the relationship between SST and Vibrio illness in BC, Canada during 1992-2017 and assess the role of SST and other environmental factors in the 2015 Vp outbreak. METHODS Cases of Vibrio infection reported to the BC Centre for Disease Control during 1992-2017 were used. SST data were obtained from NOAA and NASA. We assessed changes in incidence trend of annual Vibrio cases during 1992-2017 using a Poisson regression. We assessed the correlation between annual Vibrio cases and the average annual maximum SST using a Spearman rank-order correlation. We modeled the association between weekly Vp case counts, SST and other environmental factors during 2007-2017 using a Poisson regression. RESULTS There was a significant increase in Vibrio cases between 2008 and 2015 (annual slope = 0.163, P < 0.001). Increased Vibrio incidence was observed in most El Niño years. There was a significant correlation between annual Vibrio cases and maximum SST from 1992 to 2017 (r = 0.46, P = 0.018). Our model captured observed seasonal variation in shellfish-associated Vp in most years, but underestimated the 2015 Vp outbreak. CONCLUSIONS Vibrio incidence has been increasing concurrently with increasing SST in BC during 2008-2015. The 2015 Vp outbreak was not fully explained by climatic factors and may in part have been associated with other factors. Vp subtyping would be useful in the future to understand the combined effects of SST changes and strain emergence.
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Affiliation(s)
- Eleni Galanis
- British Columbia Centre for Disease Control, 655 W 12th Ave, Vancouver, British Columbia V5Z 4R4 Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia Canada
| | - Michael Otterstatter
- British Columbia Centre for Disease Control, 655 W 12th Ave, Vancouver, British Columbia V5Z 4R4 Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia Canada
| | - Marsha Taylor
- British Columbia Centre for Disease Control, 655 W 12th Ave, Vancouver, British Columbia V5Z 4R4 Canada
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Horizontal Plasmid Transfer Promotes the Dissemination of Asian Acute Hepatopancreatic Necrosis Disease and Provides a Novel Mechanism for Genetic Exchange and Environmental Adaptation. mSystems 2020; 5:5/2/e00799-19. [PMID: 32184363 PMCID: PMC7380584 DOI: 10.1128/msystems.00799-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Global outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the horizontal transfer of an AHPND-associated plasmid. Surprisingly, the introduction of the AHPND-associated plasmid also offers a novel mechanism of genetic exchange mediated by insertion sequences, and it improved the fitness of V. parahaemolyticus in a harsh environment. The results presented herein suggest that current shrimp farming practices promote genetic mixture between endemic and oceanic V. parahaemolyticus populations, which introduced the plasmid and accelerated bacterial adaptation by the acquisition of ecologically important functions. This entails a risk of the emergence of new virulent populations both for shrimp and humans. This study improves our understanding of the global dissemination of the AHPND-associated plasmid and highlights the urgent need to improve biosecurity for shrimp farming. Vibrio parahaemolyticus is an important foodborne pathogen and has recently gained particular notoriety because it causes acute hepatopancreatic necrosis disease (AHPND) in shrimp, which has caused significant economic loss in the shrimp industry. Here, we report a whole-genome analysis of 233 V. parahaemolyticus strains isolated from humans, diseased shrimp, and environmental samples collected between 2008 and 2017, providing unprecedented insight into the historical spread of AHPND. The results show that V. parahaemolyticus is genetically diverse and can be divided into 84 sequence types (STs). However, genomic analysis of three STs of V. parahaemolyticus identified seven transmission routes in Asia since 1996, which promoted the transfer of an AHPND-associated plasmid. Notably, the insertion sequence (ISVal1) from the plasmid subsequently mediated the genetic exchange among V. parahaemolyticus STs and resulted in the deletion of an 11-kb region regulating cell mobility and the production of capsular polysaccharides. Phenotype assays confirmed that this deletion enhanced biofilm formation, providing a novel mechanism for environmental adaptation. We conclude that the transmission mode of AHPND consists of two steps, the transmission of V. parahaemolyticus and the subsequent horizontal transfer of the AHPND-associated plasmid. This plasmid allows ISVal1 to mediate genetic exchange and improve pathogen fitness in shrimp ponds. Current shrimp farming practices promoted such genetic exchanges, which highlighted a risk of the emergence of new virulent populations, with potentially devastating consequences for both aquaculture and human health. This study addressed the basic questions regarding the transmission mechanism of AHPND and provided novel insights into shrimp and human disease management. IMPORTANCE Global outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the horizontal transfer of an AHPND-associated plasmid. Surprisingly, the introduction of the AHPND-associated plasmid also offers a novel mechanism of genetic exchange mediated by insertion sequences, and it improved the fitness of V. parahaemolyticus in a harsh environment. The results presented herein suggest that current shrimp farming practices promote genetic mixture between endemic and oceanic V. parahaemolyticus populations, which introduced the plasmid and accelerated bacterial adaptation by the acquisition of ecologically important functions. This entails a risk of the emergence of new virulent populations both for shrimp and humans. This study improves our understanding of the global dissemination of the AHPND-associated plasmid and highlights the urgent need to improve biosecurity for shrimp farming.
