Whole-Genome Sequence of a Novel Sequence Type 3136 Carbapenem-Resistant <named-content content-type='genus-species'>Klebsiella pneumoniae</named-content> Strain Isolated from a Hospitalized Patient in Durban, South Africa

Here, we describe the genome sequence of a novel sequence type 3136 (ST3136) Klebsiella pneumoniae strain isolated in South Africa. The 5,574,236-bp genome harbored 23 resistance determinants and 12 virulence factors that are of cardinal importance to infections. The genomics of Klebsiella pneumoniae offer valuable insights into its pathogenicity. Klebsiella pneumoniae is an encapsulated, nonmotile, Gram-negative pathogen of great medical significance that is implicated in a wide variety of infections in humans, including urinary tract infections, pneumonia, bacteremia, meningitis, and liver abscesses (1, 2). Carbapenem-resistant Enterobacteriaceae species, such as K. pneumoniae, are included in the World Health Organization global priority pathogen list, and carbapenems are usually the last-resort antibiotic by virtue of their broad spectrum of activity (3, 4). Here, we present the emergence of sequence type 3136 (ST3136), a novel carbapenemresistant sequence type isolated from a rectal swab of an adult female patient in an intensive care unit of a public hospital in Durban, South Africa. A chromogenic screening medium, Chromid Carba Smart (bioMérieux, France), was used for the isolation of the strain. Phenotypic microbial identification and antibiotic susceptibility testing were performed using the Vitek 2 system (bioMérieux, France). The Rapidec Carba NP (bioMérieux, France) test was used to detect carbapenem hydrolysis by carbapenemase-producing bacteria. The strain was grown on nutrient agar (Oxoid, England) and incubated overnight at 37°C prior to genomic DNA extraction. The QIAamp DNA minikit (Qiagen, Germany) was used to extract the total genomic DNA. A paired-end library (2 300 bp) was prepared using a Nextera XT DNA sample preparation kit, and wholegenome sequencing (WGS) was carried out on a MiSeq machine (Illumina, USA). The sequenced reads (3,325,060 reads) were quality trimmed using Sickle version 1.33 (https:// github.com/najoshi/sickle) and de novo assembled using SPAdes version 3.11 (5). All resultant contiguous sequences were then submitted to GenBank, where gene annotation was implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (6). Furthermore, the assembled genome was submitted to the Klebsiella multilocus sequence type (MLST) database at Institut Pasteur (Paris, France) (http:// bigsdb.pasteur.fr/klebsiella/klebsiella.html) to assign the new sequence type (7). The resistance genes and virulence factors were predicted using ResFinder (8) through the GoSeqIt tools Web platform (https://www.goseqit.com/web-services/) and the VirulenceFinder database (http://www.mgc.ac.cn/VFs/) (9), respectively. Received 27 September 2018 Accepted 5 November 2018 Published 13 December 2018 Citation Ramsamy Y, Mlisana KP, Allam M, Ismail A, Singh R, Amoako DG, Essack SY. 2018. Whole-genome sequence of a novel sequence type 3136 carbapenem-resistant Klebsiella pneumoniae strain isolated from a hospitalized patient in Durban, South Africa. Microbiol Resour Announc 7:e01300-18. https://doi.org/ 10.1128/MRA.01300-18. Editor Vincent Bruno, University of Maryland School of Medicine Copyright © 2018 Ramsamy et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Yogandree Ramsamy, Ramsamyy@ukzn.ac. za. GENOME SEQUENCES