SNP‐based genotyping and whole‐genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum , causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

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A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients

10.1101/2020.10.11.333682 ◽

2020 ◽

Author(s):

Inès Levade ◽

Ashraful I. Khan ◽

Fahima Chowdhury ◽

Stephen B. Calderwood ◽

Edward T. Ryan ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Vibrio Cholerae ◽

Genome Sequencing ◽

Asymptomatic Infection ◽

Whole Genome ◽

Metagenomic Sequencing ◽

Asymptomatic Carriers ◽

Adaptive Mutations ◽

Neutral Mutations

ABSTRACTVibrio cholerae can cause a range of symptoms in infected patients, ranging from severe diarrhea to asymptomatic infection. Previous studies using whole genome sequencing (WGS) of multiple bacterial isolates per patient have shown that Vibrio cholerae can evolve a modest amount of genetic diversity during symptomatic infection. Little is known about V. cholerae genetic diversity within asymptomatic infected patients. To achieve increased resolution in the detection of Vibrio cholerae diversity within individual infections, we applied culture-based population genomics and metagenomics to a cohort of symptomatic and asymptomatic cholera patients. While the metagenomic approach allowed us to detect more mutations in symptomatic patients compared to the culture-based approach, WGS of isolates was still necessary to detect V. cholerae diversity in asymptomatic carriers, likely due to their low Vibrio cholerae load. We found that symptomatic and asymptomatic patients contain similar levels of within-patient diversity, and discovered V. cholerae hypermutators in some patients. While hypermutators appeared to generate mostly selectively neutral mutations, non-mutators showed signs of convergent mutation across multiple patients, suggesting V. cholerae adaptation within hosts. Our results highlight the power of metagenomics combined with isolate sequencing to characterize within-patient diversity in acute V. cholerae infection and asymptomatic infection, while providing evidence for hypermutator phenotypes within cholera patients.IMPORTANCEPathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease, or asymptomatic infection. Here we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers. Despite the acuteness of cholera infections, we found evidence for adaptive mutations in the V. cholerae genome that occur independently and repeatedly within multiple symptomatic patients. We also identified V. cholerae hypermutator phenotypes within 6 out of 14 patients, which appear to generate mainly neutral or deleterious mutations. Our work sets the stage for future studies of the role of hypermutators and within-patient evolution in explaining the variation from asymptomatic carriage to symptomatic cholera.

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799. Genetic Diversity of Mycobacterium tuberculosis Strains Causing Drug-Resistant Tuberculosis in Central Region of Mozambique: The Whole-Genome Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.806 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S286-S287

Author(s):

Evangelina Namburete

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Central Region ◽

Disease Spread ◽

Whole Genome ◽

Drug Resistant ◽

Illumina Hiseq ◽

Drug Resistant Tuberculosis ◽

Resistant Tuberculosis

Abstract Background Knowing the genetic diversity of M. tuberculosis strains causing drug-resistant tuberculosis (DR-TB) in high burden TB and low resources countries such as Mozambique is a key factor to TB disease spread control and world TB epidemic control. Whole-genome sequencing (WGS) better describes molecular diversity, lineages and sub lineages, relationship between strains, underline mutations conferring drug-resistant TB, which may not be shown by molecular and phenotypic tests. As far as we know this is the first study that describes genetic diversity of M. tuberculosis strains causing DR-TB and using WGS in central region of Mozambique.We aim to describe genetic diversity of M. tuberculosis strains causing DR-TB in central Mozambique. Methods A total of 35 strains from Beira Mozambique were evaluated with genotypic tests (Genotype MTBDRplus™, and MTBDRsl™); phenotypic (MGIT-SIRE™) and DST. All isolates resistant to isoniazid (H) or rifampicin (R) or both were submitted to WGS Illumina HiSeq 2000 and analyzed with TB profiler database and phylogenetic tree was done using Figtree tool. This was a descriptive cross-sectional study. Results WGS shown that strains analyzed, belongs to three of six major lineages, with Lineage 4: 25(71.4%); Lineage 1: 5(14.3%); and Lineage 2 Beijing family: 5(14.3%)]. All pre-XDR strains 3(8.6%) were from lineage 4.3. By WGS, all 35 strains had any mutations conferring DR-TB while in one strain, mutation was not shown by genotypic neither phenotypic DST. Compared with genotypic tests, WGS had best performance in showing mutation conferring resistance to etambutol 12/35 (34.3%) and 7/35 (20%). Conclusion The DR-TB disease in Beira Mozambique is mainly caused by M. tuberculosis strains of Lineage 4, sub-lineage 3 although lineage 1 and 2 are also present. WGS shows underline mutations causing DR–TB that are not detected by genotypic and phenotypic DST test. Disclosures All authors: No reported disclosures.

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Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains

Journal of Virology ◽

10.1128/jvi.02658-09 ◽

2010 ◽

Vol 84 (12) ◽

pp. 6229-6234 ◽

Cited By ~ 16

Author(s):

Seweryn Bialasiewicz ◽

Rebecca Rockett ◽

David W. Whiley ◽

Yacine Abed ◽

Tobias Allander ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Discriminatory Power ◽

Whole Genome ◽

Nucleotide Variation ◽

Genome Sequences ◽

Typing Method ◽

Genome Characterization ◽

Wu Polyomavirus

ABSTRACT Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.