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27
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Cantrell DL, Groner ML, Ben-Horin T, Grant J, Revie CW. Modeling Pathogen Dispersal in Marine Fish and Shellfish. Trends Parasitol 2020; 36:239-249. [PMID: 32037136 DOI: 10.1016/j.pt.2019.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/19/2019] [Accepted: 12/25/2019] [Indexed: 12/12/2022]
Abstract
In marine ecosystems, oceanographic processes often govern host contacts with infectious agents. Consequently, many approaches developed to quantify pathogen dispersal in terrestrial ecosystems have limited use in the marine context. Recent applications in marine disease modeling demonstrate that physical oceanographic models coupled with biological models of infectious agents can characterize dispersal networks of pathogens in marine ecosystems. Biophysical modeling has been used over the past two decades to model larval dispersion but has only recently been utilized in marine epidemiology. In this review, we describe how biophysical models function and how they can be used to measure connectivity of infectious agents between sites, test hypotheses regarding pathogen dispersal, and quantify patterns of pathogen spread, focusing on fish and shellfish pathogens.
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Affiliation(s)
- Danielle L Cantrell
- Health Management Department, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Maya L Groner
- Prince William Sound Science Center, Cordova, AK, USA; Affiliate, US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Tal Ben-Horin
- Department of Fisheries, Animal and Veterinary Science, College of the Environment and Life Science, University of Rhode Island, Kingston, RI, USA; Center for Marine Science and Technology, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Morehead City, NC, USA
| | - Jon Grant
- Oceanography Department, Dalhousie University, Halifax, NS, Canada
| | - Crawford W Revie
- Health Management Department, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada; Department of Computer and Information Sciences, University of Strathclyde, Glasgow, UK
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28
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Yang C, Zhang X, Fan H, Li Y, Hu Q, Yang R, Cui Y. Genetic diversity, virulence factors and farm-to-table spread pattern of Vibrio parahaemolyticus food-associated isolates. Food Microbiol 2019; 84:103270. [DOI: 10.1016/j.fm.2019.103270] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/30/2019] [Accepted: 07/12/2019] [Indexed: 01/15/2023]
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29
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Watts N, Amann M, Arnell N, Ayeb-Karlsson S, Belesova K, Boykoff M, Byass P, Cai W, Campbell-Lendrum D, Capstick S, Chambers J, Dalin C, Daly M, Dasandi N, Davies M, Drummond P, Dubrow R, Ebi KL, Eckelman M, Ekins P, Escobar LE, Fernandez Montoya L, Georgeson L, Graham H, Haggar P, Hamilton I, Hartinger S, Hess J, Kelman I, Kiesewetter G, Kjellstrom T, Kniveton D, Lemke B, Liu Y, Lott M, Lowe R, Sewe MO, Martinez-Urtaza J, Maslin M, McAllister L, McGushin A, Jankin Mikhaylov S, Milner J, Moradi-Lakeh M, Morrissey K, Murray K, Munzert S, Nilsson M, Neville T, Oreszczyn T, Owfi F, Pearman O, Pencheon D, Phung D, Pye S, Quinn R, Rabbaniha M, Robinson E, Rocklöv J, Semenza JC, Sherman J, Shumake-Guillemot J, Tabatabaei M, Taylor J, Trinanes J, Wilkinson P, Costello A, Gong P, Montgomery H. The 2019 report of The Lancet Countdown on health and climate change: ensuring that the health of a child born today is not defined by a changing climate. Lancet 2019; 394:1836-1878. [PMID: 31733928 DOI: 10.1016/s0140-6736(19)32596-6] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Nick Watts
- Institute for Global Health, University College London, London, UK.
