scholarly journals Influence of Seasonality on the Genetic Diversity of Vibrio parahaemolyticus in New Hampshire Shellfish Waters as Determined by Multilocus Sequence Analysis

2012 ◽  
Vol 78 (10) ◽  
pp. 3778-3782 ◽  
Author(s):  
Crystal N. Ellis ◽  
Brian M. Schuster ◽  
Megan J. Striplin ◽  
Stephen H. Jones ◽  
Cheryl A. Whistler ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Genetic Analysis ◽  
New Hampshire ◽  
Environmental Conditions ◽  
Vibrio Parahaemolyticus ◽  
Multilocus Sequence Analysis ◽  
Content Type ◽  
High Level

ABSTRACTRisk of gastric infection withVibrio parahaemolyticusincreases with favorable environmental conditions and population shifts that increase prevalence of infective strains. Genetic analysis of New Hampshire strains revealed a unique population with some isolates similar to outbreak-causing strains and high-level diversity that increased as waters warmed.

scholarly journals Multilocus Sequence Analysis of Xanthomonads Causing Bacterial Spot of Tomato and Pepper Plants Reveals Strains Generated by Recombination among Species and Recent Global Spread of Xanthomonas gardneri

2014 ◽  
Vol 81 (4) ◽  
pp. 1520-1529 ◽  
Author(s):  
Sujan Timilsina ◽  
Mustafa O. Jibrin ◽  
Neha Potnis ◽  
Gerald V. Minsavage ◽  
Misrak Kebede ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Housekeeping Genes ◽  
Global Distribution ◽  
Multilocus Sequence Analysis ◽  
Regional Differentiation ◽  
Bacterial Spot ◽  
Content Type ◽  
Global Spread ◽  
Pathogen Populations

ABSTRACTFourXanthomonasspecies are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype ofX. gardneri, possible regional differentiation inX. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events betweenX. euvesicatoriaandX. perforans.Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.

scholarly journals Genetic Relationships of Vibrio parahaemolyticus Isolates from Clinical, Human Carrier, and Environmental Sources in Thailand, Determined by Multilocus Sequence Analysis

2013 ◽  
Vol 79 (7) ◽  
pp. 2358-2370 ◽  
Author(s):  
Chonchanok Theethakaew ◽  
Edward J. Feil ◽  
Santiago Castillo-Ramírez ◽  
David M. Aanensen ◽  
Orasa Suthienkul ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Vibrio Parahaemolyticus ◽  
Genetic Relationships ◽  
Multilocus Sequence Analysis ◽  
Clinical Samples ◽  
Intragenic Recombination ◽  
Healthy Human ◽  
Content Type ◽  
Source Of Infection ◽  
Frozen Shrimp

ABSTRACTVibrio parahaemolyticusis a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide. We investigated the genetic and evolutionary relationships of 101V. parahaemolyticusisolates originating from clinical, human carrier, and various environmental and seafood production sources in Thailand using multilocus sequence analysis. The isolates were recovered from clinical samples (n= 15), healthy human carriers (n= 18), various types of fresh seafood (n= 18), frozen shrimp (n= 16), fresh-farmed shrimp tissue (n= 18), and shrimp farm water (n= 16). Phylogenetic analysis revealed a high degree of genetic diversity within theV. parahaemolyticuspopulation, although isolates recovered from clinical samples and from farmed shrimp and water samples represented distinct clusters. The tight clustering of the clinical isolates suggests that disease-causing isolates are not a random sample of the environmental reservoir, although the source of infection remains unclear. Extensive serotypic diversity occurred among isolates representing the same sequence types and recovered from the same source at the same time. These findings suggest that the O- and K-antigen-encoding loci are subject to exceptionally high rates of recombination. There was also strong evidence of interspecies horizontal gene transfer and intragenic recombination involving therecAlocus in a large proportion of isolates. As the majority of the intragenic recombinational exchanges involvingrecAoccurred among clinical and carrier isolates, it is possible that the human intestinal tract serves as a potential reservoir of donor and recipient strains that is promoting horizontal DNA transfer, driving evolutionary change, and leading to the emergence of new, potentially pathogenic strains.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Virulence Factors ◽  
Evolutionary Dynamics ◽  
Content Type ◽  
Pan Genome ◽  
Gastrointestinal Pathogen ◽  
High Level ◽  
Core Genes ◽  
Isolated Species

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

scholarly journals Complete Nucleotide Sequence of a Novel Plasmid Bearing the High-Level Tigecycline Resistance Gene tet(X4)

