Draft Genome Sequence of a Dominant, Multidrug-Resistant
            <i>Neisseria gonorrhoeae</i>
            Strain, TCDC-NG08107, from a Sexual Group at High Risk of Acquiring Human Immunodeficiency Virus Infection and Syphilis

Chen, Chun‐Chen; Hsia, Ko-Chiang; Huang, Chung-Ter; Wong, Wing-Wai; Yen, Muh–Yong; Li, Lanhui; Lin, Kun-Yen; Chen, Kuo-Wei; Li, Shuying

doi:10.1128/jb.00007-11

Cited by 13 publications

(17 citation statements)

References 10 publications

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“…gonorrheae encodes XerC and XerD homologs as well as two FtsK homologs (19). We cloned and purified tagged versions of XerC Ng and XerD Ng (Methods, SI Text, and Fig.…”

Section: Resultsmentioning

confidence: 99%

FtsK translocation permits discrimination between an endogenous and an imported Xer/ dif recombination complex

Fournes

Crozat

Pages

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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In bacteria, the FtsK/Xer/dif (chromosome dimer resolution site) system is essential for faithful vertical genetic transmission, ensuring the resolution of chromosome dimers during their segregation to daughter cells. This system is also targeted by mobile genetic elements that integrate into chromosomal dif sites. A central question is thus how Xer/dif recombination is tuned to both act in chromosome segregation and stably maintain mobile elements. To explore this question, we focused on pathogenic Neisseria species harboring a genomic island in their dif sites. We show that the FtsK DNA translocase acts differentially at the recombination sites flanking the genomic island. It stops at one Xer/dif complex, activating recombination, but it does not stop on the other site, thus dismantling it. FtsK translocation thus permits cis discrimination between an endogenous and an imported Xer/dif recombination complex.

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“…gonorrheae encodes XerC and XerD homologs as well as two FtsK homologs (19). We cloned and purified tagged versions of XerC Ng and XerD Ng (Methods, SI Text, and Fig.…”

Section: Resultsmentioning

confidence: 99%

FtsK translocation permits discrimination between an endogenous and an imported Xer/ dif recombination complex

Fournes

Crozat

Pages

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Illumina reads were mapped to a reference strain, TCDC-NG08107 (GenBank accession number NC_017511.1), 16 using SMALT. Single nucleotide polymorphisms (SNPs) were called (ie, filtered to determine the working set of SNPs from all candidate sites) according to previous parameters 17 .…”

Section: Methodsmentioning

confidence: 99%

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

Grad

Kirkcaldy

Trees

et al. 2014

The Lancet Infectious Diseases

193

237

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SummaryBackgroundThe emergence of Neisseria gonorrhoeae with decreased susceptibility to extended spectrum cephalosporins raises the prospect of untreatable gonorrhoea. In the absence of new treatments, efforts to slow the increasing incidence of resistant gonococcus require insight into the factors that contribute to its emergence and spread. We assessed the relatedness between isolates in the USA and reconstructed likely spread of lineages through different sexual networks.MethodsWe sequenced the genomes of 236 isolates of N gonorrhoeae collected by the Centers for Disease Control and Prevention's Gonococcal Isolate Surveillance Project (GISP) from sentinel public sexually transmitted disease clinics in the USA, including 118 (97%) of the isolates from 2009–10 in GISP with reduced susceptibility to cefixime (cefRS) and 118 cefixime-susceptible isolates from GISP matched as closely as possible by location, collection date, and sexual orientation. We assessed the association between antimicrobial resistance genotype and phenotype and correlated phylogenetic clustering with location and sexual orientation.FindingsMosaic penA XXXIV had a high positive predictive value for cefRS. We found that two of the 118 cefRS isolates lacked a mosaic penA allele, and rechecking showed that these two were susceptible to cefixime. Of the 116 remaining cefRS isolates, 114 (98%) fell into two distinct lineages that have independently acquired mosaic penA allele XXXIV. A major lineage of cefRS strains spread eastward, predominantly through a sexual network of men who have sex with men. Eight of nine inferred transitions between sexual networks were introductions from men who have sex with men into the heterosexual population.InterpretationGenomic methods might aid efforts to slow the spread of antibiotic-resistant N gonorrhoeae through augmentation of gonococcal outbreak surveillance and identification of populations that could benefit from increased screening for aymptomatic infections.FundingAmerican Sexually Transmitted Disease Association, Wellcome Trust, National Institute of General Medical Sciences, and National Institute of Allergy and Infectious Diseases, National Institutes of Health.

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“…We then used Kraken to search all of the sequences placed on chromosomes 1 through 10, as a quality check on our method. We did not expect any of these contigs to match bacteria, but we unexpectedly found 2,885 small contigs that seemed to align in part to a single bacterial genome, Neisseria gonorrhoeae, strain TCDCNG08107 (Chen et al 2011). This bacterium is a human specific pathogen, and it seemed highly unlikely that it had contaminated the original DNA used for sequencing.…”

Section: Resultsmentioning

confidence: 93%

“…In an effort to determine the source of these foreign sequences in the TCDCNG08107 genome (Genbank accession CP002440), we examined the original publication (Chen et al 2011) and the GenBank entry, and found that although the genome was listed as complete in GenBank, Chen et al described an assembly that comprised 180 contigs. Neither the publication nor the GenBank entry contained any information that the gaps had been filled.…”

Section: Resultsmentioning

confidence: 99%

Peer Review #2 of "Unexpected cross-species contamination in genome sequencing projects (v0.2)"

Flot¹

2014

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Unexpected cross-species contamination in genome sequencing projects The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.

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Draft Genome Sequence of a Dominant, Multidrug-Resistant Neisseria gonorrhoeae Strain, TCDC-NG08107, from a Sexual Group at High Risk of Acquiring Human Immunodeficiency Virus Infection and Syphilis

Cited by 13 publications

References 10 publications

FtsK translocation permits discrimination between an endogenous and an imported Xer/ dif recombination complex

FtsK translocation permits discrimination between an endogenous and an imported Xer/ dif recombination complex

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

Peer Review #2 of "Unexpected cross-species contamination in genome sequencing projects (v0.2)"

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