scholarly journals A critical re-evaluation of multilocus sequence typing (MLST) efforts inWolbachia

2017 ◽  
Author(s):  
Christoph Bleidorn ◽  
Michael Gerth
Keyword(s):  
Multilocus Sequence Typing ◽  
Single Copy ◽  
Whole Genome ◽  
Strain Typing ◽  
Strain Differentiation ◽  
Phylogenetic Marker ◽  
Phylogenetic Studies ◽  
Molecular Differentiation ◽  
Genome Typing

AbstractWolbachia(Alphaproteobacteria, Rickettsiales) is the most common, and arguably one of the most important inherited symbionts. Molecular differentiation ofWolbachiastrains is routinely performed with a set of five multilocus sequence typing (MLST) markers. However, since its inception in 2006, the performance of MLST inWolbachiastrain typing has not been assessed objectively. Here, we evaluate the properties ofWolbachiaMLST markers and compare it to 252 other single copy loci present in the genome of mostWolbachiastrains. Specifically, we investigated how well MLST performs at strain differentiation, at reflecting genetic diversity of strains, and as phylogenetic marker. We find that MLST loci are outperformed by other loci at all tasks they are currently employed for, and thus that they do not reflect the properties of aWolbachiastrain very well. We argue that whole genome typing approaches should be used forWolbachiatyping in the future. Alternatively, if few-loci-approaches are necessary, we provide a characterization of 252 single copy loci for a number a criteria, which may assist in designing specific typing systems or phylogenetic studies.

Phylogenomic grouping of Listeria monocytogenes

2015 ◽  
Vol 61 (9) ◽  
pp. 637-646 ◽  
Author(s):  
Swapnil Doijad ◽  
Markus Weigel ◽  
Sukhadeo Barbuddhe ◽  
Jochen Blom ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Studies ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Subsequent Evolution ◽  
Pathogenic Potential ◽  
Core Genes ◽  
Genome Typing

The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.

scholarly journals Establishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens

2021 ◽  
Author(s):  
Mostafa Y. Abdel-Glil ◽  
Prasad Thomas ◽  
Jörg Linde ◽  
Keith A. Jolley ◽  
Dag Harmsen ◽  
...  
Keyword(s):  
High Resolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clostridium Perfringens ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Bacterial Strains

Global epidemiological surveillance of bacterial pathogens is enhanced by the availability of standard tools and sharing of typing data. The use of whole-genome sequencing has opened the possibility for high-resolution characterization of bacterial strains down to the clonal and subclonal levels.

Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

2010 ◽  
Vol 36 (4) ◽  
pp. 688-694
Author(s):  
Yi-Jun WANG ◽  
Yan-Ping LÜ ◽  
Qin XIE ◽  
De-Xiang DENG ◽  
Yun-Long BIAN
Keyword(s):  
Sorghum Bicolor ◽  
Gene Family ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Sequence Characterization ◽  
I Gene

scholarly journals Characterization of Streptococcus tigurinus Small-Colony Variants Causing Prosthetic Joint Infection by Comparative Whole-Genome Analyses

2013 ◽  
Vol 52 (2) ◽  
pp. 467-474 ◽  
Author(s):  
A. Zbinden ◽  
C. Quiblier ◽  
D. Hernandez ◽  
K. Herzog ◽  
P. Bodler ◽  
...  
Keyword(s):  
Prosthetic Joint Infection ◽  
Joint Infection ◽  
Whole Genome ◽  
Small Colony Variants ◽  
Prosthetic Joint ◽  
Small Colony ◽  
Genome Analyses

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

scholarly journals Characterization of the Major Antigenic Protein 2 of Ehrlichia canis and Ehrlichia chaffeensis and Its Application for Serodiagnosis of Ehrlichiosis

2003 ◽  
Vol 10 (4) ◽  
pp. 520-524 ◽  
Author(s):  
Tamece T. Knowles ◽  
A. Rick Alleman ◽  
Heather L. Sorenson ◽  
David C. Marciano ◽  
Edward B. Breitschwerdt ◽  
...  
Keyword(s):  
Blot Analysis ◽  
Single Copy ◽  
Ehrlichia Canis ◽  
Specific Method ◽  
Ehrlichia Chaffeensis ◽  
Antigenic Protein ◽  
Canine Monocytic Ehrlichiosis ◽  
Copy Gene ◽  
Species Specific

ABSTRACT Canine monocytic ehrlichiosis, caused by Ehrlichia canis or Ehrlichia chaffeensis, can result in clinical disease in naturally infected animals. Coinfections with these agents may be common in certain areas of endemicity. Currently, a species-specific method for serological diagnosis of monocytic ehrlichiosis is not available. Previously, we developed two indirect enzyme-linked immunosorbent assays (ELISAs) using the major antigenic protein 2 (MAP2) of E. chaffeensis and E. canis. In this study, we further characterized the conservation of MAP2 among various geographic isolates of each organism and determined if the recombinant MAP2 (rMAP2) of E. chaffeensis would cross-react with E. canis-infected dog sera. Genomic Southern blot analysis using digoxigenin-labeled species-specific probes suggested that map2 is a single-copy gene in both Ehrlichia species. Sequences of the single map2 genes of seven geographically different isolates of E. chaffeensis and five isolates of E. canis are highly conserved among the various isolates of each respective ehrlichial species. ELISA and Western blot analysis confirmed that the E. chaffeensis rMAP2 failed to serologically differentiate between E. canis and E. chaffeensis infections.

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