Whole genome sequencing for deciphering the resistome of Chryseobacterium indologenes, an emerging multidrug-resistant bacterium isolated from a cystic fibrosis patient in Marseille, France

Abstract

We decipher the resistome of Chryseobacterium indologenes MARS15, an emerging multidrug-resistant clinical strain, using the whole genome sequencing strategy. The bacterium was isolated from the sputum of a hospitalized patient with cystic fibrosis in the Timone Hospital in Marseille, France. Genome sequencing was done with Illumina MiSeq using a paired-end strategy. The in silico analysis was done by RAST, the resistome by the ARG-ANNOT database and detection of polyketide synthase (PKS) by ANTISMAH. The genome size of C. indologenes MARS15 is 4 972 580 bp with 36.4% GC content. This multidrug-resistant bacterium was resistant to all β-lactams, including imipenem, and also to colistin. The resistome of C. indologenes MARS15 includes Ambler class A and B β-lactams encoding bla CIA and bla IND-2 genes and MBL (metallo-β-lactamase) genes, the CAT (chloramphenicol acetyltransferase) gene and the multidrug efflux pump AcrB. Specific features include the presence of an urease operon, an intact prophage and a carotenoid biosynthesis pathway. Interestingly, we report for the first time in C. indologenes a PKS cluster that might be responsible for secondary metabolite biosynthesis, similar to erythromycin. The whole genome sequence analysis provides insight into the resistome and the discovery of new details, such as the PKS cluster.

Keywords: Carotenoid; Chryseobacterium indologenes; microbial genomics; nonribosomal polyketide synthase; polyketide synthase; resistome; urease.

Fig. 1

(A) Chryseobacterium indologenes MARS15 isolated on Mueller-Hinton agar. (B) Electron microscopic image of C. indologenes MARS15 using TechnaiG2 Cryo at operating voltage of 200 keV.

Fig. 2

From genotype to phenotype of Chryseobacterium indologenes MARS15. (A) Antibiotic sensitivity testing. AK, amikacin; AMC, amoxicillin–clavulanate acid; ATM, aztreonam; AX, amoxicillin; CIP, ciprofloxacin; CN, gentamicin; CRO, ceftriaxone; CT, colistin; CTX, cefotaxime; ETP, ertapenem; FOX, cefoxitin; IPM, imipenem; SXT, trimethoprim–sulfamethoxazole; TIC, ticarcillin; TIM, ticarcillin–clavulanate acid; TOB, tobramycin. (B) Results of modified Carba NP test; colour change of sample revealed presence of lactamases. (C) List of antibiotic-resistant genes. (D) Circular map of chromosome. From outside to center: genes on forward and reverse strand rRNA and tRNA (green), GC content and GC skew.

Fig. 3

Proteomic comparison and in silico DNA-DNA hybridization between MARS15 strain and most closely related species. (A) Colour code referring to percentage of similarity of protein sequence. It refers to average of number of proteins with similarity ≥80% with Chryseobacterium indologenes MARS15 proteome. (B.1) Graphic representation of proteomic comparison between C. indologenes J31 and (B.2) C. indologenes NBRC 14944 and (B.3) Chryseobacterium spp. (C) Representation of prophage absence in other Chryseobacterium analysed.

Fig. 4

Modular organization of polyketide synthase in Chryseobacterium indologenes MARS15, C. indologenes NBRC 14944, C. indologenes STRB126 and Saccharopolispora erythraea NRRL 2338.