Comparative genomic analysis of Myroides odoratimimus isolates

Abstract

Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related. Various prophages were identified in the four clinical isolate genomes, which possibly contributed to the genome evolution among the Myroides strains. CRISPR elements were only detected in the two clinical (PR63039 and CCUG10230) isolates and two environmental (CCUG12700 and H1bi) strains. With more stringent cutoff parameters in CARD analysis, the four clinical M. odoratimimus contained roughly equal antibiotic resistance genes, indicating their similar antibiotic resistance profiles. The three clinical (CCUG10230, CCUG12901, CIP101113) and three environmental (CCUG12700, L41, H1bi) M. odoratimimus strains were speculated to carry the indistinguishable virulent factors (VFs), which may involve in the similar pathogenesis mechanism. Moreover, some VFs might confer to the high capacity of dissemination, attacking tissue cells and induction of autoimmune complications. Our results facilitate the research of antibiotic resistance and the development of therapeutic regimens for the M. odoratimimus infections.

The antibiotic resistance and pathogenicity of a multidrug‐resistant Elizabethkingia anophelis isolate

“…The presence of IlpA in our strain 12012‐2 PRCM implied that it might also have the potential to cause septicemia. Other virulence factor genes such as clpP , tuf , r mlA , htpB, and DnaK may be involved in defense or invasion during the course of pathogenesis, already discussed in our previous report (Hu et al ). In addition, it is worth noting that E. anophelis isolates from mosquitoes also shared these conserved virulence factors.…”

“…One can assume the same physiological roles in 12012-2-PRCM due to their good amino acid sequence homology. The presence of IlpA in our strain 12012-2 TA B L E 2 The predicted antibiotic resistance genes in five E. anophelis isolates: 12012-2PRCM, CSID3000521207, NUHP1, Ag1, R26 htpB, and DnaK may be involved in defense or invasion during the course of pathogenesis, already discussed in our previous report (Hu et al 2018). In addition, it is worth noting that E. anophelis isolates from mosquitoes also shared these conserved virulence factors.…”

“…All five E. anophelis strains contained many catB genes or cat variants (Table ), which usually play a role in the composition of gene cassette or integron, and confer to the ability of antibiotic resistance. The resistance action mechanisms of catB were already clarified in our previous report (Hu et al ). Genes such as LpxC and SPM‐1 , ErmF, and Erm(35) as well as dfrE conferred resistance to diaminopyrimidine, streptogramin, and elfamycin, respectively.…”

“…The resistance action mechanisms of catB were already clarified in our previous report (Hu et al 2018). Genes such as LpxC and SPM-1, ErmF, and Erm(35) as well as dfrE conferred resistance to diaminopyrimidine, streptogramin, and elfamycin, respectively.…”

“…The CRISPs (Clustered Regularly Interspaced Short Palindromic repeat sequences) were predicted by CRISPR recognition tool (CRT) (Bland et al, 2007). ICEberg database was used to detect for integrative and conjugative elements (ICE) (Bi et al, 2012).The resistance genes and VFs were searched (BLASTp) against the CARD database (Jia et al, 2017;McArthur et al, 2013;McArthur & Wright, 2015) and the VFDB protein Set B database (Chen, Xiong, Sun, Yang, & Jin, 2012;Chen, Zheng, Liu, Yang, & Jin, 2016), respectively, by collaborating with Beijing Novogene Bioinformatics Technology Co., Ltd. (BNNT), followed by filtering with more stringent cutoff parameters as described previously (Hu et al, 2018) and two additional cutoff parameters, Match length >100 amino acids and Identical >100 amino acids.…”