High-throughput genome sequencing of Enterobacteriaceae resistance plasmids isolated from poultry

• Grant number: 17/26311-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: March 18, 2018
• End date: September 17, 2018
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Ana Lúcia da Costa Darini
• Grantee: Renata Galetti
• Supervisor: Lars Jelsbak
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Institution abroad: Technical University of Denmark (DTU), Denmark
• Associated to the scholarship: 15/11728-0 - 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, BP.PD

Abstract

Enterobacteriaceae bacterial family has become increasingly important in human and animal infections. According to the Ministry of Agriculture, Livestock and Supply, Brazil is the main exporter of broiler chicken in the world, making chicken farming one of the main economic activities in Brazil. The research of pathogenic and antibiotic-resistant bacteria isolated from chicken meat has an important impact on public health aiming at the risk of dissemination of these bacteria via the food chain. Based on these problems, it has become increasingly important to study and investigate these bacteria, since the indiscriminate use of antibiotics in recent decades has selected multidrug antibiotic resistant isolates. The aim of this study is to sequence and analyse the whole genome of Enterobacteriaceae (Salmonella sp. and Enterobacter sp.) harbouring plasmids carrying several different resistance genes, with clinical and veterinary importance. Whole genome sequencing of Enterobacteriaceae isolates will be performed using the Illumina (©Illumina) and/or Pacbio (Pacific Bioscience) platforms. De novo assembly will be carried out using a CLC Genomics Workbench 8.0 and SMRT Analysis Software. Gene prediction will be performed for the whole genome sequence of each isolate using the Prokka pipeline and RAsT Server. The annotation will be manually curate using BLASTN and BLASTP homology search. The investigation of particularities in each genome sequence will be done using additional tools provided by Center for Genomic Epidemiology

Scientific publications

(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; 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; 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)