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Genotypic Characterization of Multidrug Resistant Chryseobacterium Indologenes Isolates by Whole Genome Sequencing

ขวัญจิต ดวงสงค์; Kwanjit Duangsonk; อรทัย ยินใส; Orathai Yinsai; ผดุงเกียรติ แข็มน้อย; Phadungkiat Khamnoi; ศิริพงษ์ ตองใจ; Siripong Tongjai;
Date: 2567-09
Abstract
Members of genera Chryseobacterium and Elizabethkingia are non-glucose-fermenting Gram-negative bacilli. Some members of these two genera, particularly, Chryseobacterium indologenes and Elizabethkingia anophelis are classified as emerging multidrug resistant opportunistic nosocomial pathogens. They can cause serious infections in newborns and immunocompromised patients. The purpose of this study was to investigate characteristics of the genomes of C. indologenes, C. flavum, C. rhizoplanae and E. anophelis isolated from hospitalized patients from Maharaj Nakhon Chiang Mai hospital using whole genome sequencing. Most of these isolates were resistant to most of the antibiotics tested, including β-lactams, aminoglycosides, and quinolones. Their genomes were studied by next generation sequencing with Illumina and Nanopore, the sequences were then hybrid assembled and annotated. Features detected included orthologous groups, resistance genes, virulence genes and mobile genetic elements using various software tools. Preliminary genome analysis showed that 20 out of 28 isolates were pure and could be assembled into complete genomes. These included 8 isolates of Chryseobacterium indologenes, 2 isolates of Chryseobacterium flavum, 2 isolates of Chryseobacterium rhizoplanae and 8 isolates of Elizabethkingia anophelis. Three isolates of other genera were excluded from the study. The remaining 20 genomes of the isolates were analyzed in this study. Genomes of Chryseobacterium indologenes, Chryseobacterium flavum, Chryseobacterium rhizoplanae range in size from 4.83 – 5.25 Mb as a single circular chromosome, with a G + C content of 36.3-37.5%, containing 4,344 - 4,830 CDSs of coding sequences (CDSs), 18-21 genes for rRNAs, 84-91 for genes for transfer RNAs (tRNAs), and CRISPR-Cas were found in the genomes of two isolates, CI17 and CI18. There were genes involved in cellular processes essential to bacteria and genes corresponding to the drug resistance phenotype. Genes involved in pathogenic factors were also present, including genomic islands (GIs) in all isolates, mobile genetic elements (MGEs) such as integrative and conjugative elements (ICE) in some isolates, insertion sequences, but not plasmids. and integron. Genomes of 8 isolates of Elizabethkingia anophelis range in size from 3.87 – 4.31 Mb, as a single circular chromosome, with a G + C content of 35.5-35.7%, containing 3,503 -3,999 coding sequences (CDSs). CDSs contain 12-15 rRNAs genes. 49-52 transfer RNAs (tRNAs) genes. CRISPR-Cas are found in the genomes of 2 isolates, EM02 and EM08. There were genes corresponding to the drug resistance phenotype like the genus Chryseobacterium. Genes involved in pathogenic factors are also present, including genomic islands (GIs) in all isolates, integrative and conjugative elements (ICE) in some isolates, and mobile genetic elements (MGEs), such as insertion sequences, but not plasmids, and integron.
Copyright ผลงานวิชาการเหล่านี้เป็นลิขสิทธิ์ของสถาบันวิจัยระบบสาธารณสุข หากมีการนำไปใช้อ้างอิง โปรดอ้างถึงสถาบันวิจัยระบบสาธารณสุข ในฐานะเจ้าของลิขสิทธิ์ตามพระราชบัญญัติสงวนลิขสิทธิ์สำหรับการนำงานวิจัยไปใช้ประโยชน์ในเชิงพาณิชย์
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