scholarly journals Genomic Analysis of a Serotype 5Streptococcus pneumoniaeOutbreak in British Columbia, Canada, 2005–2009

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Ruth R. Miller ◽  
Morgan G. I. Langille ◽  
Vincent Montoya ◽  
Anamaria Crisan ◽  
Aleksandra Stefanovic ◽  
...  
Keyword(s):  
British Columbia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Wide Spectrum ◽  
Health Agency ◽  
Genomic Islands ◽  
Great Promise ◽  
Whole Genome ◽  
Serotype 5

Background.Streptococcus pneumoniaecan cause a wide spectrum of disease, including invasive pneumococcal disease (IPD). From 2005 to 2009 an outbreak of IPD occurred in Western Canada, caused by aS. pneumoniaestrain with multilocus sequence type (MLST) 289 and serotype 5. We sought to investigate the incidence of IPD due to thisS. pneumoniaestrain and to characterize the outbreak in British Columbia using whole-genome sequencing.Methods. IPD was defined according to Public Health Agency of Canada guidelines. Two isolates representing the beginning and end of the outbreak were whole-genome sequenced. The sequences were analyzed for single nucleotide variants (SNVs) and putative genomic islands.Results. The peak of the outbreak in British Columbia was in 2006, when 57% of invasiveS. pneumoniaeisolates were serotype 5. Comparison of two whole-genome sequenced strains showed only 10 SNVs between them. A 15.5 kb genomic island was identified in outbreak strains, allowing the design of a PCR assay to track the spread of the outbreak strain.Discussion. We show that the serotype 5 MLST 289 strain contains a distinguishing genomic island, which remained genetically consistent over time. Whole-genome sequencing holds great promise for real-time characterization of outbreaks in the future and may allow responses tailored to characteristics identified in the genome.

scholarly journals Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005–2014

2018 ◽  
Vol 218 (7) ◽  
pp. 1155-1163 ◽  
Author(s):  
Jennifer L Guthrie ◽  
Andy Delli Pizzi ◽  
David Roth ◽  
Clare Kong ◽  
Danielle Jorgensen ◽  
...  
Keyword(s):  
British Columbia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Pediatric Patients ◽  
Whole Genome ◽  
Tuberculosis Transmission

scholarly journals Integration of Whole-Genome Sequencing into Infection Control Practices: the Potential and the Hurdles

2015 ◽  
Vol 53 (4) ◽  
pp. 1054-1055 ◽  
Author(s):  
Elizabeth Robilotti ◽  
Mini Kamboj
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Epidemiology ◽  
Great Promise ◽  
Whole Genome ◽  
Related Article ◽  
Link Type ◽  
Article Type ◽  
Transmission Pathways

Microbial whole-genome sequencing (WGS) is poised to transform many of the currently used approaches in medical microbiology. Recent reports on the application of WGS to understand genetic evolution and reconstruct transmission pathways have provided valuable information that will influence infection control practices. While this technology holds great promise, obstacles to full implementation remain. Two articles in this issue of the Journal of Clinical Microbiology (S. Octavia, Q. Wang, M. M. Tanaka, S. Kaur, V. Sintchenko, and R. Lan, J Clin Microbiol 53:1063–1071, 2015, doi:10.1128/JCM.03235-14, andS. J. Salipante, D. J. SenGupta, L. A. Cummings, T. A. Land, D. R. Hoogestraat, and B. T. Cookson, J Clin Microbiol 53:1072–1079, 2015, doi:10.1128/JCM.03385-14) describe the breadth of application of WGS to the field of clinical epidemiology.

scholarly journals Digital-WGS: Automated, highly efficient whole-genome sequencing of single cells by digital microfluidics

2020 ◽  
Vol 6 (50) ◽  
pp. eabd6454
Author(s):  
Qingyu Ruan ◽  
Weidong Ruan ◽  
Xiaoye Lin ◽  
Yang Wang ◽  
Fenxiang Zou ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Whole Genome Sequencing ◽  
Single Cell ◽  
Genome Sequencing ◽  
Single Cells ◽  
Digital Microfluidics ◽  
Dropout Rate ◽  
Great Promise ◽  
Whole Genome ◽  
Exogenous Dna

Single-cell whole-genome sequencing (WGS) is critical for characterizing dynamic intercellular changes in DNA. Current sample preparation technologies for single-cell WGS are complex, expensive, and suffer from high amplification bias and errors. Here, we describe Digital-WGS, a sample preparation platform that streamlines high-performance single-cell WGS with automatic processing based on digital microfluidics. Using the method, we provide high single-cell capture efficiency for any amount and types of cells by a wetted hydrodynamic structure. The digital control of droplets in a closed hydrophobic interface enables the complete removal of exogenous DNA, sufficient cell lysis, and lossless amplicon recovery, achieving the low coefficient of variation and high coverage at multiple scales. The single-cell genomic variations profiling performs the excellent detection of copy number variants with the smallest bin of 150 kb and single-nucleotide variants with allele dropout rate of 5.2%, holding great promise for broader applications of single-cell genomics.

