scholarly journals Development of a multi-locus typing scheme for anEnterobacteriaceaelinear plasmid that mediates inter-species transfer of flagella

2019 ◽  
Author(s):  
James Robertson ◽  
Janet Lin ◽  
Amie Wren-Hedegus ◽  
Gitanjali Arya ◽  
Catherine Carrillo ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phase Variation ◽  
Public Health Importance ◽  
The Public ◽  
Mlst Scheme ◽  
Population Structure Analysis ◽  
Phenotypic Novelty ◽  
Sequence Types ◽  
Core Genes ◽  
Flagellar Genes

AbstractDue to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified inSalmonellaTyphi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758Salmonellapublic genomes. Pangenome analysis of pBSSB1-family contigs was performed using Roary and we identified three core genes amenable to a minimal MLST scheme. Population structure analysis based on the newly developed MLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This MLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name “pBSSB1-family”.

scholarly journals Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group

2004 ◽  
Vol 70 (1) ◽  
pp. 191-201 ◽  
Author(s):  
Erlendur Helgason ◽  
Nicolas J. Tourasse ◽  
Roger Meisal ◽  
Dominique A. Caugant ◽  
Anne-Brit Kolstø
Keyword(s):  
Population Structure ◽  
Bacillus Cereus ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Industrial Applications ◽  
Enzyme Electrophoresis ◽  
Mlst Scheme ◽  
High Level ◽  
Sequence Types

ABSTRACT In this study we developed a multilocus sequence typing (MLST) scheme for bacteria of the Bacillus cereus group. This group, which includes the species B. cereus, B. thuringiensis, B. weihenstephanensis, and B. anthracis, is known to be genetically very diverse. It is also very important because it comprises pathogenic organisms as well as bacteria with industrial applications. The MLST system was established by using 77 strains having various origins, including humans, animals, food, and soil. A total of 67 of these strains had been analyzed previously by multilocus enzyme electrophoresis, and they were selected to represent the genetic diversity of this group of bacteria. Primers were designed for conserved regions of housekeeping genes, and 330- to 504-bp internal fragments of seven such genes, adk, ccpA, ftsA, glpT, pyrE, recF, and sucC, were sequenced for all strains. The number of alleles at individual loci ranged from 25 to 40, and a total of 53 allelic profiles or sequence types (STs) were distinguished. Analysis of the sequence data showed that the population structure of the B. cereus group is weakly clonal. In particular, all five B. anthracis isolates analyzed had the same ST. The MLST scheme which we developed has a high level of resolution and should be an excellent tool for studying the population structure and epidemiology of the B. cereus group.

scholarly journals A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure

2009 ◽  
Vol 191 (9) ◽  
pp. 2934-2943 ◽  
Author(s):  
Sabine Kaiser ◽  
Klaus Biehler ◽  
Daniel Jonas
Keyword(s):  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Stenotrophomonas Maltophilia ◽  
Sequence Data ◽  
Clinical Isolates ◽  
Mlst Scheme ◽  
Tree Topologies ◽  
Significant Linkage ◽  
Sequence Types ◽  
Selection Of

ABSTRACT Stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including the S. maltophilia type strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.

scholarly journals Nextstrain: real-time tracking of pathogen evolution

2017 ◽  
Author(s):  
James Hadfield ◽  
Colin Megill ◽  
Sidney M. Bell ◽  
John Huddleston ◽  
Barney Potter ◽  
...  
Keyword(s):  
Public Health ◽  
Real Time ◽  
Web Application ◽  
Sequence Data ◽  
Data Types ◽  
Bioinformatics Pipeline ◽  
Public Health Importance ◽  
Viral Genomes ◽  
Effective Public Health ◽  
Interactive Visualisation

AbstractSummaryUnderstanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike.Availability and implementationAll code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within Progamotaenia festiva (Cestoda: Anoplocephalidae) from macropodid marsupials

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1465-1476 ◽  
Author(s):  
I. BEVERIDGE ◽  
S. SHAMSI ◽  
M. HU ◽  
N. B. CHILTON ◽  
R. B. GASSER
Keyword(s):  
Genetic Variation ◽  
Host Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Enzyme Electrophoresis ◽  
Single Strand Conformational Polymorphism ◽  
Oxidase Subunit ◽  
Single Host ◽  
Distinct Sequence ◽  
Sequence Types

