Study of resistance, virulence and epidemiological profile of Escherichia coli isolated from environment

• Grant number: 18/01890-3
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: August 01, 2019
• End date: April 30, 2022
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Eliana Guedes Stehling
• Grantee: João Pedro Rueda Furlan
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Bacterial resistance is a frequent problem in the hospital environment. Increased resistance among members of the Enterobacteriaceae family has resulted in the emergence of multidrug-resistant species, which represent an important public health problem. Among the enterobacteria, the most commonly reported in hospital infections are Escherichia coli, which belongs to the commensal microbiota and may act as an opportunistic pathogen, especially in immunocompromised patients. Different classes of antimicrobials can be used to treat infections caused by this pathogen, including the ²-lactams, quinolones and fluoroquinolones, tetracyclines, aminoglycosides, folate pathway inhibitors, phenicols and polymyxins. Several virulence factors are correlated to the pathogenicity of this bacterium, including toxins and hemolysins. The objective of this research project is to characterize 100 Escherichia coli isolates obtained from the environment regarding antimicrobial resistance, virulence, clonal relationship and epidemiology. Among the 100 isolates, 64 isolates were classified as Multidrug-Resistant (MDR), presenting non-susceptibility mainly to ampicillin (89%), streptomycin (75%), cefazoline and cefuroxime (67%), trimethoprim + sulfamethoxazole, sulfonamide and trimethoprim (52%). Seven isolates have already been characterized for resistance genes, plasmid typing and virulence. The resistance genes blaCMY, blaOXA-1-like, blaSHV, tetA, tetB were detected in all isolates, followed by the sul1 (4), sul2 (3), aadA (3), sul2, aac(6 ')-Ib (2) and floR (1). According to the plasmid typing, IncF, IncY and ColE-like were detected in all isolates, followed by IncFIB (6), IncFIA (1), IncFIC (1), IncHI1 (1) and IncN (1). Among the virulence genes, the ipaH gene was the most prevalent, being detected in four isolates, followed by the stx2 gene (n = 1). Thus, these isolates were classified into two different pathotypes, being EIEC and STEC, respectively. Two isolates did not present any of the virulence genes investigated. MLST analysis was performed on six of the seven previously characterized isolates, and six different STs (ST10/CC10, ST942, ST1684, ST2600, ST6658 and ST8067) were detected. Two isolates from the soil were characterized by the whole genome sequencing, which presented several genes of resistance, virulence and plasmids. (AU)

Scientific publications

(29)

(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)

NAKAMURA-SILVA, RAFAEL; OLIVEIRA-SILVA, MARIANA; RUEDA FURLAN, JOAO PEDRO; STEHLING, ELIANA GUEDES; SARAIVA MIRANDA, CARLOS EDUARDO; PITONDO-SILVA, ANDRE. Characterization of multidrug-resistant and virulent Klebsiella pneumoniae strains belonging to the high-risk clonal group 258 (CG258) isolated from inpatients in northeastern Brazil. Archives of Microbiology, JUN 2021. (18/01890-3)

FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; RAMOS, MICAELA SANTANA; GALLO, INARA FERNANDA LAGE; MORETTO, JESSICA APARECIDA SILVA; STEHLING, ELIANA GUEDES. ccurrence of clinically relevant antimicrobial resistance genes, including mcr-3 and mcr-7.1, in soil and water from a recreation clu. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH, v. 32, n. 4, AUG 2020. (18/01890-3)

NAKAMURA-SILVA, RAFAEL; OLIVEIRA-SILVA, MARIANA; RUEDA FURLAN, JOAO PEDRO; STEHLING, ELIANA GUEDES; SARAIVA MIRANDA, CARLOS EDUARDO; PITONDO-SILVA, ANDRE. Characterization of multidrug-resistant and virulent Klebsiella pneumoniae strains belonging to the high-risk clonal group 258 (CG258) isolated from inpatients in northeastern Brazil. Archives of Microbiology, v. 203, n. 7, p. 4351-4359, SEP 2021. (18/01890-3)

DOS SANTOS, L. D. R.; FURLAN, J. P. R.; GALLO, I. F. L.; RAMOS, M. S.; SAVAZZI, E. A.; STEHLING, E. G.. Occurrence of multidrug-resistant Enterococcus faecium isolated from environmental samples. Letters in Applied Microbiology, v. 73, n. 2, p. 237-246, AUG 2021. (18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; LAGE GALLO, INARA FERNANDA; DE CAMPOS, TATIANA AMABILE; STEHLING, ELIANA GUEDES. Genomic Characterization of a Multidrug-Resistant and Hypermucoviscous/Hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae ST4417 Isolated from a Sewage Treatment Plant. MICROBIAL DRUG RESISTANCE, v. 26, n. 11, JAN 2020. (18/01890-3, 18/19539-0)

SILVA MORETTO, JESSICA APARECIDA; RUEDA FURLAN, JOAO PEDRO; BRAZ, VANIA SANTOS; BITENCOURT, TAMIRES APARECIDA; STEHLING, ELIANA GUEDES. Presence of bla(OXA-48)-carrying IncF plasmid in an Escherichia fergusonii strain isolated from a sugarcane soil. Pedosphere, v. 30, n. 2, p. 293-294, APR 2020. (18/01890-3, 18/19539-0)

