Nonencapsulated or nontypeableHaemophilus influenzaeare more likely than their encapsulated or serotypeable counterparts to have mutations in their fucose operon

2011 ◽  
Vol 57 (12) ◽  
pp. 982-986 ◽  
Author(s):  
Michelle L. Shuel ◽  
Kathleen E. Karlowsky ◽  
Dennis K.S. Law ◽  
Raymond S.W. Tsang
Keyword(s):  
Nucleotide Sequence ◽  
Haemophilus Influenzae ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Housekeeping Genes ◽  
Sequence Variations ◽  
Sequence Types ◽  
Complete Deletion

Population biology of Haemophilus influenzae can be studied by multilocus sequence typing (MLST), and isolates are assigned sequence types (STs) based on nucleotide sequence variations in seven housekeeping genes, including fucK. However, the ST cannot be assigned if one of the housekeeping genes is absent or cannot be detected by the current protocol. Occasionally, strains of H. influenzae have been reported to lack the fucK gene. In this study, we examined the prevalence of this mutation among our collection of H. influenzae isolates. Of the 704 isolates studied, including 282 encapsulated and 422 nonencapsulated isolates, nine were not typeable by MLST owing to failure to detect the fucK gene. All nine fucK-negative isolates were nonencapsulated and belonged to various biotypes. DNA sequencing of the fucose operon region confirmed complete deletion of genes in the operon in seven of the nine isolates, while in the remaining two isolates, some of the genes were found intact or in parts. The significance of these findings is discussed.

scholarly journals Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries

2007 ◽  
Vol 56 (11) ◽  
pp. 1460-1466 ◽  
Author(s):  
Seon Young Choi ◽  
Yoon-Seong Jeon ◽  
Je Hee Lee ◽  
Boram Choi ◽  
Sun Hwa Moon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
Shigella Flexneri ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Asian Countries ◽  
Allelic Variants ◽  
Sequence Types

The multilocus sequence typing scheme used previously for phylogenetic analysis of Escherichia coli was applied to 107 clinical isolates of Shigella flexneri. DNA sequencing of 3423 bp throughout seven housekeeping genes identified eight new allele types and ten new sequence types among the isolates. S. flexneri serotypes 1–5, X and Y were clustered together in a group containing many allelic variants while serotype 6 formed a distinct group, as previously established.

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.

scholarly journals First Insights into the Evolution of Streptococcus uberis: a Multilocus Sequence Typing Scheme That Enables Investigation of Its Population Biology

2006 ◽  
Vol 72 (2) ◽  
pp. 1420-1428 ◽  
Author(s):  
Tracey J. Coffey ◽  
Gillian D. Pullinger ◽  
Rachel Urwin ◽  
Keith A. Jolley ◽  
Stephen M. Wilson ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Mastitis ◽  
Housekeeping Gene ◽  
Global Scale ◽  
Streptococcus Uberis ◽  
Capsule Production ◽  
Sequence Types ◽  
Better Than

ABSTRACT Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis throughout the world. Several procedures to differentiate S. uberis isolates have been proposed. However, all are prone to interlaboratory variation, and none is suitable for the description of the population structure. We describe here the development of a multilocus sequence typing (MLST) scheme for S. uberis to help address these issues. The sequences of seven housekeeping gene fragments from each of 160 United Kingdom milk isolates of S. uberis were determined. Between 5 and 17 alleles were obtained per locus, giving the potential to discriminate between 1.3 × 107 sequence types. In this study, 57 sequence types (STs) were identified. Statistical comparisons between the maximum-likelihood trees constructed by using the seven housekeeping gene fragments showed that the congruence was no better than that between each tree and trees of random topology, indicating there had been significant recombination within these loci. The population contained one major lineage (designated the ST-5 complex). This dominated the population, containing 24 STs and representing 112 isolates. The other 33 STs were not assigned to any clonal complex. All of the isolates in the ST-5 lineage carried hasA, a gene that is essential for capsule production. There was no clear association between ST or clonal complex and disease. The S. uberis MLST system offers researchers a valuable tool that allows further investigation of the population biology of this organism and insights into the epidemiology of this disease on a global scale.

scholarly journals Analysis of Genetic Relatedness of Haemophilus influenzae Isolates by Multilocus Sequence Typing