| | - Markus Amann
- Air Quality and Greenhouse Gases Programme, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Nigel Arnell
- Department of Meteorology, University of Reading, Reading, UK
| | | | - Kristine Belesova
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Maxwell Boykoff
- Cooperative Institute for Research in Environmental Sciences and Environmental Studies, University of Colorado Boulder, Boulder, CO, USA
| | - Peter Byass
- Department of Epidemiology and Global Health, Umeå University, Umeå, Sweden
| | - Wenjia Cai
- Department of Earth System Science, Tsinghua University, Beijing, China
| | | | | | - Jonathan Chambers
- Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Carole Dalin
- Institute for Sustainable Resources, University College London, London, UK
| | - Meaghan Daly
- Department of Environmental Studies, University of New England, Biddeford, ME, USA
| | - Niheer Dasandi
- School of Government, University of Birmingham, Birmingham, UK
| | - Michael Davies
- Institute for Environmental Design and Engineering, University College London, London, UK
| | - Paul Drummond
- Institute for Sustainable Resources, University College London, London, UK
| | - Robert Dubrow
- Yale Climate Change and Health Initiative, Yale University, New Haven, CT, USA
| | - Kristie L Ebi
- Department of Global Health, University of Washington, Washington, DC, USA
| | - Matthew Eckelman
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Paul Ekins
- Institute for Sustainable Resources, University College London, London, UK
| | - Luis E Escobar
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | | | - Hilary Graham
- Department of Health Sciences, University of York, York, UK
| | - Paul Haggar
- School of Psychology, Cardiff University, Cardiff, UK
| | - Ian Hamilton
- Energy Institute, University College London, London, UK
| | - Stella Hartinger
- The Integrated Development, Health and Environment Unit, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeremy Hess
- Centre for Health and the Global Environment, University of Washington, Washington, DC, USA
| | - Ilan Kelman
- Institute for Global Health, University College London, London, UK
| | - Gregor Kiesewetter
- Air Quality and Greenhouse Gases Programme, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Tord Kjellstrom
- Health and Environment International Trust, Nelson, New Zealand
| | | | - Bruno Lemke
- Nelson Marlborough Institute of Technology, Nelson, New Zealand
| | - Yang Liu
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Melissa Lott
- Center on Global Energy Policy School of International and Public Affairs, Columbia University, New York City, NY, USA
| | - Rachel Lowe
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Mark Maslin
- Department of Geography, University College London, London, UK
| | - Lucy McAllister
- History and Society Division, Babson College, Wellesley, MA, USA
| | - Alice McGushin
- Institute for Global Health, University College London, London, UK
| | | | - James Milner
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Maziar Moradi-Lakeh
- Preventive Medicine and Public Health Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Karyn Morrissey
- European Centre for Environment and Human Health, University of Exeter, Exeter, UK
| | - Kris Murray
- Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | | | - Maria Nilsson
- Department of Epidemiology and Global Health, Umeå University, Umeå, Sweden
| | - Tara Neville
- Department of Public Health and the Environment, WHO, Geneva, Switzerland
| | | | - Fereidoon Owfi
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Olivia Pearman
- Center for Science and Technology Policy Research, University of Colorado Boulder, Boulder, CO, USA
| | | | - Dung Phung
- School of Medicine, Griffith University, Brisbane, QLD, Australia
| | - Steve Pye
- Energy Institute, University College London, London, UK
| | - Ruth Quinn
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Mahnaz Rabbaniha
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Elizabeth Robinson
- School of Agriculture, Policy, and Development, University of Reading, Reading, UK
| | - Joacim Rocklöv
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Jan C Semenza
- Scientific Assessment Section, European Centre for Disease Prevention and Control, Solna, Sweden
| | - Jodi Sherman
- Department of Anesthesiology, Yale University, New Haven, CT, USA
| | | | - Meisam Tabatabaei
- Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, Shah Alam, Malaysia
| | - Jonathon Taylor
- Institute for Environmental Design and Engineering, University College London, London, UK
| | - Joaquin Trinanes
- Physical Oceanography Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | - Paul Wilkinson
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Anthony Costello
- Office of the Vice Provost for Research, University College London, London, UK
| | - Peng Gong
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Hugh Montgomery
- Institute for Human Health and Performance, University College London, London, UK
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30
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Yang C, Pei X, Wu Y, Yan L, Yan Y, Song Y, Coyle NM, Martinez-Urtaza J, Quince C, Hu Q, Jiang M, Feil E, Yang D, Song Y, Zhou D, Yang R, Falush D, Cui Y. Recent mixing of Vibrio parahaemolyticus populations. THE ISME JOURNAL 2019; 13:2578-2588. [PMID: 31235840 PMCID: PMC6775990 DOI: 10.1038/s41396-019-0461-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 02/07/2023]
Abstract
Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.
