Complete sequencing of plasmids carrying antibiotic resistance genes in bacteria of interest and genome analysis of Pseudomonas aeruginosa-producing SPM-1 and KPC-2 lines by large-scale sequencing

• Grant number: 15/11728-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: August 01, 2015
• End date: April 06, 2019
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Ana Lúcia da Costa Darini
• Grantee: Renata Galetti
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 14/14494-8 - Molecular epidemiology of gram-negative bacteria and genetic of antibiotic resistance, AP.TEM
• Associated scholarship(s): 17/26311-3 - High-throughput genome sequencing of Enterobacteriaceae resistance plasmids isolated from poultry, BE.EP.PD

Abstract

Nowadays, the main mechanism of resistance to antibiotics in gram-negative bacteria is the production of enzymes that degrade antibiotics, highlighting the beta-lactamase. Most beta-lactamase genes encoding are inserted in mobile genetic elements (MGE- Mobile Genetic Elements -Integrons, transposons, and insertion sequences) carried or not by plasmids. Sequencing of complete genome and bacterial plasmid allows knowledge of their entire gene content, such as MGE, resistance genes and virulence genes carried by epidemic strains. New generation sequencing are available and provide accurate sequencing of these genomes at a relatively low cost. Objectives: Sequence and annotation of draft genome of two strains of P. aeruginosa, one carrying blaSPM-1 gene and other carrying blaKPC-2 gene, identify the possible presence of MGE, virulence and pathogenicity islands in each of these genomes and identify probable presence of plasmids inserted in the chromosome of these P. aeruginosa, and/or analyze the presence of "scar" that indicate how and how often transposable elements were inserted and/or excised from the bacterial chromosome; Complete sequencing of plasmid not typeable by conventional techniques or major epidemiological concern that carrying resistance genes in gram-negative bacteria of clinical and/or veterinarian interest; To compare the sequenced plasmids of this project with the plasmids deposited in public databases. Materials and Methods: Selection of genomes and plasmids: Two draft genomes of P. aeruginosa strains previously characterized in our laboratory, P. aeruginosa HC84 carrying blaSPM-1 gene from Hospital das Clinicas-Ribeirao Preto in 2007 and P. aeruginosa BH6 carrying the blaKPC-2 gene from hospital-Belo Horizonte in 2012. Approximately 4-6 plasmids non-typable will be selected for complete sequencing from enterobacteria and/or gram-negative non-fermenting. Those plasmids carrying more than one resistance gene and those in epidemiologically important bacteria may also be selected. Sequencing of genome and plasmids: plasmideal DNA will be extracted using the PureLinkTM HiPure Plasmid Filter Midiprep (Invitrogen) and experiments of electroporation and/or conjugation will be realized in selected isolates, when necessary, using techniques already described. The sequencing will be carried out using Illumina platform MiSeq (Illumina, Inc. Assembly and annotation of genomes and plasmids: The quality of the sequencing will be checked using the FastQC program (Babraham Bioinformatics) and the assembly 'denovo' will be performed using the Velvet program (European Bioinformatics Institute (EMBL-EBI). The union of contigs will be confirmed by PCR followed by sequencing by the Sanger method. Then, the data will be analyzed using Prokka tool and CLC Genomics Workbench (CLCbio, Qiagen), the softwares Artemis Version 8 (Sanger Institute) and Sequin. The confirmation and validation of ORFs will be held using BLASTN and BLASTP. Project Execution: The performance of sequencing analysis will be carried out at the Laboratório Especial de Bacteriologia e Epidemiologia Molecular-LEBEM by the selected postdoctoral researcher. For sequencing analysis support, Dr. Alessandra Carattoli, researcher at the Istituto Superiore di Sanita, Rome, IT, and Dr. Alessandro de Mello Varani, Researcher III of the Department of Technology Faculty of Agriculture and Veterinary Sciences - UNESP will be consulted. Expected results: It is expected, with the conclusion of these projects, unravels the genome of two strains of P. aeruginosa and completely sequenced plasmids carrying carbapenemases genes. (AU)

Scientific publications

(10)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

GALETTI, RENATA; CASARIN PENHA FILHO, RAFAEL ANTONIO; FERREIRA, JOSEANE CRISTINA; VARANI, ALESSANDRO M.; COSTA DARINI, ANA LIICIA. Antibiotic resistance and heavy metal tolerance plasmids: the antimicrobial bulletproof properties of Escherichia fergusonii isolated from poultry. INFECTION AND DRUG RESISTANCE, v. 12, p. 1029-1033, 2019. (15/11728-0, 14/14494-8, 16/12293-0)

