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

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Damas, Marcelo Silva Folhas ; Ferreira, Roumayne Lopes ; Campanini, Emeline Boni ; Soares, Gabriela Guerrera ; Campos, Leslie Camelo ; Laprega, Pedro Mendes ; da Costa, Andrea Soares ; Freire, Caio Cesar de Melo ; Pitondo-Silva, Andre ; Cerdeira, Louise Teixeira ; da Cunha, Anderson Ferreira ; Pranchevicius, Maria-Cristina da Silva

• Document type: Journal article
• Source: FRONTIERS IN MEDICINE; v. 9, p. 20-pg., 2022-07-28.

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 beta-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 beta-lactamases (bla(IND-13), bla(CIA-3), bla(TEM-116), bla(OXA-209), bla(VEB-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. (AU)

• FAPESP's process: 18/24213-7 - Analysis of the presence of virulence and resistance genes encoding antibiotic resistance and virulence determinants in S. marcescens and identification of vaccine candidates against S. marcescens using reverse vaccinology
• Grantee: Marcelo Silva Folhas Damas
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 21/08423-4 - Characterization of multidrug-resistant Brevundimonas isolated from intensive-care-unit patient sample using whole-genome sequencing
• Grantee: Gabriela Guerrera Soares
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 20/11964-4 - Characterization molecular and phenotypic of opportunistic bacteria: development of vaccines and drugs using subtractive proteomics
• Grantee: Maria Cristina da Silva Pranchevicius
• Support Opportunities: Regular Research Grants
• FAPESP's process: 18/20697-0 - Selection and directed evolution of yeasts - Identification and analysis of important metabolic pathways for application in the bioethanol and fermented beverage industries.
• Grantee: Anderson Ferreira da Cunha
• Support Opportunities: Regular Research Grants
• FAPESP's process: 21/00425-8 - Production of human recombinant Peptidoglycan recognition protein (rPGLYRP3) and antimicrobial peptide (AMP-rPGLYRP3) in Pichia pastoris and analysis of antibacterial activity in opportunistic strains
• Grantee: Pedro Mendes Laprega
• Support Opportunities: Scholarships in Brazil - Scientific Initiation