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Affiliation(s)
- Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiaoyan Pei
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lin Yan
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yuqin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | | | | | | | - Qinghua Hu
- Shenzhen Centre for Disease Control and Prevention, Shenzhen, 518055, China
| | - Min Jiang
- Shenzhen Centre for Disease Control and Prevention, Shenzhen, 518055, China
| | | | - Dajin Yang
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | | | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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31
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Cohen ML, Mashanova EV, Rosen NM, Soto W. Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes). Evolution 2019; 73:1885-1897. [PMID: 31397886 DOI: 10.1111/evo.13819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 11/29/2022]
Abstract
For microorganisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether adaptation to stress during the free-living stage can impact microbial fitness in the host. To address this topic, the mutualism between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bioluminescent bacterium Vibrio fischeri was utilized. Using microbial experimental evolution, V. fischeri was selected to low (8°C), high (34°C), and fluctuating temperature stress (8°C/34°C) for 2000 generations. The temperatures 8°C and 34°C were the lower and upper growth limits, respectively. V. fischeri was also selected to benign temperatures (21°C and 28°C) for 2000 generations, which served as controls. V. fischeri demonstrated significant adaptation to low, high, and fluctuating temperature stress. V. fischeri did not display significant adaptation to the benign temperatures. Adaptation to stressful temperatures facilitated V. fischeri's ability to colonize the squid host relative to the ancestral lines. Bioluminescence levels also increased. Evolution to benign temperatures did not manifest these results. In summary, microbial adaptation to stress during the free-living stage can promote coevolution between hosts and microorganisms.
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Affiliation(s)
- Meagan Leah Cohen
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
| | | | | | - William Soto
- Department of Biology, College of William & Mary, Williamsburg, Virginia, 23185
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32
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González-Escalona N, Allard MA, Brown EW, Sharma S, Hoffmann M. Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli. PLoS One 2019; 14:e0220494. [PMID: 31361781 PMCID: PMC6667211 DOI: 10.1371/journal.pone.0220494] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 02/02/2023] Open
Abstract
Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete Shiga toxin-producing Escherichia coli (STEC) O26:H11/H- genomes from two different sequence types (ST21 and 29), each acquired using the Nextera XT MiSeq, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read whole genome sequencing (WGS) using Nextera XT MiSeq failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobial genes, and composition/location of Stx phages. Taken together, positive correlations between the two long-read methods for determining plasmids, virulome, antimicrobial resistance genes, and phage composition support MinION sequencing as one accurate and economical option for closing STEC genomes and identifying specific virulence markers.
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Affiliation(s)
- Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
- * E-mail:
| | - Marc A. Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Shashi Sharma
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
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33
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Edlind T, Richards GP. Development and Evaluation of Polymorphic Locus Sequence Typing for Epidemiological Tracking of Vibrio parahaemolyticus. Foodborne Pathog Dis 2019; 16:752-760. [PMID: 31144991 DOI: 10.1089/fpd.2019.2649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vibrio parahaemolyticus is a common inhabitant of coastal estuaries, and can accumulate to high levels in the shellfish that populate those waters. Human gastrointestinal infection occasionally follows ingestion of raw oysters, and it can lead to extended closures of implicated oyster beds with serious economic consequences. To track down the source of human infection, and to monitor strain variation in the environment, a user-friendly and affordable typing method that provides sufficient resolution for epidemiological analysis is needed. Polymorphic locus sequence typing (PLST) is based on conventional PCR and dideoxynucleotide sequencing of the one or two most phylogenetically informative genomic loci. Bioinformatic analyses of GenBank databases identified the V. parahaemolyticus polymorphic tandem repeat-containing loci VpMT1 and VpMT2 on chromosomes 1 and 2, respectively, as promising PLST targets, yielding diversity indexes of 0.99. Phylogenetic analysis identified multiple clusters representing strains known or likely to be epidemiologically related. Correlations with serotype and multilocus sequence type were strong but resolution was higher; for example, North American ST36 strains yielded 16 VpMT1 alleles. In the laboratory, VpMT1 and VpMT2 were robust, resolving 16 of 17 strains following PCR and sequencing directly from heat-killed colonies. Finally, 4 of 13 retail oyster enrichments yielded VpMT sequences that were unique but closely related to previously characterized clinical or environmental V. parahaemolyticus isolates.
