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. 2016 Oct 27;4(5):e01215-16. doi: 10.1128/genomeA.01215-16

Draft Genome Sequence of Elizabethkingia anophelis Strain EM361-97 Isolated from the Blood of a Cancer Patient

Jiun-Nong Lin a,b,c, Chih-Hui Yang d, Chung-Hsu Lai b, Yi-Han Huang a, Hsi-Hsun Lin b,
PMCID: PMC5084871  PMID: 27789647

Abstract

Elizabethkingia anophelis EM361-97 was isolated from the blood of a patient with nasopharyngeal carcinoma and lung cancer. We report the draft genome sequence of EM361-97, which contains a G+C content of 35.7% and 3,611 candidate protein-encoding genes.

GENOME ANNOUNCEMENT

Elizabethkingia, previously belonging to genus Flavobacterium and then Chryseobacterium, is a Gram-negative, nonfermentative rod that is ubiquitously distributed in soil, water, and reservoirs (1). This microorganism has rarely been reported to cause diseases in humans before. However, Elizabethkingia has recently emerged as an important pathogen in the opportunistic infections of immunocompromised patients and neonates. The most common infections of Elizabethkingia include pneumonia, bacteremia, meningitis, and neutropenic fever (24). The genus Elizabethkingia includes four species: E. meningoseptica, E. miricola, E. anophelis, and E. endophytica (5). E. anophelis, first isolated from the mosquito Anopheles gambiae in 2011, has caused several outbreaks of infections in the United States (3) and Hong Kong (4). Infections of E. anophelis are associated with a mortality rate of 24% to 30% in humans (3, 4).

E. anophelis strain EM361-97 was isolated from the blood of a patient with advanced nasopharyngeal carcinoma and lung cancer in Taiwan. This patient has received several courses of radiotherapy and chemotherapy. This isolate was identified as E. anophelis according to the results of 16S rRNA gene sequencing (6).

Total DNA of the isolate was prepared using a Wizard genomic DNA purification kit according to the manufacturer’s instructions (Promega, WI, USA). The genomic DNA was sequenced using an Illumina HiSeq 2000 sequencing platform (Illumina, CA, USA). A total of 1,463 Mb data was produced and the short reads were assembled into a genome sequence using the SOAP de novo method (7). The total length of the draft genome was 4,077,699 bp with a mean G+C content of 35.7%. The assembly contained 26 scaffolds and 27 contigs. Gene prediction was performed by the NCBI Prokaryotic Genome Annotation Pipeline (8). The methods of best-placed reference protein set and GeneMarkS+ were used for the annotation of genes, coding sequences (CDSs), rRNAs, tRNAs, noncoding RNAs (ncRNAs), and repeat regions (8). A total of 3,738 genes and 3,663 CDSs were identified. The total length of genes makes up approximately 87.9% of genome. There were 52 pseudo genes. The predicted number of coding genes was 3,611. The number of RNA genes was 75, including 21 rRNAs (5S: 5; 16S: 7; 23S: 9), 51 tRNAs, and three ncRNAs.

Among the species of genus Elizabethkingia, E. meningosepticum is the most well-known species (911). In contrast, less information is available about the epidemiology, virulence factors, antibiotics resistance, and clinical manifestations of E. anophelis. Knowledge of the genome sequence of E. anophelis will provide researchers important information to understand the pathogenicity of this emerging microorganism.

Accession number(s).

This whole-genome shotgun project has been deposited at GenBank under the accession number LWDS00000000.

ACKNOWLEDGMENTS

This work was supported by a grant (MOST 105-2314-B-214-008) from the Ministry of Science and Technology, Taiwan.

Footnotes

Citation Lin J-N, Yang C-H, Lai C-H, Huang Y-H, Lin H-H. 2016. Draft genome sequence of Elizabethkingia anophelis strain EM361-97 isolated from the blood of a cancer patient. Genome Announc 4(5):e01215-16. doi:10.1128/genomeA.01215-16.

REFERENCES

  • 1.Henriques IS, Araújo S, Azevedo JSN, Alves MS, Chouchani C, Pereira A, Correia A. 2012. Prevalence and diversity of carbapenem-resistant bacteria in untreated drinking water in Portugal. Microb Drug Resist 18:531–537. doi: 10.1089/mdr.2012.0029. [DOI] [PubMed] [Google Scholar]
  • 2.da Silva PSL, Pereira GH. 2013. Elizabethkingia meningoseptica: emergent bacteria causing pneumonia in a critically ill child. Pediatr Int 55:231–234. doi: 10.1111/j.1442-200X.2012.03650.x. [DOI] [PubMed] [Google Scholar]
  • 3.Wisconsin Department of Health Services, Division of Public Health 2016. Wisconsin 2016 Elizabethkingia anophelis outbreak. Accessed: 4 September 2016 https://www.dhs.wisconsin.gov/disease/elizabethkingia.htm. [Google Scholar]
  • 4.Lau SKP, Chow WN, Foo C-H, Curreem SOT, Lo GC-S, Teng JLL, Chen JHK, Ng RHY, Wu AKL, Cheung IYY, Chau SKY, Lung DC, Lee RA, Tse CWS, Fung KSC, Que TL, Woo PCY. 2016. Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality. Sci Rep 6:26045. doi: 10.1038/srep26045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Nicholson AC, Humrighouse BW, Graziano JC, Emery B, McQuiston JR. 2016. Draft genome sequences of strains representing each of the Elizabethkingia genomospecies previously determined by DNA-DNA hybridization. Genome Announc 4(2):e00045-16. doi: 10.1128/genomeA.00045-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Hantsis-Zacharov E, Shakéd T, Senderovich Y, Halpern M. 2008. Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow’s milk. Int J Syst Evol Microbiol 58:2635–2639. doi: 10.1099/ijs.0.65819-0. [DOI] [PubMed] [Google Scholar]
  • 7.Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. doi: 10.1093/bioinformatics/btn025. [DOI] [PubMed] [Google Scholar]
  • 8.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Sun G, Wang L, Bao C, Li T, Ma L, Chen L. 2015. Complete genome sequence of Elizabethkingia meningoseptica, isolated from a T-cell non-Hodgkin’s lymphoma patient. Genome Announc 3(3):e00673-15. doi: 10.1128/genomeA.00673-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Moore LSP, Owens DS, Jepson A, Turton JF, Ashworth S, Donaldson H, Holmes AH. 2016. Waterborne Elizabethkingia meningoseptica in adult critical care. Emerg Infect Dis 22:9–17. doi: 10.3201/eid2201.150139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Rastogi N, Mathur P, Bindra A, Goyal K, Sokhal N, Kumar S, Sagar S, Aggarwal R, Soni KD, Tandon V. 2016. Infections due to Elizabethkingia meningoseptica in critically injured trauma patients: a seven-year study. J Hosp Infect 92:30–32. doi: 10.1016/j.jhin.2015.07.008. [DOI] [PubMed] [Google Scholar]

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