GONCALVES DE ALMEIDA, AVIO GUILHERME; RUEDA FURLAN, JOAO PEDRO; STEHLING, ELIANA GUEDES; PEREIRA DE MARTINIS, ELAINE CRISTINA. Comparative phylo-pangenomics reveals generalist lifestyles in representative Acinetobacter species and proposes candidate gene markers for species identification. Gene, v. 791, JUL 30 2021. (18/01890-3)

LOPES, RALF; FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; GALLO, INARA FERNANDA LAGE; STEHLING, ELIANA GUEDES. Colistin-Resistant mcr-1-Positive Escherichia coli ST131-H22 Carrying bla(CTX-M-15) and qnrB19 in Agricultural Soil. FRONTIERS IN MICROBIOLOGY, v. 12, APR 9 2021. (18/01890-3, 18/19539-0)

FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; RAMOS, MICAELA SANTANA; GALLO, INARA FERNANDA LAGE; MORETTO, JESSICA APARECIDA SILVA; STEHLING, ELIANA GUEDES. Occurrence of clinically relevant antimicrobial resistance genes, including mcr-3 and mcr-7.1, in soil and water from a recreation club. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH, v. 32, n. 4, p. 10-pg., 2020-08-01. (18/01890-3)

RUEDA FURLAN, JOAO PEDRO; STEHLING, ELIANA GUEDES. Molecular characterization of an extensively drug-resistant Acinetobacter baumannii isolated from a corn culture soil. Pedosphere, v. 31, n. 6, p. 973-976, OCT 2021. (18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; RODRIGUES DOS SANTOS, LUCAS DAVID. Presence of Colistin Resistancemcr-4Gene and Clinically Relevant Antimicrobial Resistance Genes in Sand Samples from a Public Beach. WATER AIR AND SOIL POLLUTION, v. 231, n. 7, JUN 17 2020. (18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; GONCALVES DE ALMEIDA, OTAVIO GUILHERME; PEREIRA DE MARTINIS, ELAINE CRISTINA; STEHLING, ELIANA GUEDES. Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants. FRONTIERS IN MICROBIOLOGY, v. 10, SEP 18 2019. (18/01890-3, 18/19539-0, 17/13759-6)

RUEDA FURLAN, JOAO PEDRO; ROSA, RAFAEL DA SILVA; RAMOS, MICAELA SANTANA; RODRIGUES DOS SANTOS, LUCAS DAVID; LOPES, RALF; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Genetic plurality of bla(KPC-2)-harboring plasmids in high-risk clones of Klebsiella pneumoniae of environmental origin. Science of The Total Environment, v. 881, p. 8-pg., 2023-04-19. (21/01655-7, 18/01890-3)

FURLAN, JOAO PEDRO RUEDA; RAMOS, MICAELA SANTANA; DOS SANTOS, LUCAS DAVID RODRIGUES; ROSA, RAFAEL DA SILVA; STEHLING, ELIANA GUEDES. Multidrug-resistant Shiga toxin-producing Escherichia coli and hybrid pathogenic strains of bovine origin. VETERINARY RESEARCH COMMUNICATIONS, v. N/A, p. 7-pg., 2023-05-18. (18/01890-3)

FURLAN, JOAO PEDRO RUEDA; RIBEIRO, TERESA GONSALVES; NOVAIS, ANGELA; CABRAL, HAMILTON; PEIXE, LUISA; STEHLING, ELIANA GUEDES. Citrobacter meridianamericanus sp. nov., isolated from a soil sample. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, v. 73, n. 3, p. 5-pg., 2023-01-01. (21/01655-7, 18/01890-3, 20/14426-3)

ROSA, RAFAEL DA SILVA; FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; RAMOS, MICAELA SANTANA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Early dissemination of novel NDM-1-producing Klebsiella pneumoniae ST6326 to the environment. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 34, p. 2-pg., 2023-09-01. (21/01655-7, 18/01890-3)

LOPES, RALF; FURLAN, JOAO PEDRO RUEDA; STEHLING, ELIANA GUEDES. Acquisition of bla(IMP-13) on a novel IncP-7 plasmid in XDR VIM-2-positive Pseudomonas aeruginosa belonging to the global high-risk clone ST235 in an agricultural ecosystem. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 30, p. 3-pg., 2022-08-22. (18/01890-3, 21/01655-7)

FURLAN, JOAO PEDRO RUEDA; RAMOS, MICAELA SANTANA; ROSA, RAFAEL DA SILVA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Occurrence and genetic characteristics of multidrug-resistant Escherichia coli isolates co-harboring antimicrobial resistance genes and metal tolerance genes in aquatic ecosystems. INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH, v. 244, p. 8-pg., 2022-06-29. (18/01890-3, 21/01655-7)