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Affiliation(s)
- Tom Edlind
- MicrobiType LLC, Plymouth Meeting, Pennsylvania
| | - Gary P Richards
- U.S. Department of Agriculture, Agricultural Research Service, Dover, Delaware
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34
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Jesser KJ, Valdivia-Granda W, Jones JL, Noble RT. Clustering of Vibrio parahaemolyticus Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting. Front Public Health 2019; 7:66. [PMID: 31139608 PMCID: PMC6519141 DOI: 10.3389/fpubh.2019.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/06/2019] [Indexed: 01/22/2023] Open
Abstract
Vibrio parahaemolyticus is a ubiquitous and abundant member of native microbial assemblages in coastal waters and shellfish. Though V. parahaemolyticus is predominantly environmental, some strains have infected human hosts and caused outbreaks of seafood-related gastroenteritis. In order to understand differences among clinical and environmental V. parahaemolyticus strains, we used high quality DNA sequencing data to compare the genomes of V. parahaemolyticus isolates (n = 43) from a variety of geographic locations and clinical and environmental sample matrices. We used phylogenetic trees inferred from multilocus sequence typing (MLST) and whole-genome (WG) alignments, as well as a novel classification and genome clustering approach that relies on protein motif fingerprints (MFs), to assess relationships between V. parahaemolyticus strains and identify novel molecular targets associated with virulence. Differences in strain clustering at more than one position were observed between the MLST and WG phylogenetic trees. The WG phylogeny had higher support values and strain resolution since isolates of the same sequence type could be differentiated. The MF analysis revealed groups of protein motifs that were associated with the pathogenic MLST type ST36 and a large group of clinical strains isolated from human stool. A subset of the stool and ST36-associated protein motifs were selected for further analysis and the motif sequences were found in genes with a variety of functions, including transposases, secretion system components and effectors, and hypothetical proteins. DNA sequences associated with these protein motifs are candidate targets for future molecular assays in order to improve surveys of pathogenic V. parahaemolyticus in the environment and seafood.
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Affiliation(s)
- Kelsey J Jesser
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
| | | | - Jessica L Jones
- Gulf Coast Seafood Laboratory, Division of Seafood Science and Technology, U.S. Food and Drug Administration, Dauphin Island, AL, United States
| | - Rachel T Noble
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, NC, United States
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35
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Yang Q, Dong X, Xie G, Fu S, Zou P, Sun J, Wang Y, Huang J. Comparative genomic analysis unravels the transmission pattern and intra-species divergence of acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus strains. Mol Genet Genomics 2019; 294:1007-1022. [PMID: 30968246 DOI: 10.1007/s00438-019-01559-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a recently discovered shrimp disease that has become a severe threat to global shrimp-farming industry. The causing agents of AHPND were identified as Vibrio parahaemolyticus and other vibrios harboring a plasmid encoding binary toxins PirAvp/PirBvp. However, the epidemiological involvement of environmental vibrios in AHPND is poorly understood. In this study, with an aim to reveal the possible transmission route of AHPND-causing V. parahaemolyticus, we sequenced and analyzed the genomes of four pairs of V. parahaemolyticus strains from four representative regions of shrimp farming in China, each including one strain isolated from diseased shrimp during an AHPND outbreak and one strain isolated from sediment before AHPND outbreaks. Our results showed that all the four shrimp-isolated and three of the sediment-isolated strains encode and secret PirAvp/PirBvp toxins and, therefore, are AHPND-causing strains. In silico multilocus sequence typing and high-resolution phylogenomic analysis based on single-nucleotide polymorphisms, as well as comparison of genomic loci in association with prophages and capsular polysaccharides (CPSs) consistently pointed to a close genetic relationship between the shrimp- and sediment-isolated strains obtained from the same region. In addition, our analyses revealed that the sequences associated with prophages, CPSs, and type VI secretion system-1 are highly divergent among strains from different regions, implying that these genes may play vital roles in environmental adaptation for AHPND-causing V. parahaemolyticus and thereby be potential targets for AHPND control. Summing up, this study provides the first direct evidence regarding the transmission route of AHPND-causing V. parahaemolyticus and underscores that V. parahaemolyticus in shrimp are most likely originated from local environment. The importance of environmental disinfection measures in shrimp farming was highlighted.
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Affiliation(s)
- Qian Yang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xuan Dong
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Guosi Xie
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Songzhe Fu
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China.
| | - Peizhuo Zou
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Jing Sun
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yi Wang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
| | - Jie Huang
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.
