Genome sequence-based curation of PubMLST data challenges interspecies recombination in the Burkholderia cepacia complex

We report here the draft genome sequence of the Flavobacterium sp. TAB 87 strain, isolated from Antarctic seawater during a summer campaign near the French Antarctic station Dumont d’Urville (60°40′S, 40°01′E). It will allow for comparative genomics and the fulfillment of both fundamental and application-oriented investigations. It allowed the recognition of genes associated with the production of bioactive compounds and antibiotic resistance.

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A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex

Journal of Clinical Microbiology ◽

10.1128/jcm.01741-20 ◽

2020 ◽

Vol 58 (11) ◽

Author(s):

Honghui Wang ◽

Ousmane H. Cissé ◽

Thomas Bolig ◽

Steven K. Drake ◽

Yong Chen ◽

...

Keyword(s):

Species Identification ◽

Burkholderia Cepacia ◽

Species Level ◽

Diagnostic Methods ◽

Burkholderia Cenocepacia ◽

Burkholderia Cepacia Complex ◽

Diagnostic Classification ◽

Content Type ◽

Proteomics Approach ◽

Interspecies Recombination

ABSTRACT Ancestral genetic exchange between members of many important bacterial pathogen groups has resulted in phylogenetic relationships better described as networks than as bifurcating trees. In certain cases, these reticulated phylogenies have resulted in phenotypic and molecular overlap that challenges the construction of practical approaches for species identification in the clinical microbiology laboratory. Burkholderia cepacia complex (Bcc), a betaproteobacteria species group responsible for significant morbidity in persons with cystic fibrosis and chronic granulomatous disease, represents one such group where network-structured phylogeny has hampered the development of diagnostic methods for species-level discrimination. Here, we present a phylogeny-informed proteomics approach to facilitate diagnostic classification of pathogen groups with reticulated phylogenies, using Bcc as an example. Starting with a set of more than 800 Bcc and Burkholderia gladioli whole-genome assemblies, we constructed phylogenies with explicit representation of inferred interspecies recombination. Sixteen highly discriminatory peptides were chosen to distinguish B. cepacia, Burkholderia cenocepacia, Burkholderia multivorans, and B. gladioli and multiplexed into a single, rapid liquid chromatography-tandem mass spectrometry multiple reaction monitoring (LC-MS/MS MRM) assay. Testing of a blinded set of isolates containing these four Burkholderia species demonstrated 50/50 correct automatic negative calls (100% accuracy with a 95% confidence interval [CI] of 92.9 to 100%), and 70/70 correct automatic species-level positive identifications (100% accuracy with 95% CI 94.9 to 100%) after accounting for a single initial incorrect identification due to a preanalytic error, correctly identified on retesting. The approach to analysis described here is applicable to other pathogen groups for which development of diagnostic classification methods is complicated by interspecies recombination.

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Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex

Genome Announcements ◽

10.1128/genomea.00351-17 ◽

2017 ◽

Vol 5 (20) ◽

Cited By ~ 2

Author(s):

Valentina Maggini ◽

Luana Presta ◽

Elisangela Miceli ◽

Marco Fondi ◽

Emanuele Bosi ◽

...

Keyword(s):

Medicinal Plant ◽

Genome Sequence ◽

Burkholderia Cepacia ◽

Draft Genome ◽

Echinacea Purpurea ◽

Burkholderia Cepacia Complex ◽

Draft Genome Sequence ◽

Antimicrobial Compounds ◽

Pseudomonas Sp ◽

Opportunistic Pathogens

ABSTRACT In this announcement, we detail the draft genome sequence of the Pseudomonas sp. strain Ep R1, isolated from the roots of the medicinal plant Echinacea purpurea. The elucidation of this genome sequence may allow the identification of genes associated with the production of antimicrobial compounds.

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Draft Genome Sequence of a Burkholderia cepacia Complex Strain Isolated from a Human Intra-abdominal Abscess

Microbiology Resource Announcements ◽

10.1128/mra.00091-21 ◽

2021 ◽

Vol 10 (11) ◽

Author(s):

Yuting Zhai ◽

Kathryn E. DeSear ◽

Kartik Cherabuddi ◽

J. Glenn Morris ◽

Kwangcheol C. Jeong

Keyword(s):

Genome Sequence ◽

Burkholderia Cepacia ◽

Draft Genome ◽

Immunocompetent Patient ◽

Burkholderia Cepacia Complex ◽

Draft Genome Sequence ◽

Abdominal Abscess ◽

Opportunistic Pathogens ◽

Content Type ◽

Complex Strain

ABSTRACT Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens with high transmissibility and mortality. Here, we report the draft genome sequence of a Bcc strain isolated from a deep abscess culture in an immunocompetent patient with no relevant prior medical history.

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Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2019.11.017 ◽

2020 ◽

Vol 20 ◽

pp. 28-30

Author(s):

Asif Hameed ◽

Mariyam Shahina ◽

Wei-An Lai ◽

Paul Stothard ◽

Li-Sen Young ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Genome Sequence ◽

Burkholderia Cepacia ◽

Draft Genome ◽

Rice Root ◽

Burkholderia Cepacia Complex ◽

Draft Genome Sequence

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Antimicrobial activity of essential oils toward clinical and environmental strains of the opportunistic pathogen of Cystic Fibrosis patients Burkholderia cepacia complex

Planta Medica ◽

10.1055/s-0033-1352360 ◽

2013 ◽

Vol 79 (13) ◽

Author(s):

A Lo Nostro ◽

M Barnabei ◽

E Perrin ◽

A Bilia ◽

G Pesavento ◽

...

Keyword(s):

Cystic Fibrosis ◽

Antimicrobial Activity ◽

Essential Oils ◽

Burkholderia Cepacia ◽

Opportunistic Pathogen ◽

Burkholderia Cepacia Complex

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Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections

Microorganisms ◽

10.3390/microorganisms9010051 ◽

2020 ◽

Vol 9 (1) ◽

pp. 51

Author(s):

Min Yi Wong ◽

Yuan-Hsi Tseng ◽

Tsung-Yu Huang ◽

Bor-Shyh Lin ◽

Chun-Wu Tung ◽

...

Keyword(s):

Genetic Diversity ◽

Vascular Access ◽

Burkholderia Cepacia ◽

Bacterial Species ◽

Diversity Indices ◽

Burkholderia Cepacia Complex ◽

Reca Gene ◽

Clinical Effects ◽

Environmental Distribution ◽

Microbiological Characteristics

Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.

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