Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

Autor(es)

Borelli, Tiago Cabral ^[1] ; Lovate, Gabriel Lencioni ^[1] ; Scaranello, Ana Flavia Tonelli ^[1] ; Ribeiro, Lucas Ferreira ^[1] ; Zaramela, Livia ^[2] ; Pereira-dos-Santos, Felipe Marcelo ^[3] ; Silva-Rocha, Rafael ^[3] ; Guazzaroni, Maria-Eugenia ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, Dept Biol, Ave Bandeirantes 3900, BR-14049901 Ribeirao Preto, SP - Brazil

^[2] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92161 - USA

^[3] Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Cell & Mol Biol, Ave Bandeirantes 3900, BR-14049900 Ribeirao Preto, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: ANTIBIOTICS-BASEL; v. 10, n. 4 APR 2021.
• Citações Web of Science: 0

Resumo

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities. (AU)

• Processo FAPESP: 19/00390-0 - Resistoma e mobiloma em genomas de bactérias oriundas de diversas regiões brasileiras
• Beneficiário: Tiago Cabral Borelli
• Modalidade de apoio: Bolsas no Brasil - Mestrado
• Processo FAPESP: 15/04309-1 - Novas abordagens para melhorar a prospecção funcional de biocatalizadores em bibliotecas metagenômicas
• Beneficiário: María Eugenia Guazzaroni
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 19/06672-7 - Montagem de genoma para identificação de genes de resistência a antibióticos em isolados clínicos do Hospital das Clínicas de Ribeirão Preto
• Beneficiário: Murilo Henrique Anzolini Cassiano
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 16/18827-7 - Integrando engenharia de proteínas e biologia sintética para desenvolver novos sistemas de high-throughput selection
• Beneficiário: Lucas Ferreira Ribeiro
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 19/15675-0 - Desvendando a complexidade das redes de regulação gênica microbianas
• Beneficiário: Rafael Silva Rocha
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 18/18158-3 - Busca por determinantes da resistência a antibióticos no interior paulista utilizando metagenômica funcional
• Beneficiário: Gabriel Lencioni Lovate
• Modalidade de apoio: Bolsas no Brasil - Mestrado