Genome Sequence of Acinetobacter baumannii TYTH-1

Liou, Ming-Li; Liu, Chih‐Chin; Lu, Chia-Wei; Hsieh, Ming‐Feng; Chang, Kai‐Chih; Kuo, Han-Yueh; Lee, Chi-Ching; Chang, Chun-Tien; Yang, Cheng‐Yao; Tang, Chuan Yi

doi:10.1128/jb.01860-12

Cited by 15 publications

(6 citation statements)

References 10 publications

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“…PCR primer pairs specific for each gene of the eight-gene hemO cluster 35 were designed based on alignment of gene cluster sequences of six A. baumannii strains [strains ACICU 21 , SDF 22 , MDR-ZJ06 25 , TYTH-1 27 , TCDC-AB07115 26 , and AB0057 18 ], available as of May, 2013. The sequence alignment was performed by using Lasergene MegAlign program from DNASTAR, Inc. (Madison, WI).…”

Section: Methodsmentioning

confidence: 99%

“…Despite the clinical significance of A. baumannii infections, the molecular basis on the virulence and acquisition of multidrug resistance by A. baumannii remains largely unknown. To better understand the genome plasticity, natural history, epidemiology and acquisition of resistance and pathogenicity islands/genes of A. baumannii , the complete genomes of 21 A. baumannii strains, including LAC-4, became available as of December 31, 2014 17 18 19 20 21 22 23 24 25 26 27 28 29 30 . In addition, the genomes of hundreds of A. baumannii strains have been sequenced to scaffold or contig levels ( http://www.ncbi.nlm.nih.gov/genome/genomes/403 ).…”

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confidence: 99%

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Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

Kuang

et al. 2015

Sci Rep

101

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Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

Kuang

et al. 2015

Sci Rep

101

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“…1). This structure has been identified on plasmids associated with Klebsiella oxytoca and Citrobacter freundii (GenBank accession numbers CP003684.1 and JX182975.1, respectively) and on the chromosome of A. baumannii MDR-TJ and TYTH-1 (21,22). The second region also includes multiple antibiotic resistance genes, including the tetracycline efflux gene tetB, the streptomycin resistance genes strA and strB, and the dihydropteroate synthase gene sul2.…”

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confidence: 99%

Bacterial Peritonitis Due to Acinetobacter baumannii Sequence Type 25 with Plasmid-Borne New Delhi Metallo-β-Lactamase in Honduras

Waterman

McGann

Snesrud

et al. 2013

Antimicrob Agents Chemother

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A carbapenem-resistant Acinetobacter baumannii strain was isolated from the peritoneal fluid of a patient with complicated intra-abdominal infection and evaluated at the Multidrug-resistant Organism Repository and Surveillance Network by wholegenome sequencing and real-time PCR. The isolate was sequence type 25 and susceptible to colistin and minocycline, with low MICs of tigecycline. bla NDM-1 was located on a plasmid with >99% homology to pNDM-BJ02. The isolate carried numerous other antibiotic resistance genes, including the 16S methylase gene, armA.

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“…It is worth mentioning that Clover was involved in two sequencing projects to respectively sequence bacterial genomes Acinetobacter baumannii TYTH-1 (4.0 Mb and 165 contigs) [ 14 ] and Morganella morganii KT (3.8 Mb and 58 contigs) [ 15 ]. The contigs generated by Clover were then used to build the draft sequences, which were confirmed by optical mapping and PCR.…”

Section: Resultsmentioning

confidence: 99%

Clover: a clustering-oriented de novo assembler for Illumina sequences

Hsieh

Tang

2020

BMC Bioinformatics

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Background Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. Results In this paper, we develop a de Bruijn assembler, called Clover (clustering-oriented de novo assembler), that utilizes a novel k-mer clustering approach from the overlap-layout-consensus concept to deal with the sequencing errors generated by the Illumina platform. We further evaluate Clover’s performance against several de Bruijn graph assemblers (ABySS, SOAPdenovo, SPAdes and Velvet), overlap-layout-consensus assemblers (Bambus2, CABOG and MSR-CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromosome 14). The results show that Clover achieves a superior assembly quality in terms of corrected N50 and E-size while remaining a significantly competitive in run time except SOAPdenovo. In addition, Clover was involved in the sequencing projects of bacterial genomes Acinetobacter baumannii TYTH-1 and Morganella morganii KT. Conclusions The marvel clustering-based approach of Clover that integrates the flexibility of the overlap-layout-consensus approach and the efficiency of the de Bruijn graph method has high potential on de novo assembly. Now, Clover is freely available as open source software from https://oz.nthu.edu.tw/~d9562563/src.html.

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Genome Sequence of Acinetobacter baumannii TYTH-1

Cited by 15 publications

References 10 publications

Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

Bacterial Peritonitis Due to Acinetobacter baumannii Sequence Type 25 with Plasmid-Borne New Delhi Metallo-β-Lactamase in Honduras

Clover: a clustering-oriented de novo assembler for Illumina sequences

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