Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review

被引：5

作者：

Singh, Reema ^{[1
]}

Kusalik, Anthony ^{[2
,3
]}

Dillon, Jo-Anne R. ^{[1
,4
]}

机构：

[1] Univ Saskatchewan, Coll Med, Dept Biochem Microbiol & Immunol, Saskatoon, SK, Canada

[2] Univ Saskatchewan, Dept Comp Sci, Saskatoon, SK, Canada

[3] Univ Saskatchewan, Bioinformat Program, Saskatoon, SK, Canada

[4] Vaccine & Infect Dis Org, Saskatoon, SK, Canada

来源：

BRIEFINGS IN FUNCTIONAL GENOMICS | 2022年 / 21卷 / 02期

基金：

加拿大健康研究院;

关键词：

bioinformatics; Neisseria gonorrhoeae; whole genome sequencing; antimicrobial resistance; molecular epidemiology; strain typing; population structure; EXTENDED-SPECTRUM CEPHALOSPORINS; MOLECULAR RESISTANCE MECHANISMS; ANTIMICROBIAL RESISTANCE; ANTIBIOTIC-RESISTANCE; DECREASED SUSCEPTIBILITY; TRANSMISSION CLUSTERS; REVEALS TRANSMISSION; PHYLOGENETIC TREES; FC428; CLONE; SINGLE-CELL;

D O I：

10.1093/bfgp/elab028

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.

引用

页码：78 / 89

页数：12

共 201 条

[51]

Gernert KM, 2020, LANCET MICROBE, V1, pE154, DOI 10.1016/S2666-5247(20)30059-8

[52] Modern technologies and algorithms for scaffolding assembled genomes [J].

Ghurye, Jay ;

Pop, Mihai .

PLOS COMPUTATIONAL BIOLOGY, 2019, 15 (06)

[53] Use of Whole Genome Sequencing for the Molecular Comparison of Neisseria gonorrhoeae Isolates With Decreased Susceptibility to Extended Spectrum Cephalosporins From 2 Geographically Different Regions in America [J].

Gianecini, Ricardo A. ;

Zittermann, Sandra ;

Oviedo, Claudia ;

Galas, Marcelo ;

Pardo, Pilar Ramon ;

Allen, Vanessa G. ;

Galarza, Patricia ;

Melano, Roberto G. .

SEXUALLY TRANSMITTED DISEASES, 2019, 46 (08) :548-555

[54] Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16 [J].

Gianecini, Ricardo A. ;

Golparian, Daniel ;

Zittermann, Sandra ;

Litvik, Ana ;

Gonzalez, Silvia ;

Oviedo, Claudia ;

Melano, Roberto G. ;

Unemo, Magnus ;

Galarza, Patricia ;

Cristaldo, P. ;

Gonzalez, M. ;

Cuenca, N. ;

Caniggia, L. ;

Montibello, S. ;

Buscemi, L. ;

Smayevski, J. ;

Turco, M. ;

Garbaz, C. ;

Morales, M. ;

Alfonso, C. ;

Montoto, M. ;

Marcato, M. ;

Casimiro, A. ;

Cervetto, M. ;

Giovanakis, M. ;

Apestey, N. ;

Casanova, N. ;

Di Bartolomeo, S. ;

Machain, M. ;

Garrone, M. ;

Padlog, R. ;

Vilches, V. ;

Sparo, M. ;

Retes, A. ;

Tognieri, A. ;

Almuzara, M. ;

Rizzo, M. ;

Cagnoni, V. ;

Littvik, A. ;

Gonzalez, S. ;

Mendez, E. ;

Morano, S. ;

Valles, J. ;

Nepote, A. ;

Piccoli, L. ;

Solis, H. ;

Guillen, A. ;

Amador, S. ;

Guantay, C. ;

Arias, C. .

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2019, 74 (06) :1551-1559

[55] Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions [J].

Golparian, Daniel ;

Sanchez-Buso, Leonor ;

Cole, Michelle ;

Unemo, Magnus .

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2021, 76 (04) :940-944

[56] Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16 [J].

Golparian, Daniel ;

Bazzo, Maria Luiza ;

Golfetto, Lisleia ;

Gaspar, Pamela Cristina ;

Schorner, Marcos Andre ;

Benzaken, Adele Schwartz ;

Ramos, Mauro Cunha ;

Ferreira, William Antunes ;

Alonso Neto, Jose Boullosa ;

Mendes Pereira, Gerson Fernando ;

Unemo, Magnus .

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2020, 75 (11) :3163-3172

[57] Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928-2013): antimicrobial use/misuse selects for resistance and drives evolution [J].

Golparian, Daniel ;

Harris, Simon R. ;

Sanchez-Buso, Leonor ;

Hoffmann, Steen ;

Shafer, William M. ;

Bentley, Stephen D. ;

Jensen, Jorgen S. ;

Unemo, Magnus .

BMC GENOMICS, 2020, 21 (01)

[58] Multidrug-resistant Neisseria gonorrhoeae isolate, belonging to the internationally spreading Japanese FC428 clone, with ceftriaxone resistance and intermediate resistance to azithromycin, Ireland, August 2018 [J].

Golparian, Daniel ;

Rose, Lisa ;

Lynam, Almida ;

Mohamed, Aia ;

Bercot, Beatrice ;

Ohnishi, Makoto ;

Crowley, Brendan ;

Unemo, Magnus .

EUROSURVEILLANCE, 2018, 23 (47) :6-9

[59] Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013 [J].

Grad, Yonatan H. ;

Harris, Simon R. ;

Kirkcaldy, Robert D. ;

Green, Anna G. ;

Marks, Debora S. ;

Bentley, Stephen D. ;

Trees, David ;

Lipsitch, Marc .

JOURNAL OF INFECTIOUS DISEASES, 2016, 214 (10) :1579-1587

[60] Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study [J].

Grad, Yonatan H. ;

Kirkcaldy, Robert D. ;

Trees, David ;

Dordel, Janina ;

Harris, Simon R. ;

Goldstein, Edward ;

Weinstock, Hillard ;

Parkhill, Julian ;

Hanage, William P. ;

Bentley, Stephen ;

Lipsitch, Marc .

LANCET INFECTIOUS DISEASES, 2014, 14 (03) :220-226

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