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

Abstract

Neisseria gonorrhoeae infection is the second major cause of sexually transmitted diseases worldwide. Development of resistance to multiple classes of antimicrobials in N. gonorrhoeae has compromised treatment and disease control. Herein, we report the availability of the draft genome sequence of a multidrug-resistant N. gonorrhoeae isolate, TCDC-NG08107, which spread in groups of men who have sex with men (MSM) in Taiwan.

The Neisseria gonorrhoeae isolate TCDC-NG08107 was obtained from a 17-year-old male patient in May 2008. The isolate was identified as sequence types ST2253 and ST7363 by multiantigen sequence typing (NG-MAST) and multilocus sequence typing (MLST), respectively. NG-MAST ST2253 is closely related to a worldwide-prevalent ST835 clone (9), and furthermore, MLST ST7363 has been reported to be a dominant ST with reduced susceptibility to cefixime in Japan (6). Interestingly, TCDC-NG08107 belongs to a dominant NG-MAST N. gonorrhoeae sequence type prevalent in groups of men who have sex with men (MSM), with an 11.1% syphilis and 38.9% HIV coinfection rate during 2006 to 2009 in Taiwan. The isolate was resistant to cefixime (MIC, 0.5 mg/liter) and had reduced susceptibility to ceftriaxone (0.19 mg/liter) (10).

The genome of TCDC-NG08107 was sequenced with an Illumina genome analyzer II. The sequence coverage was about 700×. Automated DNA sequencing chromatograms were analyzed by the CLC bio software package. In particular, the order of 180 contigs was predicted by comparison with the chromosome sequences of N. gonorrhoeae FA1090 (GenBank accession no. AE004969) and NCCP11945 (GenBank accession no. CP001050) (1) and then confirmed by optical mapping (8). The length of the draft sequence of the TCDC-NG08107 circular chromosome is 2,154,835 bp. By MUMmer (5), the overall chromosome sequence identities are 94.5 and 97.7% to FA1090 and NCCP11945, respectively. We also isolated a 39,054-bp circular plasmid, pNGTCDC08107, whose sequence was ∼3 kb shorter than but nearly identical to that of pEP5289 (GenBank accession no. GU479466), which has a Dutch-type backbone (7).

In the TCDC-NG08107 genome, the most abundant repeat type is the DNA uptake sequence (5′-GCCGTCTGAA-3′), comprising 1,931 copies (FA1090, 1,965 copies; and NCCP11945, 1,966 copies). Open reading frame (ORF) prediction and functional assignment of genes were performed with GLIMMER (2), BioNumerics software (version 6.5; Applied Maths), and BLAST. The chromosome and the plasmid have 2,151 and 45 predicted ORFs, respectively. In addition, there are 46 tRNAs and 4 copies of 16S-23S-5S rRNA operons in the chromosome. Particularly, isolate TCDC-NG08107 has a mosaic penA gene, encoding a type X penicillin-binding protein 2, which is the dominant type found in multidrug-resistant gonorrhea in Asia (4). The G+C content of the genome is 52.5%, which is similar to those of FA1090 (52.7%) and NCCP11945 (52.4%). The TCDC-NG08107 chromosome is more sequentially similar to NCCP11945 than FA1090 but is ∼77 kb smaller than NCCP11945. Interestingly, this difference in chromosome size is mainly caused by a gonococcal genetic island (GGI) in NCCP11945, which encodes a type IV secretion system (1, 3).

A detailed report on our isolate will be included in a future publication, including the results of a full comparative analysis between the N. gonorrhoeae genomes.

Nucleotide sequence accession numbers.

The draft genome sequence of N. gonorrhoeae TCDC-NG08107 has been assigned GenBank accession no. CP002440 and CP002441.