SUMMARYGenetic variation was examined in the anoplocephalid cestode Progamotaenia festiva, from Australian marsupials, in order to test the hypothesis that P. festiva, is a complex of sibling species and to assess the extent of host switching reported previously based on multilocus enzyme electrophoresis (MEE). Polymerase chain reaction (PCR)-based single-strand conformational polymorphism (SSCP) was used for the analysis of sequence variation in the cytochrome c oxidase subunit 1 (cox1) gene among 179 specimens of P. festiva (identified based on morphology and predilection site in the host) from 13 different host species, followed by selective DNA sequencing. Fifty-three distinct sequence types (haplotypes) representing all specimens were defined. Phylogenetic analyses of these sequence data (utilizing maximum parsimony and neighbour-joining methods) revealed 12 distinct clades. Other heterologous species, P. ewersi and P. macropodis, were used as outgroups and the remaining bile-duct inhabiting species, P. diaphana and P. effigia, were included in the analysis for comparative purposes. The latter 2 species were nested within the clades representing P. festiva. Most clades of P. festiva identified were restricted to a single host species; one clade primarily in Macropus robustus was also found in the related host species M. antilopinus in an area of host sympatry; another clade occurring primarily in M. robustus occurred also in additional kangaroo species, M. rufus and M. dorsalis. High levels of genetic divergence, the existence of distinct clades and their occurrence in sympatry provide support for the hypothesis that P. festiva represents a complex of numerous species, most of which, but not all, are host specific. Three distinct clades of cestodes were found within a single host, M. robustus, but there was no evidence of within-host speciation.

The Swine Flu Immunization Program: Scientific Venture or Political Folly?

1978 ◽  
Vol 3 (4) ◽  
pp. 425-445 ◽  
Author(s):  
Cyril H. Wecht
Keyword(s):  
Swine Flu ◽  
Allegheny County ◽  
Public Health Importance ◽  
Immunization Program ◽  
The Public ◽  
Kennedy Assassination ◽  
Commission Report ◽  
Human Costs ◽  
Political Value ◽  
Great Public Health

AbstractThe author of this Article, an internationally recognized coroner perhaps best known among laymen for his incisive and tenacious criticism of the Warren Commission report on the Kennedy assassination, turns his attention to the federal government's 1976-1977 Swine Flu Immunization Program. Dr. Wecht contends that although this program may have been viewed by its key proponents as having great public health importance, or perhaps even political value, its creation and continuation nevertheless were scientifically unjustified. Furthermore, he contends, the federal government failed to inform the public adequately of important facts about the program's origins and progress, and it mismanaged the program in several important respects. Among the topics he discusses are swine flu's epidemiological history (including the 1976 Fort Dix outbreak that propelled swine flu into the national consciousness); the key elements leading to the government's decision to immunize; the government's failure to reevaluate the program seriously as problems arose; the shortcomings of the federal swine flu statute; the inadequacy of the government's investigation of the deaths of three persons in Pittsburgh within a few hours after being vaccinated (a matter that was of immediate concern to the author in his role as Coroner of Allegheny County, Pennsylvania); the long-delayed termination of the program following the emergence of a possible statistical link between the immunizations and an increase in the incidence of the Guillain-Barré Syndrome; the financial and human costs of the program; and the need for calmer, more objective decision making in future situations where immunization of the general populace is being considered.

Exposure of Campylobacter jejuni to 6°C: Effects on Heat Resistance and Electron Transport Activity

2010 ◽  
Vol 73 (4) ◽  
pp. 729-733 ◽  
Author(s):  
REBECCA-AYME HUGHES ◽  
TRISTAN COGAN ◽  
TOM HUMPHREY
Keyword(s):  
Electron Transport ◽  
Heat Resistance ◽  
Campylobacter Jejuni ◽  
Weibull Model ◽  
Human Infection ◽  
Marginal Effect ◽  
Public Health Importance ◽  
The Public ◽  
Electron Transport Activity ◽  
Increased Sensitivity

Human infection with Campylobacter jejuni is frequently associated with the consumption of foods, especially chicken meat, which have been exposed to a range of temperatures during processing, storage, and cooking. Despite the public health importance of C. jejuni, little is known about the effects of cold exposure (refrigeration) on the subsequent ability of this pathogen to survive heat challenge. This work examined the effect of rapid exposure to 6°C for 24 h on the heat resistance at 52°Cof19 C. jejuni strains originally isolated from various sources. The resulting death curves were analyzed with the Weibull model. Unlike cold-exposed cells of Escherichia coli and Salmonella, which have been reported to show significant increased sensitivity to heat, such exposure had only a marginal effect on heat resistance of the C. jejuni strains in this study. A possible explanation for this effect is that rapid chilling renders C. jejuni cells unable to adapt to reduced temperatures in an active manner. This hypothesis is supported by the observation that exposure to 6°C for 24 h resulted in a significant and marked reduction in electron transport system activity when compared with controls at 37°C.

scholarly journals Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

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