2019 ◽  
Vol 63 (11) ◽  
Author(s):  
Liang-Xing Fang ◽  
Chong Chen ◽  
Dong-Ling Yu ◽  
Ruan-Yang Sun ◽  
Chao-Yue Cui ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Hybrid Plasmid ◽  
Content Type ◽  
Clinically Significant ◽  
High Level ◽  
Plasmid Backbone

ABSTRACT We reported the complete nucleotide sequence of a tet(X4)-carrying plasmid, pSTB20-1T, from a tigecycline-resistant Escherichia coli isolate in China. Sequence analysis indicated that pSTB20-1T contains a hybrid plasmid backbone and a tet(X4)-containing multidrug resistance region, likely originated through recombination of multiple plasmids. tet(X4) was flanked by two ISCR2, which may be responsible for tet(X4) mobilization. The occurrence and transmission of this novel hybrid plasmid may exacerbate the spread of the clinically significant tet(X4) gene.

scholarly journals The Cypriot Indigenous Grapevine Germplasm Is a Multi-Clonal Varietal Mixture

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1034 ◽  
Author(s):  
Apostolis Grigoriou ◽  
Georgios Tsaniklidis ◽  
Marianna Hagidimitriou ◽  
Nikolaos Nikoloudakis
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Stress Tolerance ◽  
Eastern Mediterranean ◽  
Microsatellite Primer ◽  
Mediterranean Island ◽  
Sexual Propagation ◽  
High Level ◽  
Additional Value ◽  
Vitis Spp

Cypriot vineyards are considered as one among the earliest niches of viticulture and a pivotal hub for the domestication and dissemination of grapevine. The millennial presence of Vitis spp. in this Eastern Mediterranean island has given rise to a plethora of biotypes that have not been adequately characterized, despite their unique attributes and stress tolerance. This ancient germplasm also has an additional value since it survived the phylloxera outbreak; hence, it possesses a large amount of genetic diversity that has been unnoticed. In order to provide useful insights to the lineage of Cypriot vineyards, a two-year-spanning collection of centennial grapevine cultivars mostly regarded to belong to four indigenous variety clusters (“Mavro”, “Xynisteri”, “Maratheftiko”, and “Veriko”) was initiated. There were 164 accessions across the broader Commandaria wine zone sampled and characterized using a universal microsatellite primer set. Genetic analysis indicated that considered indigenous Cypriot germplasm has a polyclonal structure with a high level of heterozygosity. Moreover, several lineages or unexplored varieties may exist, since a larger than considered number of discrete genotypes was discovered. Furthermore, it was established that grapevine lineages in Cyprus were shaped across eras via clonal, as well as, sexual propagation. The special attributes of the Cypriot landscape are discussed.

scholarly journals Environmental Conditions Associated with Elevated Vibrio parahaemolyticus Concentrations in Great Bay Estuary, New Hampshire

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0155018 ◽  
Author(s):  
Erin A. Urquhart ◽  
Stephen H. Jones ◽  
Jong W. Yu ◽  
Brian M. Schuster ◽  
Ashley L. Marcinkiewicz ◽  
...  
Keyword(s):  
New Hampshire ◽  
Environmental Conditions ◽  
Vibrio Parahaemolyticus ◽  
Great Bay ◽  
Great Bay Estuary

scholarly journals Population Structure of Clinical Vibrio parahaemolyticus from 17 Coastal Countries, Determined through Multilocus Sequence Analysis

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e107371 ◽  
Author(s):  
Dongsheng Han ◽  
Hui Tang ◽  
Jun Lu ◽  
Guangzhou Wang ◽  
Lin Zhou ◽  
...  
Keyword(s):  
Population Structure ◽  
Sequence Analysis ◽  
Vibrio Parahaemolyticus ◽  
Multilocus Sequence Analysis

scholarly journals Draft Genome Sequence of Neisseria mucosa Strain HSUH001, Isolated from an Aggressive Periodontal Lesion

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Masatoshi Yamashita ◽  
Toshiyuki Nagasawa ◽  
Satsuki Kato ◽  
Hiroshi Miyakawa ◽  
Mari Fujita ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Multilocus Sequence Analysis ◽  
Content Type ◽  
Total Length ◽  
Neisseria Mucosa

ABSTRACT We report the draft genome sequence (143 contigs, with a total length of 2,424,805 bp and an N50 value of 36,066 bp) of a bacterium isolated from an aggressive periodontal lesion in a patient. We assigned strain HSUH001 to Neisseria mucosa through a multilocus sequence analysis.

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