Draft Genome Sequence of Neisseria gonorrhoeae Strain NG_869 with Penicillin, Tetracycline and Ciprofloxacin Resistance Determinants Isolated from Malaysia

Abstract

Gonorrhea is a sexually transmitted infection caused by Neisseria gonorrhoeae and the increasing reports of multidrug-resistant gonococcal isolates are a global public health care concern. Herein, we report the genome sequence of N. gonorrhoeae strain NG_869 isolated from Malaysia which may provide insights into the drug resistance determinants in gonococcal bacteria.Keywords Drug resistance Á Genome sequence Á N. gonorrhoeae Á Sexual transmitted diseases Á Gonorrhea New cases of sexually transmitted infection caused by Neisseria gonorrhoeae were estimated to be a staggering 106.1 million in 2008 [1]. The emergence and dissemination of antimicrobial-resistant N. gonorrhoeae is undermining the management and control of gonococcal infections as effective therapeutic options continued to dwindle. Isolation of penicillinase-producing N. gonorrhoeae in Malaysia was first reported in 1977 followed by tetracycline-and quinolone-resistant strains in 1990 and 2001, respectively [2-4]. Although the resistance rate for penicillin amongst tested isolates from Malaysia has dropped from 61 % in 2007 to 23.5 % in 2010, resistance rate for quinolone remained above 80 % whilst tetracycline was between 35 and 70 % [1,5].The clinical isolate of N. gonorrhoeae strain NG_869 was obtained from a male patient in June 2014 and the genomic DNA was extracted using Epicenter MasterPure DNA Purification Kit (Madison, WI). The genome was sequenced using llumina HiSeq 2000 platform (San Diego, CA) with a 300-bp paired-end library template and a total of 3,251,582 reads with an average length of 98 bp were obtained. De novo assembly performed using CLC Genomics Workbench version 7.0 (Aarhus, Denmark) yielded 220 contigs with an average coverage of 218.13-fold. The contigs were annotated using Rapid Annotation using Subsystem Technology version 2.0 [6], Prokka [7] and NCBI Prokaryotic Genome Annotation Pipeline version 2.10 [8]. The genome was found to be 99.71 % complete when analyzed using CheckM [9]. The genome size of NG_869 is 2,124,678 bp out of which 2,072,962 bp (52.6 % G ? C content) are chromosomal and the remaining 51,716 bp belong to three circular plasmids. A total of 2572 protein coding genes, 346 subsystems and 49 RNA genes (3 rRNA and 46 tRNA) were predicted. In the RAST-annotated genome, most of the genes were assigned into amino acids and derivatives (14.8 %) followed by protein metabolism (12.2 %) and cofactors, vitamins, prosthetic groups and pigment (10.7 %) subsystems (Table 1). Genes encoding iron acquisition system, multidrug resistance efflux pumps and type IV secretion system were also identified in the genome.The 42,005-bp plasmid pNG869_1 (47.94 % G ? C content) harboured the Dutch-type tetracycline resistance gene (tetM). Another tetracycline resistance gene which was chromosomally mediated was also found as Val-57-toMet point mutation in the ribosomal protein S10 was identified [10,11]. The bla TEM-1B gene was found within