The in vitro antimicrobial susceptibility testing demonstrates that the strain J31 is only susceptible to TMP-SMZ, but resistant to all the other tested antibiotics including ampicillin, amikacin, ciprofloxacin, levofloxacin, cefoperazone, nitrofurantoin, imipenem, iobramycin, piperacillin-tazobactam, colistin and cephalosporins (Additional file
1: Table S1). We screened the antibiotic resistance genes (ARGs) in the genome-wide scale in order to further explore the genetic basis of extensive resistance in this strain. In silico analysis revealed the presence of a considerable number of putative ARGs from different drug classes, 90 genes in total (Additional file
2: Table S2), which was more than that observed in
Chryseobacterium oranimense [
16]. This isolate encoded 30 β-lactamase genes, which included amber class A, MBL, class C, and other novel β-lactamases genes. These ARGs might confer high-level resistance to cefepime, cefoperazone and piperacillin-tazobactam, which have been active in previous studies [
11,
28]. In addition, we detected genes corresponding to rifampin, aminoglycosides, phenicols, sulfonamide, macrolide and trimethoprim resistance, which are consistent with the phenotypic results (Additional file
2: Table S2). Moreover, Multidrug efflux pumps including ABC-type transporter, MFS superfamily transporter and RND family transporter are also scattered among the genome. Therefore, these predicted ARGs might contribute to the multidrug resistance of stain J31 to the tested antibiotics and other non-tested antibiotics.
To further explore the resistance mechanism of J31, we used PlasmidFinder to detect the potential plasmids among the whole genome sequence. However, PlasmidFinder did not find any plasmid, and the result was also verified by conjugation experiments. We further investigated the other three assemblies of
C. indologenes in NCBI genome database (
https://www.ncbi.nlm.nih.gov/genome/) and no typing plasmid replicons could be found in all the contigs. For the genus
Chryseobacterium, only two in thirty-eight draft or complete genomes consist of chromosomes and plasmids, which suggests
Chryseobacterium, unlike the genus
Enterococcus, might carry the resistant genes in the chromosome [
16,
29].
We scanned each ARG flanking sequences in a range of 10-kb for IS sequences and junction associated proteins. Only one partial IS sequence, 107 bp ISR of ISBbi1 in IS1595 family, was found locating at 8958 bp upstream of one subclass B1 MBL (Additional file
3: Table S3). We found two integrases, a 304-aa-long site-specific tyrosine recombinase XerD at 2908 bp downstream of the penicillin-binding protein gene and a 422-aa-long hypothetical integrase at 4146 bp downstream of the putative ABC transporter gene, and two crossover junction endodeoxyribonucleases, a 184-aa-long RuvC protein at 5578 bp downstream of one β-lactamase gene and a 138-aa-long RuvA protein at 1748 bp downstream of another β-lactamase gene (Additional file
3: Table S3). Maybe there are some unknown proteins flanking the predicted ARGs which might function as the insertion elements or transposases for transferring antibiotic resistance.