2007 ◽  
Vol 190 (4) ◽  
pp. 1473-1483 ◽  
Author(s):  
Alice L. Erwin ◽  
Sara A. Sandstedt ◽  
Paul J. Bonthuis ◽  
Jennifer L. Geelhood ◽  
Kevin L. Nelson ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Multilocus Sequence Typing ◽  
Genetic Relatedness ◽  
Geographic Origin ◽  
Maximum Parsimony Analysis ◽  
Negative Bacterium ◽  
Phylogenetic Groups ◽  
Capsule Production ◽  
Metabolic Reactions ◽  
Sequence Types

ABSTRACT The gram-negative bacterium Haemophilus influenzae is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of H. influenzae respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656 H. influenzae strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.

scholarly journals Multilocus Sequence-Typing of Anthrax Microbe Strains Isolated in Russia and Neighboring Countries

2021 ◽  
pp. 95-102
Author(s):  
Yu. O. Goncharova ◽  
I. V. Bakhteeva ◽  
R. I. Mironova ◽  
A. G. Bogun ◽  
K. V. Khlopova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Multilocus Sequence Typing ◽  
Software Package ◽  
Housekeeping Genes ◽  
Common Mutation ◽  
Whole Genome ◽  
New Generation Sequencing ◽  
New Generation ◽  
Sequence Types ◽  
Generation Sequencing

Objective – genotyping by multilocus sequence-typing (MLST) and phylogenetic analysis of 40 Bacillus anthracis strains isolated in Russia and neighboring countries.Materials and methods. In this study, the sequences of seven housekeeping genes of B. anthracis strains were assembled based on the data of a whole genome new generation sequencing, after which the identified mutations and their coordinates were described. The obtained sequences were used for genotyping of the investigated sample using the MLST method. The results are compared with the data presented in PubMLST database. A phylogenetic analysis was performed for the in silico fused sequences of the seven loci of the identified sequence types. The MEGA 7.0 software package was used to build the dendrograms.Results and discussion. Two sequence types (ST) have been found in the examined sample: 35 strains belong to ST-1, and five strains that differed by one common mutation at the glpF locus – to ST-3 (according to PubMLST coding), which emphasizes the genetic separation of this group of strains. One strain has a unique mutation in the gmk gene located outside the region used for MLST. 

scholarly journals MLSTar: automatic multilocus sequence typing of bacterial genomes in R

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5098 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Multilocus Sequence Typing ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Bacterial Genomes ◽  
Standard Tool ◽  
Comparable Performance ◽  
R Packages ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii

Microbiology ◽  
2011 ◽  
Vol 157 (3) ◽  
pp. 727-738 ◽  
Author(s):  
Kana Tanigawa ◽  
Koichi Watanabe
Keyword(s):  
Multilocus Sequence Typing ◽  
Fragment Length Polymorphism ◽  
Housekeeping Genes ◽  
Lactobacillus Delbrueckii ◽  
Single Strain ◽  
Discriminatory Ability ◽  
Identification Methods ◽  
Subspecies Level ◽  
Genotypic Identification ◽  
Sequence Types

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080T, was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

scholarly journals Multilocus Sequence Typing of Aggregatibacter actinomycetemcomitans Competently Depicts the Population Structure of the Species

2021 ◽  
Author(s):  
Signe Nedergaard ◽  
Anne B. Jensen ◽  
Dorte Haubek ◽  
Niels Nørskov-Lauritsen
Keyword(s):  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Housekeeping Genes ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Content Type ◽  
Typing Scheme ◽  
Sequence Types

We developed a multilocus sequence typing scheme (MLST) for Aggregatibacter actinomycetemcomitans based on seven housekeeping genes, adk , atpG , frdB , mdh , pgi , recA , and zwf . A total of 188 strains of seven serotypes were separated into 57 sequence types.

scholarly journals Update on Pneumocystis carinii f. sp.hominis Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes

1998 ◽  
Vol 36 (3) ◽  
pp. 734-741 ◽  
Author(s):  
Chao-Hung Lee ◽  
Jannik Helweg-Larsen ◽  
Xing Tang ◽  
Shaoling Jin ◽  
Baozheng Li ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Internal Transcribed Spacer ◽  
Pneumocystis Carinii ◽  
Rrna Genes ◽  
Its1 Sequence ◽  
Clinical Specimens ◽  
Internal Transcribed Spacer Regions ◽  
Sequence Variations ◽  
Sequence Types ◽  
Its1 And Its2

Pneumocystis carinii f. sp. hominisisolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study.

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