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

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Soares, Gabriela Guerrera ; Campanini, Emeline Boni ; Ferreira, Roumayne Lopes ; Damas, Marcelo Silva Folhas ; Rodrigues, Saulo Henrique ; Campos, Leslie Camelo ; Galvao, Jucimaria Dantas ; Fuentes, Andrea Soares da Costa ; Freire, Caio Cesar de Melo ; Malavazi, Iran ; Pitondo-Silva, Andre ; da Cunha, Anderson Ferreira ; Pranchevicius, Maria-Cristina da Silva

• Document type: Journal article
• Source: MICROBIOLOGY SPECTRUM; v. 11, n. 3, p. 21-pg., 2023-04-17.

Abstract

To increase knowledge on Brevundimonas pathogens, we conducted indepth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to beta-lactams (penP, bla(TEM-16), and bla(BKC-1)) and aminoglycosides [strA, strB, aac(6 ')-Ib, and aac(6 ')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas. (AU)

• 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: 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: 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: 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