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.
