Recombinational Switching of the Clostridium difficile S-Layer and a Novel Glycosylation Gene Cluster Revealed by Large-Scale Whole-Genome Sequencing

AbstractIntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR)-TB. The large amount of publicly available whole-genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analysis at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR-TB isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.ResultsWe aggregated a dataset that includes 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.

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Independent Microevolution Mediated by Mobile Genetic Elements of IndividualClostridium difficileIsolates from Clade 4 Revealed by Whole-Genome Sequencing

mSystems ◽

10.1128/msystems.00252-18 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 4

Author(s):

Yuan Wu ◽

Chen Liu ◽

Wen-Ge Li ◽

Jun-Li Xu ◽

Wen-Zhu Zhang ◽

...

Keyword(s):

Drug Resistance ◽

Clostridium Difficile ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mobile Genetic Elements ◽

High Rate ◽

Whole Genome ◽

Content Type ◽

Genetic Elements ◽

Sequence Types

ABSTRACTHorizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome ofClostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37C. difficileisolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly,catD, known to be harbored by Tn4453a/b, was replaced byaac(6′) aph(2′′)in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges betweenC. difficileand other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified inC. difficileisolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number ofC. difficileisolates resistant to all antibiotics tested here suggests the ease with which resistance is acquiredin vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.IMPORTANCEMobile genetic elements play a key role in the continuing evolution ofClostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4C. difficileisolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/bwithaac(6′) aph(2′′)instead ofcatD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

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Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of InvasiveStaphylococcus aureusin Europe

mBio ◽

10.1128/mbio.00444-16 ◽

2016 ◽

Vol 7 (3) ◽

Cited By ~ 123

Author(s):

David M. Aanensen ◽

Edward J. Feil ◽

Matthew T. G. Holden ◽

Janina Dordel ◽

Corin A. Yeats ◽

...

Keyword(s):

Public Health ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Bacterial Pathogens ◽

Epidemiological Surveillance ◽

Data Sets ◽

Whole Genome ◽

Bioinformatic Tools ◽

Road Map

ABSTRACTThe implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasiveStaphylococcus aureusisolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show thatin silicopredictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools.IMPORTANCEThe spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.

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Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework

Nucleic Acids Research ◽

10.1093/nar/gkx019 ◽

2017 ◽

pp. gkx019 ◽

Cited By ~ 6

Author(s):

Miaoxin Li ◽

Jiang Li ◽

Mulin Jun Li ◽

Zhicheng Pan ◽

Jacob Shujui Hsu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Whole Genome ◽

Integrative Framework ◽

Downstream Analysis

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Whole-Genome Sequencing Demonstrates That Fidaxomicin Is Superior to Vancomycin for Preventing Reinfection and Relapse of Infection With Clostridium difficile

The Journal of Infectious Diseases ◽

10.1093/infdis/jit598 ◽

2013 ◽

Vol 209 (9) ◽

pp. 1446-1451 ◽

Cited By ~ 35

Author(s):

David W. Eyre ◽

Farah Babakhani ◽

David Griffiths ◽

Jaime Seddon ◽

Carlos Del Ojo Elias ◽

...

Keyword(s):

Clostridium Difficile ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Fast and inexpensive whole genome sequencing library preparation from intact yeast cells

10.1101/2020.09.03.280990 ◽

2020 ◽

Author(s):

Sibylle C Vonesch ◽

Shengdi Li ◽

Chelsea Szu Tu ◽

Bianca P Hennig ◽

Nikolay Dobrev ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Dna ◽

Large Scale ◽

Massively Parallel Sequencing ◽

Yeast Cells ◽

Whole Genome ◽

High Quality ◽

Rapid Preparation ◽

Yeast Cultures

ABSTRACTThrough the increase in the capacity of sequencing machines massively parallel sequencing of thousands of samples in a single run is now possible. With the improved throughput and resulting drop in the price of sequencing, the cost and time for preparation of sequencing libraries have become the major bottleneck in large-scale experiments. Methods using a hyperactive variant of the Tn5 transposase efficiently generate libraries starting from cDNA or genomic DNA in a few hours and are highly scalable. For genome sequencing, however, the time and effort spent on genomic DNA isolation limits the practicability of sequencing large numbers of samples. Here, we describe a highly scalable method for preparing high quality whole-genome sequencing libraries directly from yeast cultures in less than three hours at 34 cents per sample. We skip the rate-limiting step of genomic DNA extraction by directly tagmenting yeast spheroplasts and add a nucleosome release step prior to enrichment PCR to improve the evenness of genomic coverage. Resulting libraries do not show any GC-bias and are comparable in quality to libraries processed from genomic DNA with a commercially available Tn5-based kit. We use our protocol to investigate CRISPR/Cas9 on- and off-target edits and reliably detect edited variants and shared polymorphisms between strains. Our protocol enables rapid preparation of unbiased and high-quality, sequencing-ready indexed libraries for hundreds of yeast strains in a single day at a low price. By adjusting individual steps of our workflow we expect that our protocol can be adapted to other organisms.

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