CACADOR, NATALIA CANDIDO; DA COSTA CAPIZZANI, CAROLINA PAULINO; MONTEIRO MARIN TORRES, LFDIA ALICE GOMES; GALETTI, RENATA; CIOFU, OANA; DA COSTA DARINI, ANA LTICIA; FLEFIBY, NIELS. Adaptation of Pseudomonas aeruginosa to the chronic phenotype by mutations in the algTmucABD operon in isolates from Brazilian cystic fibrosis patients. PLoS One, v. 13, n. 11, NOV 29 2018. (13/13455-6, 15/11728-0, 14/14494-8, 13/13358-0)

BALLABEN, ANELISE STELLA; GALETTI, RENATA; ANDRADE, LEONARDO NEVES; FERREIRA, JOSEANE CRISTINA; GARCIA, DOROTI DE OLIVEIRA; DA SILVA, PAULO; DOI, YOHEI; COSTA DARINI, ANA LUCIA. Plasmid Carrying bla(CTX-M-2) and bla(GES-1) in Extensively Drug-Resistant Pseudomonas aeruginosa from Cerebrospinal Fluid. Antimicrobial Agents and Chemotherapy, v. 63, n. 7, JUL 2019. (15/23484-9, 14/14494-8, 15/11728-0)

GALETTI, RENATA; ANDRADE, LEONARDO NEVES; SAZINAS, PAVELAS; JELSBAK, LARS; DARINI, ANA LUCIA COSTA. pST15-IncHI2 plasmids co-harboring mcr-9 and several other antibiotic resistance genes in heavy metal tolerant Enterobacter cloacae complex isolates from hospital infections. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 31, p. 2-pg., 2022-10-07. (14/14494-8, 17/26311-3, 15/11728-0)

GALETTI, RENATA; ANDRAD, LEONARDO NEVES; VARANI, ALESSANDRO M.; COSTA DARINI, ANA LUCIA. SPM-1-producing Pseudomonas aeruginosa ST277 carries a chromosomal pack of acquired resistance genes: An example of high-risk clone associated with 'intrinsic resistome'. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 16, p. 4-pg., 2019-03-01. (15/11728-0, 14/14494-8)

BALLABEN, ANELISE STELLA; GALETTI, RENATA; FERREIRA, JOSEANE CRISTINA; PAZIANI, MARIO HENRIQUE; KRESS, MARCIA REGINA VON ZESKA; GARCIA, DOROTI DE OLIVEIRA; DA SILVA, PAULO; DOI, YOHEI; DARINI, ANA LUCIA COSTA; ANDRADE, LEONARDO NEVES. Different virulence genetic context of multidrug-resistant CTX-M- and KPC-producing Klebsiella pneumoniae isolated from cerebrospinal fluid. DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, v. 104, n. 3, p. 5-pg., 2022-08-19. (15/11728-0, 14/14494-8, 15/23484-9)

BALLABEN, ANELISE S.; ANDRADE, LEONARDO N.; GALETTI, RENATA; FERREIRA, JOSEANE C.; MCELHENY, CHRISTI L.; METTUS, ROBERTA T.; DA SILVA, PAULO; GARCIA, DOROTI DE OLIVEIRA; DARINI, ANA LUCIA C.; DOI, YOHEI. Diversity of High-Level Aminoglycoside Resistance Mechanisms among Gram-Negative Nosocomial Pathogens in Brazil. Antimicrobial Agents and Chemotherapy, v. 62, n. 11, NOV 2018. (15/23484-9, 17/11707-9, 15/11728-0, 14/14494-8)

GALETTI, RENATA; ANDRADE, LEONARDO NEVES; VARANI, ALESSANDRO M.; COSTA DARINI, ANA LUCIA. A Phage-Like Plasmid Carrying bla(KPC-2) Gene in Carbapenem-Resistant Pseudomonas aeruginosa. FRONTIERS IN MICROBIOLOGY, v. 10, MAR 20 2019. (14/14494-8, 15/11728-0)

GALETTI, RENATA; CASARIN PENHA FILHO, RAFAEL ANTONIO; FERREIRA, JOSEANE CRISTINA; VARANI, ALESSANDRO M.; SAZINAS, PAVELAS; JELSBAK, LARS; COSTA DARINI, ANA LUCIA. The plasmidome of multidrug-resistant emergent Salmonella serovars isolated from poultry. INFECTION GENETICS AND EVOLUTION, v. 89, APR 2021. (15/11728-0, 17/26311-3, 14/14494-8)

BALLABEN, ANELISE STELLA; GALETTI, RENATA; ANDRADE, LEONARDO NEVES; FERREIRA, JOSEANE CRISTINA; GARCIA, DOROTI DE OLIVEIRA; DOI, YOHEI; COSTA DARINI, ANA LUCIA. Extensively drug-resistant IMP-16-producing Pseudomonas monteilii isolated from cerebrospinal fluid. INFECTION GENETICS AND EVOLUTION, v. 87, JAN 2021. (14/14494-8, 15/11728-0, 15/23484-9)