LOPES, RALF; FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; STEHLING, ELIANA GUEDES. Detection of CTX-M-27-positive endophytic Escherichia coli ST131 lineage C1/H30R subclade carrying bla(KPC-2) on an IncX3-IncU plasmid in a fresh vegetable. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 30, p. 2-pg., 2022-07-11. (18/01890-3, 21/01655-7)

DE MELO, FERNANDA MACIEL; RUEDA FURLAN, JOAO PEDRO; SANCHEZ, DANILO GARCIA; LAGE GALLO, INARA FERNANDA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Dispersion of merA and catabolic genes in Brazilian water sources. ECOLOGICAL INDICATORS, v. 108, JAN 2020. (18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; LOPES, RALF; STEHLING, ELIANA GUEDES. Whole-genome sequence-based analysis of the Paenibacillus aquistagni strain DK1, a polyethylene-degrading bacterium isolated from landfill. WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, v. 37, n. 5, MAY 2021. (18/01890-3)

FURLAN, JOAO PEDRO RUEDA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Widespread high-risk clones of multidrug-resistant extended-spectrum beta-lactamase-producing Escherichia coli B2-ST131 and F-ST648 in public aquatic environments. INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS, v. 56, n. 1, JUL 2020. (18/01890-3)

RUEDA FURLAN, JOAO PEDRO; LAGE GALLO, INARA FERNANDA; STEHLING, ELIANA GUEDES. enomic characterization of multidrug-resistant extraintestinal pathogenic Escherichia coli isolated from grain culture soil. Pedosphere, v. 32, n. 3, p. 495-502, JUN 2022. (18/19539-0, 18/01890-3)

RUEDA FURLAN, JOAO PEDRO; LOPES, RALF; RAMOS, MICAELA SANTANA; RODRIGUES DOS SANTOS, LUCAS DAVID; ROSA, RAFAEL DA SILVA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Colistin-resistant mcr-1-positive Escherichia coli ST1775-H137 co-harboring bla(CTX-M-2) and bla(CMY-2) recovered from an urban stream. INFECTION GENETICS AND EVOLUTION, v. 96, DEC 2021. (18/01890-3, 18/19539-0)

RAMOS, MICAELA SANTANA; RUEDA FURLAN, JOAO PEDRO; LAGE GALLO, INARA FERNANDA; RODRIGUES DOS SANTOS, LUCAS DAVID; DE CAMPOS, TATIANA AMABILE; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. High Level of Resistance to Antimicrobials and Heavy Metals in Multidrug-Resistant Pseudomonas sp. Isolated from Water Sources. Current Microbiology, v. 77, n. 10, MAY 2020. (18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; RODRIGUES DOS SANTOS, LUCAS DAVID; SILVA MORETTO, JESSICA APARECIDA; RAMOS, MICAELA SANTANA; LAGE GALLO, INARA FERNANDA; DIAS ALVES, GEORGIA DE ASSIS; PAULELLI, ANA CAROLINA; DE SOUZA ROCHA, CECILIA CRISTINA; CESILA, CIBELE APARECIDA; GALLIMBERTI, MATHEUS; et al. Occurrence and abundance of clinically relevant antimicrobial resistance genes in environmental samples after the Brumadinho dam disaster, Brazil. Science of The Total Environment, v. 726, JUL 15 2020. (18/24069-3, 18/01890-3, 18/19539-0)

RUEDA FURLAN, JOAO PEDRO; LOPES, RALF; LIMA GONZALEZ, IRYS HANY; RAMOS, PATRICIA LOCOSQUE; STEHLING, ELIANA GUEDES. Comparative analysis of multidrug resistance plasmids and genetic background of CTX-M-producing Escherichia coli recovered from captive wild animals. Applied Microbiology and Biotechnology, v. 104, n. 15, JUN 2020. (18/01890-3)

FURLAN, JOAO PEDRO RUEDA; LOPES, RALF; STEHLING, ELIANA GUEDES. Multidrug resistance IncC plasmid carrying bla(CMY-97) in Shiga toxin-producing Escherichia coli ST215-H54 of ovine origin. INFECTION GENETICS AND EVOLUTION, v. 93, SEP 2021. (18/19539-0, 18/01890-3)

RAMOS, MICAELA SANTANA; FURLAN, JOAO PEDRO RUEDA; DOS SANTOS, LUCAS DAVID RODRIGUES; ROSA, RAFAEL DA SILVA; SAVAZZI, EDUARDO ANGELINO; STEHLING, ELIANA GUEDES. Patterns of antimicrobial resistance and metal tolerance in environmental Pseudomonas aeruginosa isolates and the genomic characterization of the rare O6/ST900 clone. ENVIRONMENTAL MONITORING AND ASSESSMENT, v. 195, n. 6, p. 14-pg., 2023-06-01. (18/01890-3)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

FURLAN, João Pedro Rueda. Molecular characterization of multidrug-resistant Escherichia coli isolates obtained from the environment. 2022. Doctoral Thesis - Universidade de São Paulo (USP). Faculdade de Ciências Farmacêuticas de Ribeirão Preto (PCARP/BC) Ribeirão Preto.