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

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Protocol publication

[…] Elizabethkingia, previously belonging to genus Flavobacterium and then Chryseobacterium, is a Gram-negative, nonfermentative rod that is ubiquitously distributed in soil, water, and reservoirs (). 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 (). The genus Elizabethkingia includes four species: E. meningoseptica, E. miricola, E. anophelis, and E. endophytica (). E. anophelis, first isolated from the mosquito Anopheles gambiae in 2011, has caused several outbreaks of infections in the United States () and Hong Kong (). Infections of E. anophelis are associated with a mortality rate of 24% to 30% in humans (, ).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 ().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 (). 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 (). 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 (). 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 (). 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. […]

Pipeline specifications

Software tools SOAP, PGAP
Application 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Carcinoma, Lung Neoplasms, Neoplasms