scholarly journals A Novel erm(44) Gene Variant from a Human Staphylococcus saprophyticus Isolate Confers Resistance to Macrolides and Lincosamides but Not Streptogramins

2016 ◽  
Vol 61 (1) ◽  
Author(s):  
Christian Strauss ◽  
Yanmin Hu ◽  
Anthony Coates ◽  
Vincent Perreten
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Healthy Person ◽  
Whole Genome ◽  
Gene Variant ◽  
Content Type ◽  
Staphylococcus Saprophyticus ◽  
Associated Proteins

ABSTRACT A novel erm(44) gene variant, erm(44)v, has been identified by whole-genome sequencing in a Staphylococcus saprophyticus isolate from the skin of a healthy person. It has the particularity to confer resistance to macrolides and lincosamides but not to streptogramin B when expressed in S. aureus. The erm(44)v gene resides on a 19,400-bp genomic island which contains phage-associated proteins and is integrated into the chromosome of S. saprophyticus.

scholarly journals Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kah Ern Ten ◽  
Muhammad Zarul Hanifah Md Zoqratt ◽  
Qasim Ayub ◽  
Hock Siew Tan
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Gc Content ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Whole Genome ◽  
Strain Atcc ◽  
Circular Chromosome ◽  
Genome Data

Abstract Objective The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. Results One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.

scholarly journals Optimizing SARS-CoV-2 Variant of Concern Screening: Experience from British Columbia, Canada, Early 2021

2021 ◽  
Author(s):  
Catherine A Hogan ◽  
Hind Sbihi ◽  
Agatha Jassem ◽  
Natalie Prystajecky ◽  
John R Tyson ◽  
...  
Keyword(s):  
Public Health ◽  
British Columbia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Screening Strategy ◽  
Strategy Implementation ◽  
Whole Genome ◽  
Testing Strategy

Comprehensive and timely testing is required for SARS-CoV-2 variant of concern (VoC) screening. This study demonstrated the feasibility of a combined targeted and whole genome sequencing testing strategy for VoC prevalence assessment in British Columbia, which directly informed provincial VoC screening strategy implementation, and public health efforts.

scholarly journals Whole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials

2021 ◽  
Vol 12 ◽  
Author(s):  
Emma Stubberfield ◽  
Jonathan Sheldon ◽  
Roderick M. Card ◽  
Manal AbuOun ◽  
Jon Rogers ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Intervention Program ◽  
Core Genome ◽  
Health Agency ◽  
Whole Genome ◽  
Swine Dysentery ◽  
England And Wales ◽  
Economic Productivity ◽  
Brachyspira Hyodysenteriae

Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009–2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance. The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies.

scholarly journals A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A

2009 ◽  
Vol 53 (6) ◽  
pp. 2283-2288 ◽  
Author(s):  
Mathilde Lescat ◽  
Alexandra Calteau ◽  
Claire Hoede ◽  
Valérie Barbe ◽  
Marie Touchon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Hot Spot ◽  
Whole Genome ◽  
Clonal Group ◽  
E Coli ◽  
Group A

ABSTRACT Escherichia coli clonal group A (CGA) commonly exhibits a distinctive multidrug antimicrobial resistance phenotype—i.e., resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, and trimethoprim (ACSSuTTp)—and has accounted for up to 50% of trimethoprim-sulfamethoxazole-resistant E. coli urinary tract infections in some locales. Annotation of the whole-genome sequencing of UMN026, a reference CGA strain, clarified the genetic basis for this strain's ACSSuTTp antimicrobial resistance phenotype. Most of the responsible genes were clustered in a unique 23-kbp chromosomal region, designated the genomic resistance module (GRM), which occurred within a 105-kbp genomic island situated at the leuX tRNA. The GRM is characterized by numerous remnants of mobilization and rearrangement events suggesting multiple horizontal transfers. Additionally, comparative genomic analysis of the leuX tRNA genomic island in 14 sequenced E. coli genomes showed that this region is a hot spot of integration, with the presence/absence of specific subregions being uncorrelated with either the phylogenetic group or the pathotype. Our data illustrate the importance of whole-genome sequencing in the detection of genetic elements involved in antimicrobial resistance. Additionally, this is the first documentation of the bla TEM and dhfrVII genes in a chromosomal location in E. coli strains.

scholarly journals Using Whole-genome Sequencing to Determine the Timing of Secondary Tuberculosis in British Columbia, Canada

2020 ◽  
Author(s):  
Kamila Romanowski ◽  
Benjamin Sobkowiak ◽  
Jennifer L Guthrie ◽  
Victoria J Cook ◽  
Jennifer L Gardy ◽  
...  
Keyword(s):  
British Columbia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Epidemiological Data ◽  
Whole Genome ◽  
Patient Level Data ◽  
Patient Level ◽  
Level Data

Abstract Combined with epidemiological data, whole-genome sequencing (WGS) can help better resolve individual tuberculosis (TB) transmission events to a degree not possible with traditional genotyping. We combine WGS data with patient-level data to calculate the timing of secondary TB among contacts of people diagnosed with active TB in British Columbia, Canada.

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