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

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.

scholarly journals A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients

mSystems ◽  
2021 ◽  
Author(s):  
Inès Levade ◽  
Ashraful I. Khan ◽  
Fahima Chowdhury ◽  
Stephen B. Calderwood ◽  
Edward T. Ryan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Diarrheal Disease ◽  
Asymptomatic Infection ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Content Type ◽  
Life Threatening

Pathogen 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.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

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.

scholarly journals Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

2018 ◽  
Author(s):  
David R. Greig ◽  
Ulf Schafer ◽  
Sophie Octavia ◽  
Ebony Hunter ◽  
Marie A. Chattaway ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Species Identification ◽  
Genome Sequencing ◽  
National Level ◽  
Whole Genome ◽  
Surveillance Programs ◽  
El Tor ◽  
The Impact

AbstractEpidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.

scholarly journals Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae

2018 ◽  
Vol 56 (11) ◽  
Author(s):  
David R. Greig ◽  
Ulf Schaefer ◽  
Sophie Octavia ◽  
Ebony Hunter ◽  
Marie A. Chattaway ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Species Identification ◽  
Genome Sequencing ◽  
National Level ◽  
Whole Genome ◽  
Content Type ◽  
El Tor ◽  
The Impact

ABSTRACT Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 and March 2018 (n = 836) and held at the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived species identification and serotype for a subset of isolates (n = 152). Of the 836 isolates, 750 (89.7%) were from a fecal specimen, 206 (24.6%) belonged to serogroup O1, and 7 (0.8%) were serogroup O139; 792 (94.7%) isolates were from patients reporting recent travel abroad, most commonly to India (n = 209) and Pakistan (n = 104). Of the 152 V. cholerae isolates identified by use of kmer, 149 (98.1%) were concordant with those identified using the traditional biochemical approach. Traditional serotyping results were 100% concordant with those of the whole-genome sequencing (WGS) analysis for the identification of serogroups O1 and O139 and classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type 69 (ST69) and in V. cholerae O1 classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from U.K. travelers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from U.K. travelers will contribute to global surveillance programs and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travelers and mitigate the impact of imported infections and the associated risks to public health.

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

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.

scholarly journals High-throughput screening and whole genome sequencing identifies an antimicrobially active inhibitor of Vibrio cholerae

2014 ◽  
Vol 14 (1) ◽  
pp. 49 ◽  
Author(s):  
Galina Sergeev ◽  
Sambit Roy ◽  
Michael Jarek ◽  
Viktor Zapolskii ◽  
Dieter E Kaufmann ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
High Throughput ◽  
High Throughput Screening ◽  
Whole Genome ◽  
Active Inhibitor

scholarly journals Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains

2010 ◽  
Vol 84 (12) ◽  
pp. 6229-6234 ◽  
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.

scholarly journals Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

2020 ◽  
Vol 8 (5) ◽  
pp. 716
Author(s):  
Xueling Wu ◽  
Han Zhou ◽  
Liangzhi Li ◽  
Enhui Wang ◽  
Xiangyu Zhou ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Industrial Wastewater ◽  
Treatment Plant ◽  
Cod Removal ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Toxic Compound ◽  
Adaptive Mutations ◽  
Metabolic Versatility

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

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