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36
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González-Escalona N, Kase JA. Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017. PLoS One 2019; 14:e0214620. [PMID: 30934002 PMCID: PMC6443163 DOI: 10.1371/journal.pone.0214620] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/15/2019] [Indexed: 11/19/2022] Open
Abstract
Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA's Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a. Here we described the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, and determined their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by FDA field labs (ORA), and food testing by a contract company. Only 276 (83%) strains were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% saa (26%)]. Virulence gene prevalence was also determined: stx1 only (19%); stx2 only (66%); and stx1/sxt2 (15%). Our data form a new WGS dataset that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods.
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Affiliation(s)
- Narjol González-Escalona
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
| | - Julie Ann Kase
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States of America
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37
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Han D, Yu F, Chen X, Zhang R, Li J. Challenges in Vibrio parahaemolyticus infections caused by the pandemic clone. Future Microbiol 2019; 14:437-450. [PMID: 30855189 DOI: 10.2217/fmb-2018-0308] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vibrio Parahaemolyticus infections caused by the pandemic clone have become a global public health issue. The pandemic clone includes over ten sequence types and 49 serotypes. Several markers such as toxRS/new, orf8 and genomic islands were considered specific for pandemic strains, but subsequent studies later confirmed a lack of specificity. Thus, identifying stable indicators for the pandemic clone is still an open question. In recent years, several environmental pandemic strains are growing, constituting a new threat to seafood safety and human health. Traditional methods show limited discrimination in studying the microevolution of pandemic strains. For example, multilocus sequence typing divides many pandemic strains into ST3 type, making it difficult to further distinguish the variability within ST3 strains from different contexts. When using a whole genome sequencing-based technique, strains including those with the same sequence type, could be well separated. Whole genome sequencing-based technology also played important roles in dissecting the evolution process and revealing the mechanism underlying rapid serotype conversion within pandemic strains. In addition, the emergence of multiple-antibiotic resistant pandemic strains needs attention. Altogether, we are facing many challenges posed by pandemic V. parahaemolyticus strains, which need to be resolved in future studies.
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Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Fei Yu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiao Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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38
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Ina-Salwany MY, Al-Saari N, Mohamad A, Mursidi FA, Mohd-Aris A, Amal MNA, Kasai H, Mino S, Sawabe T, Zamri-Saad M. Vibriosis in Fish: A Review on Disease Development and Prevention. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:3-22. [PMID: 30246889 DOI: 10.1002/aah.10045] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/16/2018] [Indexed: 05/19/2023]
Abstract
Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.
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Affiliation(s)
- M Y Ina-Salwany
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nurhidayu Al-Saari
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- International Institute for Halal Research and Training, International Islamic University Malaysia, KICT Building, Level 3, 53100, Gombak, Selangor, Malaysia
| | - Aslah Mohamad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Fathin-Amirah Mursidi
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Aslizah Mohd-Aris
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, School of Biology, Universiti Teknologi MARA, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
| | - M N A Amal
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hisae Kasai
- Laboratory of Fish Pathology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - M Zamri-Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Martinez-Urtaza J, Trinanes J, Abanto M, Lozano-Leon A, Llovo-Taboada J, Garcia-Campello M, Pousa A, Powell A, Baker-Austin C, Gonzalez-Escalona N. Epidemic Dynamics of Vibrio parahaemolyticus Illness in a Hotspot of Disease Emergence, Galicia, Spain. Emerg Infect Dis 2019; 24:852-859. [PMID: 29664388 PMCID: PMC5938774 DOI: 10.3201/eid2405.171700] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Galicia in northwestern Spain has been considered a hotspot for Vibrio parahaemolyticus infections. Infections abruptly emerged in 1998 and, over the next 15 years, were associated with large outbreaks caused by strains belonging to a single clone. We report a recent transition in the epidemiologic pattern in which cases throughout the region have been linked to different and unrelated strains. Global genome-wide phylogenetic analysis revealed that most of the pathogenic strains isolated from infections were associated with globally diverse isolates, indicating frequent episodic introductions from disparate and remote sources. Moreover, we identified that the 2 major switches in the epidemic dynamics of V. parahaemolyticus in the regions, the emergence of cases and an epidemiologic shift in 2015-2016, were associated with the rise of sea surface temperature in coastal areas of Galicia. This association may represent a fundamental contributing factor in the emergence of illness linked to these introduced pathogenic strains.
