<i>NGMASTER: in Silico</i>Multi-Antigen Sequence Typing for<i>Neisseria gonorrhoeae</i>

Kwong, Jason C; Silva, Anders Gonçalves da; Dyet, Kristin; Williamson, Deborah A; Stinear, Timothy P.; Howden, Benjamin P; Seemann, Torsten

doi:10.1101/057760

Cited by 5 publications

(6 citation statements)

References 12 publications

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“…The findings of the sequenced genomes analysis using the NGMASTER software [16] revealed a complete coincidence with the initial data referring the analyzed strains to the genogroups ST 1407, ST 12556, and ST 12450 ( Table 4 ). …”

Section: Resultssupporting

confidence: 58%

“…The NGMASTER software was employed for NG-MAST sequence typing of N. gonorrhoeae [16]; multilocus MLST sequence typing was performed using the SRST2 software [17]. Orthologous protein groups belonging to the genus Neisseria were inferred by OrthoFinder [18] from annotated protein sequences of the analyzed isolates and 24 previously sequenced N. gonorrhoeae strains, as well as NCBI reference annotations of N. meningitidis , N. lactamica and N. elongata .…”

Section: Methodsmentioning

confidence: 99%

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Whole-Genome Sequencing of Russian Neisseria Gonorrhoeae Isolates Related to ST 1407 Genogroup

Kubanov¹,

Runina²,

Chestkov³

et al. 2018

Acta Naturae

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The whole-genome sequencing data of three N. gonorrhoeae strains isolated in the Russian Federation in 2015 are presented. According to the NG-MAST protocol, these strains are related to the globally spread ST 1407 genogroup. The analysis of their resistomes showed the absence of ermA/B/C/F genes and the presence of wild-type alleles of rpsE, rrs, rrl, rplD, rplV, macAB, and mefA genes, and these patterns explain the susceptibility of the sequenced strains to aminocyclitols (spectinomycin) and macrolides (azithromycin). Conjugative resistance determinants (blaTEM, tetM) were absent in the genomes, and the penC/ pilQ, parE, and norM alleles were shown to be wild-type, whereas single or multiple nucleotide substitutions were identified in the genes encoding targets for β-lactams (ponA, penA), tetracyclines (rpsJ), and fluoroquinolones (gyrA, parC). The additional mutations were found in porB gene and the promoter of mtrR gene, which nonspecifically reduced the susceptibility to antimicrobials due to the membrane permeability decrease and efflux pump overexpression. The diversity of mutations observed in the analyzed genomes prompted a revision of the phylogenetic relationships between the strains by comparing more than 790 groups of housekeeping genes. A high homology between the N. gonorrhoeae ST 1407 and N. gonorrhoeae ST 12556 genomes was confirmed; the latter had probably diverged from a common ancestor as a result of single mutation events. On the other hand, N. gonorrhoeae ST 12450 was an example of phenotypic convergence which appeared in the emergence of new drug resistance determinants that partially coincide with those of the ST 1407 genogroup.

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Section: Resultssupporting

confidence: 58%

Section: Methodsmentioning

confidence: 99%

Whole-Genome Sequencing of Russian Neisseria Gonorrhoeae Isolates Related to ST 1407 Genogroup

Kubanov¹,

Runina²,

Chestkov³

et al. 2018

Acta Naturae

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“…In parallel to the mapping process, reads were assembled using the assembly and improvement iterative pipeline developed at the Wellcome Sanger Institute 57 . Multi-locus sequence typing (MLST) 58 and N. gonorrhoeae multi-antigen sequence typing (NG-MAST) 59 typing schemes were retrieved directly from the sequences using the get_sequence_type script (https://github.com/sanger-pathogens/mlst_check/blob/master/bin/get_sequence_type) and NGMASTER 60 , respectively. The presence of the β-lactamase ( bla TEM ) and tetracycline ( tetM ) genes on plasmids and the Gonococcal Genomic Island (GGI) were detected using BLAST v2.3.0+ 61 and ARIBA v2.4 62 .…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

Sánchez-Busó

Golparian

Corander

et al. 2018

Preprint

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“…AMR SNPs were detected using Ariba (35) v2.14.4 using the CARD database (36) and the built-in TB database. In silico serotyping was performed using emmtyper (37) v0.1.0 for Streptococcus pyogenes , kleborate (38) v0.3.0 for Klebsiella pneumoniae , legsta (39) v0.3.2 for Legionella pneumophilia , lissero (40) v0.2 for Listeria monocytogenes , meningotype (41) v0.8.2-beta for N. meningitidis , ngmaster (42) v0.5.5 for N. gonorrhoeae , seroba (43) v1.0.1 for Streptococcus pneumoniae , shigatyper (44) v1.0.5 for Shigella spp ., sistr (45) v1.0.2 for Salmonella enterica , and srst2 (46) v0.2.0 using the EcOH DB for Escherichia coli .…”

Section: Tablementioning

confidence: 99%