Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil

Abstract

Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.

Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil

“…Babies are more vulnerable to colonization and infection with pathogens due to an immature immune system. Novel molecular and phenotypic methods are providing more accurate and robust identification of these pathogens ( 28 – 30 ).…”

“…The penP gene encodes a narrow-spectrum β-lactamase that displays a more effective hydrolysis only of first—and second—generation penicillins and cephalosporins ( 44 – 46 ). The bla TEM-116 gene has been reported in a variety of clinical isolates ( 28 , 47 ). Studies have related that TEM-116 β-lactamase can confer resistance to ceftazidime, cefotaxime, and aztreonam ( 48 , 49 ).…”

“…Resistance to quinolones is frequently acquired by mutations in the quinolone resistance-determining regions (QRDRs) of the target genes, such as gyrA , gyrB , parC , and parE ( 28 , 63 ). Our strain displayed a double amino acid substitution in GyrA, serine to leucine at codon 83, and aspartic acid to histidine at 87 (GyrA-S83L-D87H).…”

Novel Antibiotic Resistance Genes Identified by Functional Gene Library Screening in Stenotrophomonas maltophilia and Chryseobacterium spp. Bacteria of Soil Origin

“…Although genus Chryseobacterium is composed of more than 130 species [ 50 ], the majority of information about Chryseobacterium antibiotic resistance has been obtained from three main human-infecting species: C. indologenes , C. meningosepticum , and C. gleum [ 51 ]. Clinical Chryseobacterium isolates are known to be highly resistant to most β-lactam agents, aminoglycosides, tetracyclines, macrolides, chloramphenicol, erythromycin, and ticarcillin-clavulanate [ 11 , 26 , 52 , 53 ]. Information about the resistance of the environmental Chryseobacterium spp.…”

“…However, no specific Chryseobacterium proteins responsible for tetracycline resistance have been confirmed yet. Chryseobacterium resistance to aminoglycosides is also well documented [ 11 ]; efflux pumps and antibiotic-modifying enzymes have been shown to be coded in sequenced Chryseobacterium genomes [ 53 , 60 ]. In this study, we found Chryseobacterium streptomycin resistance gene ant(6) , which is widespread in genus Chryseobacterium .…”