Whole-Genome Sequencing of Pantoea sp. Strain RIT388, a Potential Oral Opportunistic Pathogen Isolated from a Chewing Stick (Distemonanthus benthamianus)

In this study, we report the isolation, identification, characterization, and whole-genome sequence of the endophyte Pantoea sp. strain RIT388, isolated from Distemonanthus benthamianus, a plant known for its antifungal and antibacterial properties that is commonly used for chewing sticks.

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Whole-Genome Sequence of Streptococcus tigurinus Strain osk_001, Isolated from Postmortem Material

Genome Announcements ◽

10.1128/genomea.00878-17 ◽

2017 ◽

Vol 5 (35) ◽

Author(s):

Hidenori Yoshizawa ◽

Daisuke Motooka ◽

Ryuichi Katada ◽

Yuki Matsumoto ◽

Shota Nakamura ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Novel Species ◽

Infected Tissue ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Virulent Strains ◽

Highly Virulent

ABSTRACT Streptococcus tigurinus was recently described as a novel species, and some strains are highly virulent. We detected S. tigurinus in infected tissue sampled by necropsy. In order to characterize and confirm the virulence of this species, whole-genome sequencing of the pure cultured bacterium was performed. We found that the strain has specific and unique genetic elements contained in highly virulent strains of S. tigurinus.

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Whole-Genome Sequence of the Mycoplasma mucosicanis Type Strain

Microbiology Resource Announcements ◽

10.1128/mra.00799-19 ◽

2019 ◽

Vol 8 (41) ◽

Author(s):

Rebecca L. Tallmadge ◽

Patrick K. Mitchell ◽

Renee Anderson ◽

Rebecca Franklin-Guild ◽

Laura B. Goodman

Keyword(s):

Whole Genome Sequencing ◽

Clinical Significance ◽

Genome Sequencing ◽

Genome Sequence ◽

Diagnostic Tests ◽

Type Strain ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type

Whole-genome sequencing of Mycoplasma mucosicanis type strain 1642 was performed to support efforts to better understand the clinical significance of Mycoplasma infection in canine health. The availability of this sequence will also further the development of highly specific diagnostic tests.

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Whole-Genome Sequence of Chryseobacterium oranimense, a Colistin-Resistant Bacterium Isolated from a Cystic Fibrosis Patient in France

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02417-14 ◽

2015 ◽

Vol 59 (3) ◽

pp. 1696-1706 ◽

Cited By ~ 20

Author(s):

Poonam Sharma ◽

Sushim Kumar Gupta ◽

Seydina M. Diene ◽

Jean-Marc Rolain

Keyword(s):

Cystic Fibrosis ◽

Antibiotic Resistance ◽

Whole Genome Sequencing ◽

Cystic Fibrosis Patient ◽

Genome Sequencing ◽

Genome Sequence ◽

Resistant Bacterium ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type

ABSTRACTFor the first time, we report the whole-genome sequence analysis ofChryseobacterium oranimenseG311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing ofC. oranimenseG311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of theC. oranimenseG311 draft genome were compared to the other available genomes ofChryseobacterium gleumandChryseobacteriumsp. strain CF314.C. oranimenseG311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size ofC. oranimenseG311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of thepmrA(E8D),pmrB(L208F and P360Q), andlpxA(G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients.

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Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

Applied and Environmental Microbiology ◽

10.1128/aem.01049-15 ◽

2015 ◽

Vol 81 (17) ◽

pp. 6024-6037 ◽

Cited By ~ 76

Author(s):

Matthew J. Stasiewicz ◽

Haley F. Oliver ◽

Martin Wiedmann ◽

Henk C. den Bakker

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genetic Determinants ◽

Single Nucleotide ◽

Content Type ◽

Food Borne ◽

Clonal Spread

ABSTRACTWhile the food-borne pathogenListeria monocytogenescan persist in food associated environments, there are no whole-genome sequence (WGS) based methods to differentiate persistent from sporadic strains. Whole-genome sequencing of 188 isolates from a longitudinal study ofL. monocytogenesin retail delis was used to (i) apply single-nucleotide polymorphism (SNP)-based phylogenetics for subtyping ofL. monocytogenes, (ii) use SNP counts to differentiate persistent from repeatedly reintroduced strains, and (iii) identify genetic determinants ofL. monocytogenespersistence. WGS analysis revealed three prophage regions that explained differences between three pairs of phylogenetically similar populations with pulsed-field gel electrophoresis types that differed by ≤3 bands. WGS-SNP-based phylogenetics found that putatively persistentL. monocytogenesrepresent SNP patterns (i) unique to a single retail deli, supporting persistence within the deli (11 clades), (ii) unique to a single state, supporting clonal spread within a state (7 clades), or (iii) spanning multiple states (5 clades). Isolates that formed one of 11 deli-specific clades differed by a median of 10 SNPs or fewer. Isolates from 12 putative persistence events had significantly fewer SNPs (median, 2 to 22 SNPs) than between isolates of the same subtype from other delis (median up to 77 SNPs), supporting persistence of the strain. In 13 events, nearly indistinguishable isolates (0 to 1 SNP) were found across multiple delis. No individual genes were enriched among persistent isolates compared to sporadic isolates. Our data show that WGS analysis improves food-borne pathogen subtyping and identification of persistent bacterial pathogens in food associated environments.

