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

• Published in: Frontiers in medicine Vol. 9; p. 931379
• Main Authors: Damas, Marcelo Silva Folhas, Ferreira, Roumayne Lopes, Campanini, Emeline Boni, Soares, Gabriela Guerrera, Campos, Leslie Camelo, Laprega, Pedro Mendes, Soares da Costa, Andrea, Freire, Caio César de Melo, Pitondo-Silva, André, Cerdeira, Louise Teixeira, Cunha, Anderson Ferreira da, Pranchevicius, Maria-Cristina da Silva
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 28-07-2022
• Subjects: Chryseobacterium indologenes; Medicine; metabolic features; mobile genetic elements; neonatal intensive care unit; virulence and resistance genes; whole-genome sequencing
• ISSN: 2296-858X; 2296-858X
• DOI: 10.3389/fmed.2022.931379

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 (
bla
IND–
13
,
bla
CIA–
3
,
bla
TEM–
116
,
bla
OXA–
209
,
bla
VEB–
15
), quinolone (
mcb
G), tigecycline (
tet
(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (
Ran
A/
Ran
B), and colistin (
Hly
D/
Tol
C). 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.