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Watts N, Amann M, Arnell N, Ayeb-Karlsson S, Belesova K, Berry H, Bouley T, Boykoff M, Byass P, Cai W, Campbell-Lendrum D, Chambers J, Daly M, Dasandi N, Davies M, Depoux A, Dominguez-Salas P, Drummond P, Ebi KL, Ekins P, Montoya LF, Fischer H, Georgeson L, Grace D, Graham H, Hamilton I, Hartinger S, Hess J, Kelman I, Kiesewetter G, Kjellstrom T, Kniveton D, Lemke B, Liang L, Lott M, Lowe R, Sewe MO, Martinez-Urtaza J, Maslin M, McAllister L, Mikhaylov SJ, Milner J, Moradi-Lakeh M, Morrissey K, Murray K, Nilsson M, Neville T, Oreszczyn T, Owfi F, Pearman O, Pencheon D, Pye S, Rabbaniha M, Robinson E, Rocklöv J, Saxer O, Schütte S, Semenza JC, Shumake-Guillemot J, Steinbach R, Tabatabaei M, Tomei J, Trinanes J, Wheeler N, Wilkinson P, Gong P, Montgomery H, Costello A. The 2018 report of the Lancet Countdown on health and climate change: shaping the health of nations for centuries to come. Lancet 2018; 392:2479-2514. [PMID: 30503045 DOI: 10.1016/s0140-6736(18)32594-7] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/30/2018] [Accepted: 10/12/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Nick Watts
- Institute for Global Health, University College London, London, UK.
| | - Markus Amann
- Air Quality and Greenhouse Gases Programme, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Nigel Arnell
- Department of Meteorology, University of Reading, Reading, UK
| | | | - Kristine Belesova
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Helen Berry
- Sydney School of Public Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Timothy Bouley
- Health and Climate Change Unit, World Bank, Washington, DC, USA
| | - Maxwell Boykoff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Peter Byass
- Epidemiology and Global Health Unit, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Wenjia Cai
- Department of Earth System Science, Tsinghua University, Beijing, China
| | | | | | - Meaghan Daly
- Department of Environmental Studies, University of New England, Biddeford, ME, USA
| | - Niheer Dasandi
- School of Government and Society, University of Birmingham, Birmingham, UK
| | - Michael Davies
- Institute for Environmental Design and Engineering, University College London, London, UK
| | - Anneliese Depoux
- Centre Virchow-Villermé for Public Health Paris-Berlin, Université Sorbonne Paris Cité and Université Paris Sorbonne, Paris, France
| | - Paula Dominguez-Salas
- Department of Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Paul Drummond
- Institute for Sustainable Resources, University College London, London, UK
| | - Kristie L Ebi
- Department of Global Health, University of Washington, Washington, DC, USA
| | - Paul Ekins
- Institute for Sustainable Resources, University College London, London, UK
| | | | - Helen Fischer
- Department of Psychology, Heidelberg University, Heidelberg, Germany
| | | | - Delia Grace
- International Livestock Research Institute, Nairobi, Kenya
| | - Hilary Graham
- Department of Health Sciences, University of York, York, UK
| | - Ian Hamilton
- UCL Energy Institute, University College London, London, UK
| | | | - Jeremy Hess
- Centre for Health and the Global Environment, University of Washington, Washington, DC, USA
| | - Ilan Kelman
- Institute for Global Health, University College London, London, UK
| | - Gregor Kiesewetter
- Air Quality and Greenhouse Gases Programme, International Institute for Applied Systems Analysis, Laxenburg, Austria
| | - Tord Kjellstrom
- Health and Environment International Trust, Nelson, New Zealand
| | | | - Bruno Lemke
- Nelson Marlborough Institute of Technology, Nelson, New Zealand
| | - Lu Liang
- University of North Texas, Denton, TX, USA
| | - Melissa Lott
- Asia Pacific Energy Research Centre, Tokyo, Japan
| | - Rachel Lowe
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Maquins Odhiambo Sewe
- Epidemiology and Global Health Unit, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | | | - Mark Maslin
- Department of Geography, University College London, London, UK
| | - Lucy McAllister
- History and Society Division, University of Colorado Boulder, Boulder, CO, USA
| | | | - James Milner
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Maziar Moradi-Lakeh
- Preventive Medicine and Public Health Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Karyn Morrissey
- European Centre for the Environment and Human Health, University of Exeter, Exeter, UK
| | - Kris Murray
- Faculty of Medicine, School of Public Health, Imperial college London, London, UK
| | - Maria Nilsson
- Epidemiology and Global Health Unit, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Tara Neville
- Department of Public Health and the Environment, WHO, Geneva, Switzerland
| | - Tadj Oreszczyn
- UCL Energy Institute, University College London, London, UK
| | - Fereidoon Owfi
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Olivia Pearman
- Centre for Science and Technology Policy Research, University of Colorado Boulder, Boulder, CO, USA
| | | | - Steve Pye
- UCL Energy Institute, University College London, London, UK
| | - Mahnaz Rabbaniha