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Corrigendum to “Genetic diversity and capsaicinoids content association of Thai chili landraces analyzed by whole genome sequencing-based SNPs” [Sci. Hortic. 249 (2019) 401–406]

Scientia Horticulturae ◽

10.1016/j.scienta.2019.108625 ◽

2019 ◽

Vol 256 ◽

pp. 108625

Author(s):

Wassana Kethom ◽

Pumipat Tongyoo ◽

Orarat Mongkolporn

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011-2019

Journal of Clinical Microbiology ◽

10.1128/jcm.02529-20 ◽

2020 ◽

Author(s):

Justine Schaeffer ◽

Steliana Huhulescu ◽

Anna Stoeger ◽

Franz Allerberger ◽

Werner Ruppitsch

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Diphtheria Toxin ◽

Corynebacterium Diphtheriae ◽

Toxin Gene ◽

Whole Genome ◽

Skin Infections ◽

Antimicrobial Resistance Genes

Background: Diphtheria is a vaccine preventable disease with a high potential for re-emergence. One of its causative agent is Corynebacterium diphtheriae, some strains producing the diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory track or from skin infections. Objectives: The aim of the study was to investigate the genetic diversity of these C. diphtheriae isolates using whole genome sequencing. Methods: Isolates were characterized by genome wide comparison using single nucleotide polymorphism or core genome multilocus sequence typing, and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. Results: Genetic diversity between the isolates was high, with no clear distribution over time or place. C. belfantii isolates were separated from other strains, and were strongly associated with respiratory infections (OR = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin, but did not carry genes conferring β-lactam resistance. Diphtheria toxin gene with no non-synonymous mutation was found in three isolates only. Conclusion: This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistances more broadly and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole genome sequencing.

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Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex

Applied and Environmental Microbiology ◽

10.1128/aem.02919-19 ◽

2020 ◽

Vol 86 (10) ◽

Author(s):

Mélanie Mercier-Darty ◽

Guilhem Royer ◽

Brigitte Lamy ◽

Chadly Charron ◽

Olivier Lemenand ◽

...

Keyword(s):

Genetic Diversity ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Resistance Genes ◽

Stenotrophomonas Maltophilia ◽

Whole Genome ◽

Content Type ◽

Genetic Organization ◽

Animal Strains

ABSTRACT The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans. IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.

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Streptococcus gallolyticus subsp. gallolyticus from Human and Animal Origins: Genetic Diversity, Antimicrobial Susceptibility, and Characterization of a Vancomycin-Resistant Calf Isolate Carrying avanA-Tn1546-Like Element

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04083-14 ◽

2015 ◽

Vol 59 (4) ◽

pp. 2006-2015 ◽

Cited By ~ 12

Author(s):

Beatriz Romero-Hernández ◽

Ana P. Tedim ◽

José Francisco Sánchez-Herrero ◽

Pablo Librado ◽

Julio Rozas ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antibiotic Susceptibility ◽

Resistant Isolate ◽

Comparative Genomic ◽

Gene Gain ◽

Whole Genome ◽

Content Type ◽

Streptococcus Gallolyticus

ABSTRACTThe aim of this work was to characterize the antibiotic susceptibility and genetic diversity of 41Streptococcus gallolyticussubsp.gallolyticusisolates: 18 isolates obtained from animals and 23 human clinical isolates. Antibiotic susceptibility was determined by the semiautomatic Wider system and genetic diversity by pulsed-field gel electrophoresis (PFGE) with SmaI. Animal isolates grouped separately in the PFGE analysis, but no statistical differences in antimicrobial resistance were found between the two groups. The LMG 17956 sequence type 28 (ST28) strain recovered from the feces of a calf exhibited high levels of resistance to vancomycin and teicoplanin (MIC, ≥256 mg/liter). Its glycopeptide resistance mechanism was characterized by Southern blot hybridization and a primer-walking strategy, and finally its genome, determined by whole-genome sequencing, was compared with four closely relatedS. gallolyticussubsp.gallolyticusgenomes. Hybridization experiments demonstrated that a Tn1546-like element was integrated into the bacterial chromosome. In agreement with this finding, whole-genome sequencing confirmed a partial deletion of thevanY-vanZregion and partial duplication of thevanHgene. The comparative genomic analyses revealed that the LMG 17956 ST28 strain had acquired an unusually high number of transposable elements and had experienced extensive chromosomal rearrangements, as well as gene gain and loss events. In conclusion,S. gallolyticussubsp.gallolyticusisolates from animals seem to belong to lineages separate from those infecting humans. In addition, we report a glycopeptide-resistant isolate from a calf carrying a Tn1546-like element integrated into its chromosome.

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Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

10.1101/2021.06.28.450143 ◽

2021 ◽

Author(s):

Severin Einspanier ◽

Tamara Susanto ◽

Nicole Metz ◽

Pieter J. Wolters ◽

Vivianne G.A.A. Vleeshouwers ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fungicide Resistance ◽

Early Blight ◽

Management Strategies ◽

Resistance Management ◽

Alternaria Solani ◽

Whole Genome ◽

A Genome

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI-resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, five years after introduction of SDHIs. Two primary mutations in the Sdh complex (SdhB-H278Y and SdhC-H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. We performed whole-genome sequencing for A. solani isolates from potato fields across Europe (Germany, Sweden, Belgium, and Serbia) to better understand the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. We used ancestry analysis and phylogenetics to determine the genetic background of 48 isolates. The isolates can be grouped into 7 genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. The Sdh mutations appear in different genetic backgrounds, suggesting they arose independently, and the observed admixtures might indicate a higher adaptive potential in the fungus than previously thought. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes and apparent admixture in the populations indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

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