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Protocols

PhyResSE specifications

Information


Unique identifier OMICS_22057
Name PhyResSE
Alternative name Phylo-Resistance-Search-Engine
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline vschleusener
  • person_outline Stefan Niemann
  • person_outline Kurt Fellenberg

Additional information


https://bioinf.fz-borstel.de/mchips/phyresse/docu.html

Publication for Phylo-Resistance-Search-Engine

PhyResSE citations

 (12)
library_books

Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population based study

2018
PLoS One
PMCID: 5884559
PMID: 29617456
DOI: 10.1371/journal.pone.0195413

[…] number of (transmission) events within a VNTR cluster was calculated by the number of patients within the respective VNTR cluster minus the index patient (n-1 method). Fastq.gz files were uploaded to PhyResSe [] to assign a lineage to each isolate. The Chi-square test was used to analyse differences between patients clustered by WGS and patients that were not; Fisher’s exact test was used for cell […]

library_books

Molecular epidemiology of tuberculosis in Tasmania and genomic characterisation of its first known multi drug resistant case

2018
PLoS One
PMCID: 5821347
PMID: 29466411
DOI: 10.1371/journal.pone.0192351

[…] ean genome coverage of 20, and were annotated as previously described []. Mycobacterial lineage was predicted with TB Profiler [] and mutations associated with drug resistance were detected using the PhyResSE database [] followed by manual checking of the sequence. A maximum likelihood phylogenetic inference tree was built in PhyML using the generalised time reversible (GTR) substitution model []. […]

call_split

Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high confidence resistance conferring mutations

2018
Sci Rep
PMCID: 5818527
PMID: 29459669
DOI: 10.1038/s41598-018-21378-x
call_split See protocol

[…] ins, four other WHO-TDR strains had whole genome sequences available yet were excluded, three due to heteroresistance as they were found to have a mutation in katG in 21%, 29% and 43% of reads (using PhyResSE, see below) and one because a mixture of resistant as well as susceptible bacilli for multiple drugs was suggestive of mixed infection. Isoniazid MIC determination on Löwenstein-Jensen (LJ) m […]

library_books

A Predominant Variable Number Tandem Repeat Cluster of Mycobacterium tuberculosis Isolates among Asylum Seekers in the Netherlands and Denmark, Deciphered by Whole Genome Sequencing

2018
J Clin Microbiol
PMCID: 5786717
PMID: 29167288
DOI: 10.1128/JCM.01100-17

[…] n cluster 1064-32 and isolates belonging to other VNTR clusters. The phenotypic resistance profile of the MDR-TB patients was verified on the basis of detected mutations in resistance genes using the PhyResSe pipeline. Phenotypic drug susceptibility testing (DST) was performed with a MGIT 960 system. […]

library_books

Draft Genome Sequence of the First Confirmed Isolate of Multidrug Resistant Mycobacterium tuberculosis in Tasmania

2017
Genome Announc
PMCID: 5668546
PMID: 29097470
DOI: 10.1128/genomeA.01230-17

[…] SNVs and 97 were insertions/deletions. The genome of TASMDR1 displayed high-confidence single-nucleotide polymorphisms in genes correlating with antimicrobial drug resistance when analyzed using the PhyResSE database (). These include high-confidence mutations in the katG gene (aGc/aCc, S315T) and rpoB gene (gAc/gGc, D435G; tCg/tTg, S450L), which underlie M. tuberculosis resistance to isoniazid a […]

call_split

Half of rifampicin resistant Mycobacterium tuberculosis complex isolated from tuberculosis patients in Sub Saharan Africa have concomitant resistance to pyrazinamide

2017
PLoS One
PMCID: 5663438
PMID: 29088294
DOI: 10.1371/journal.pone.0187211
call_split See protocol

[…] age depth of at least >30x. was considered acceptable. The reads obtained were then aligned to M. tuberculosis H37Rv reference genome, and total variant calling was performed with the pipeline of the PhyResSE web-tool. Isolates showing a coverage of at least 20× were considered for SNP analysis.Interpretation of PZA resistance based on pncA mutations was based on published literature () [,,,–]. Si […]

Citations

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PhyResSE institution(s)
Molecular Mycobacteriology, Research Center Borstel, Borstel, Germanya, Germany; German Center for Infection Research (DZIF), Borstel Site, Borstel, Germanyb, Germany; Bioinformatics, Research Center Borstel, Borstel, Germany; Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
PhyResSE funding source(s)
Supported by the European Union TB-PANNET (FP7-223681) and PathoNgenTrace (FP7-278864-2) projects and the German Center for Infection Research (DZIF).

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