- Iranian Fisheries Science Research Institute, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Elizabeth Robinson
- School of Agriculture, Policy, and Development, University of Reading, Reading, UK
| | - Joacim Rocklöv
- Epidemiology and Global Health Unit, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Olivia Saxer
- Centre Virchow-Villermé for Public Health Paris-Berlin, Université Sorbonne Paris Cité and Université Paris Sorbonne, Paris, France
| | - Stefanie Schütte
- Centre Virchow-Villermé for Public Health Paris-Berlin, Université Sorbonne Paris Cité and Université Paris Sorbonne, Paris, France
| | - Jan C Semenza
- European Centre for Disease Control and Prevention, Solna, Sweden
| | | | - Rebecca Steinbach
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Meisam Tabatabaei
- Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organisation, Tehran, Iran
| | - Julia Tomei
- Institute for Sustainable Resources, University College London, London, UK
| | - Joaquin Trinanes
- Physical Oceanography Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | - Nicola Wheeler
- Institute for Global Health, University College London, London, UK
| | - Paul Wilkinson
- Department of Public Health, Environments, and Society, London School of Hygiene & Tropical Medicine, London, UK
| | - Peng Gong
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Hugh Montgomery
- Centre for Human Health and Performance, Department of Medicine, University College London, London, UK
| | - Anthony Costello
- Office of the Vice-Provost (Research), University College London, London, UK
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Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations. ISME JOURNAL 2018; 12:2954-2966. [PMID: 30072747 PMCID: PMC6246604 DOI: 10.1038/s41396-018-0245-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/30/2018] [Accepted: 07/06/2018] [Indexed: 11/08/2022]
Abstract
Diseases of marine animals caused by bacteria of the genus Vibrio are on the rise worldwide. Understanding the eco-evolutionary dynamics of these infectious agents is important for predicting and managing these diseases. Yet, compared to Vibrio infecting humans, knowledge of their role as animal pathogens is scarce. Here we ask how widespread is virulence among ecologically differentiated Vibrio populations, and what is the nature and frequency of virulence genes within these populations? We use a combination of population genomics and molecular genetics to assay hundreds of Vibrio strains for their virulence in the oyster Crassostrea gigas, a unique animal model that allows high-throughput infection assays. We show that within the diverse Splendidus clade, virulence represents an ancestral trait but has been lost from several populations. Two loci are necessary for virulence, the first being widely distributed across the Splendidus clade and consisting of an exported conserved protein (R5.7). The second is a MARTX toxin cluster, which only occurs within V. splendidus and is for the first time associated with virulence in marine invertebrates. Varying frequencies of both loci among populations indicate different selective pressures and alternative ecological roles, based on which we suggest strategies for epidemiological surveys.
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Audemard C, Kator HI, Reece KS. High salinity relay as a post-harvest processing method for reducing Vibrio vulnificus levels in oysters (Crassostrea virginica). Int J Food Microbiol 2018; 279:70-79. [DOI: 10.1016/j.ijfoodmicro.2018.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 11/15/2022]
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Abstract
Vibrio is a genus of ubiquitous bacteria found in a wide variety of aquatic and marine habitats; of the >100 described Vibrio spp., ~12 cause infections in humans. Vibrio cholerae can cause cholera, a severe diarrhoeal disease that can be quickly fatal if untreated and is typically transmitted via contaminated water and person-to-person contact. Non-cholera Vibrio spp. (for example, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus) cause vibriosis - infections normally acquired through exposure to sea water or through consumption of raw or undercooked contaminated seafood. Non-cholera bacteria can lead to several clinical manifestations, most commonly mild, self-limiting gastroenteritis, with the exception of V. vulnificus, an opportunistic pathogen with a high mortality that causes wound infections that can rapidly lead to septicaemia. Treatment for Vibrio spp. infection largely depends on the causative pathogen: for example, rehydration therapy for V. cholerae infection and debridement of infected tissues for V. vulnificus-associated wound infections, with antibiotic therapy for severe cholera and systemic infections. Although cholera is preventable and effective oral cholera vaccines are available, outbreaks can be triggered by natural or man-made events that contaminate drinking water or compromise access to safe water and sanitation. The incidence of vibriosis is rising, perhaps owing in part to the spread of Vibrio spp. favoured by climate change and rising sea water temperature.
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