Draft Genome Sequence of the First Isolate of Extensively Drug-
Resistant (XDR) Mycobacterium tuberculosis in Malaysia
Kee Peng Ng,aSu Mei Yew,aChai Ling Chan,aJennifer Chong,aSoo Nee Tang,aTuck Soon Soo-Hoo,aShiang Ling Na,a
Hamimah Hassan,aYun Fong Ngeow,aChee Choong Hoh,bKok Wei Lee,bWai Yan Yeeb
Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysiaa; Codon Genomics SB, Jalan Bandar Lapan Belas, Pusat Bandar
Puchong, Selangor Darul Ehsan, Malaysiab
The emergence of the global threat of extensively drug-resistant (XDR) Mycobacterium tuberculosis reveals weaknesses in tuber-
bacterium tuberculosis strain isolated in Malaysia. The sequence was also compared against a reference strain to elucidate the
Received 24 October 2012 Accepted 14 November 2012 Published 24 January 2013
Citation Ng KP, Yew SM, Chan CL, Chong J, Tang SN, Soo-Hoo TS, Na SL, Hassan H, Ngeow YF, Hoh CC, Lee KW, Yee WY. 2013. Draft genome sequence of the first isolate of
extensively drug-resistant (XDR) Mycobacterium tuberculosis in Malaysia. Genome Announc. 1(1):e00056-12. doi:10.1128/genomeA.00056-12.
Copyright © 2013 Ng et al. This is an open-access article distributed under the terms of the Attribution 3.0 Unported Creative Commons License.
Address correspondence to Kee Peng Ng, firstname.lastname@example.org.
public health problem that threatens tuberculosis (TB) care and
control in many countries (1). XDR Mycobacterium tuberculosis
strain UM 1072388579 was isolated from a 57-year-old man. The
isolate was resistant to amikacin, capreomycin, ciprofloxacin,
ethionamide, isoniazid, kanamycin, ofloxacin, rifampin, and
streptomycin but sensitive to ethambutol and para-salicylic acid.
of 5,861,112 paired-end reads, using the Illumina HiSeq 2000 se-
quencer machine. After preprocessing, 2,800,000 high-quality
paired-end reads (100-fold depth) were subsampled and assem-
bled using Velvet v1.1.07 (2), producing 213 contigs (?200 bp).
(3) and GapFiller v1.10 (4) programs by utilizing all paired-end
information available. Final assembly consisted of 89 scaffolds
The assembly has an N50 scaffold size of 108,779 bp and G?C
content of 65.4%. Protein coding sequences, rRNAs, and tRNAs
of the XDR M. tuberculosis genome were predicted using
GeneMarkS (5), RNAmmer 1.2 server (6), and tRNAscan-SE
v1.23 (7), respectively. Our pipeline predicted 4,099 coding DNA
sequences (CDS) with length ?33 amino acids (aa), 45 tRNAs,
and 3 rRNAs (5S, 16S, and 23S). Annotation of the coding se-
quences predicted was performed by a BLAST search against the
NCBI nonredundant database with 4,069 (99.3%) genes anno-
tated with function. All annotated genes were subjected to Gene
Ontology classification and Kyoto Encyclopedia of Genes and
Genomes (KEGG) pathways analysis.
tify the difference between intergenic and coding regions of drug-
he emergence of multidrug-resistant (MDR) and extensively
drug-resistant (XDR) Mycobacterium tuberculosis is a major
susceptible versus extensively drug-resistant strains. A total of 1,455
served. Mutations of other drug resistance sites such as ethA (ethio-
namide), gidB (streptomycin), gyrA and gyrB (fluoroquinolones),
were also observed. The draft sequence of the XDR M. tuberculosis
to better understanding of the genetic molecular differences in ac-
quired drug resistance of XDR M. tuberculosis isolates locally and in
Nucleotide sequence accession number. The nucleotide se-
deposited in DDBJ/EMBL/GenBank under accession number
the University of Malaya.
writing and editing of the manuscript. K.P.N., J.C., S.N.T., T.S.S.H.,
C.L.C., and S.L.N. were responsible for the isolation, identification, and
DNA extraction. S.M.Y., C.C.H., K.W.L., and W.Y.Y. performed the ge-
nome sequencing and bioinformatics analysis.
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