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Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype

Genome Announcements ◽

10.1128/genomea.01324-17 ◽

2017 ◽

Vol 5 (49) ◽

Cited By ~ 3

Author(s):

Taylor W. Bailey ◽

Naila C. do Nascimento ◽

Arun K. Bhunia

Keyword(s):

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Illumina Sequencing ◽

Foodborne Pathogen ◽

Whole Genome ◽

Content Type ◽

Serotype 1 ◽

Serotype 4B

ABSTRACT Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we performed whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b) using Illumina sequencing. The sequence showed 94.5% identity with strain F2365, serotype 4b, and 90.6% with EGD-e, serotype 1/2a.

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Draft Genome Sequence of a Mycobacterium porcinum Strain Isolated from a Pet Cat with Atypical Mycobacterial Panniculitis

Microbiology Resource Announcements ◽

10.1128/mra.00006-20 ◽

2020 ◽

Vol 9 (11) ◽

Author(s):

Anthony Mannion ◽

Tina McCollester ◽

Alexander Sheh ◽

Zeli Shen ◽

Hilda Holcombe ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Fast Growing

A fast-growing Mycobacterium species was cultured from draining, purulent lesions on the caudal abdomen of a 12-year-old male domestic long-haired cat. Whole-genome sequencing identified the organism as Mycobacterium porcinum.

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Five-year Microevolution of a Multidrug-Resistant Mycobacterium Tuberculosis Strain within a Patient with Inadequate Compliance to Treatment.

10.21203/rs.3.rs-251738/v1 ◽

2021 ◽

Author(s):

Dario Fernández Do Porto ◽

Johana Monteserin ◽

Josefina Campos ◽

Ezequiel J Sosa ◽

Mario Matteo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Treatment Compliance ◽

Whole Genome Sequence ◽

Intermittent Therapy ◽

Whole Genome ◽

Short Term ◽

Depth Analysis

Abstract BackgroundWhole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported.Case Presentations In this work, we applied whole genome sequencing for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium. tuberculosis isolates obtained from a patient within 57-month of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patience, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy.ConclusionsThis report highlights the relevance of whole-genome sequencing in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

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Whole-genome sequencing reveals progressive versus stable myeloma precursor conditions as two distinct entities

Nature Communications ◽

10.1038/s41467-021-22140-0 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Bénedith Oben ◽

Guy Froyen ◽

Kylee H. Maclachlan ◽

Daniel Leongamornlert ◽

Federico Abascal ◽

...

Keyword(s):

Multiple Myeloma ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Monoclonal Gammopathy ◽

Whole Genome Sequence ◽

Whole Genome ◽

Driver Genes ◽

Smoldering Myeloma ◽

Undetermined Significance

AbstractMultiple myeloma (MM) is consistently preceded by precursor conditions recognized clinically as monoclonal gammopathy of undetermined significance (MGUS) or smoldering myeloma (SMM). We interrogate the whole genome sequence (WGS) profile of 18 MGUS and compare them with those from 14 SMMs and 80 MMs. We show that cases with a non-progressing, clinically stable myeloma precursor condition (n = 15) are characterized by later initiation in the patient’s life and by the absence of myeloma defining genomic events including: chromothripsis, templated insertions, mutations in driver genes, aneuploidy, and canonical APOBEC mutational activity. This data provides evidence that WGS can be used to recognize two biologically and clinically distinct myeloma precursor entities that are either progressive or stable.

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Whole-Genome Sequence of Lactobacillus plantarum SPC-SNU 72-2 as a Probiotic Starter for Sourdough Fermentation

Microbiology Resource Announcements ◽

10.1128/mra.00708-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Seul-Ah Kim ◽

Geonhee Kim ◽

Bo Bo ◽

Sangmin Shim ◽

Deukbuhm Lee ◽

...

Keyword(s):

Lactobacillus Plantarum ◽

Genome Sequencing ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Pacific Biosciences ◽

Microbial Characteristics ◽

The Pacific

ABSTRACT We report the whole-genome sequence of Lactobacillus plantarum SPC-SNU 72-2, a probiotic starter for sourdough. Genome sequencing was completed using the Pacific Biosciences RS II and Illumina platforms. This study will facilitate the understanding of microbial characteristics of L. plantarum SPC-SNU 72-2 and its roles during sourdough fermentation.

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Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment

BMC Infectious Diseases ◽

10.1186/s12879-021-06069-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Darío A. Fernandez Do Porto ◽

Johana Monteserin ◽

Josefina Campos ◽

Ezequiel J. Sosa ◽

Mario Matteo ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Intermittent Therapy ◽

Whole Genome ◽

Sequencing Analysis ◽

Short Term ◽

Depth Analysis

Abstract Background Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. Case presentation In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5′ untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. Conclusions This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

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