AUTHOR=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 

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

JOURNAL=Frontiers in Medicine

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2022.931379

DOI=10.3389/fmed.2022.931379

ISSN=2296-858X

ABSTRACT=<p>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 <italic>C. indologenes</italic> 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 <italic>C. indologenes</italic> 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, <italic>C. indologenes</italic> 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 <italic>C. indologenes</italic> revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (<italic>bla</italic><sub><italic>IND–</italic>13</sub>, <italic>bla</italic><sub><italic>CIA–</italic>3</sub>, <italic>bla</italic><sub><italic>TEM–</italic>116</sub>, <italic>bla</italic><sub><italic>OXA–</italic>209</sub>, <italic>bla</italic><sub><italic>VEB–</italic>15</sub>), quinolone (<italic>mcb</italic>G), tigecycline (<italic>tet</italic>(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (<italic>Ran</italic>A/<italic>Ran</italic>B), and colistin (<italic>Hly</italic>D/<italic>Tol</italic>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). <italic>Chryseobacterium indologenes</italic> 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 <italic>C. indologenes</italic> 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 <italic>C. indologenes</italic>, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.</p>