Comparative analysis of the resistome of Klebsiella pneumoniae XDR (NDM-1/KPC-2) belonging to the endemic high-risk clonal complex CC258

• Grant number: 15/21325-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): March 01, 2016
• Effective date (End): November 03, 2018
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Nilton Erbet Lincopan Huenuman
• Grantee: Louise Teixeira Cerdeira
• Host Institution: Faculdade de Ciências Farmacêuticas (FCF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 17/25909-2 - Comparative genomic analysis of Klebsiella pneumoniae belonging to the endemic high-risk clonal complex CC258 (ST11, ST437, ST340, ST258) in the Human-Animal-Environment Interface in Brazil, BE.EP.DR

Abstract

The dissemination of Klebsiella pneumoniae strains showing a multidrug-resistant (MDR) or extreme drug resistance (XDR) profile is a worldwide issue that for countries with a high prevalence of infection it has acquired an endemic character. In Brazil, previous studies have shown that endemic genotypes, within many hospitals in the country, are associated with the production of KPC-2-type carbapenemases, with a rapid adaptation of high-risk clonal complexes (CCs) (eg., CC258). Additionally, to make matters worse for public health, recent studies have reported the presence of these clonal complexes in urban aquatic environments and food-producing animals. Most likely the genetic versatility of CC258 has contributed in this process of adaptation and persistence in the different ecosystems, so far studied, indeed, strains belonging to CC258 are largely considered responsible for the global spread of KPC. This study aims to conduct a pan-resistoma comparative analysis of K. pneumoniae XDR strains (NDM-1/KPC-2), belonging to the high-risk clonal complex CC258, endemic in Brazil. Strains of K. pneumoniae KPC-2/ST340, previously isolated from clinical cases, urban aquatic environments and farm animals will be subjected to complete genome sequencing with subsequent analysis of the pan-resistoma using complete and draft genome sequences, previuosly published, and different strategies and bioinformatics tools for assembly and analysis. The results may contribute to creating a platform that can be used by several researchers, for purposes of diagnosis, therapeutic and epidemiological control, among others; elucidating "a priori" genetic aspects of adaptation, antimicrobial resistance and virulence of this endemic clone.

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)

FERNANDES, MIRIAM R.; CERDEIRA, LOUISE; SILVA, MEIRE M.; SELLERA, FABIO P.; MUNOZ, MARIA; JUNIOR, FELICIO G.; AZEVEDO, SERGIO S.; POWER, PABLO; GUTKIND, GABRIEL; LINCOPAN, NILTON. Novel mcr-5.3 variant in a CTX-M-8-producing Escherichia coli ST711 isolated from an infected horse. Journal of Antimicrobial Chemotherapy, v. 73, n. 12, p. 3520-3522, DEC 2018. (16/08593-9, 15/21325-0, 15/13527-2)

LOPES, RALF; FUENTES-CASTILLO, DANNY; FONTANA, HERRISON; RODRIGUES, LARISSA; DANTAS, KARINE; CERDEIRA, LOUISE; HENRIQUES, ISABEL; LINCOPAN, NILTON. Endophytic Lifestyle of Global Clones of Extended-Spectrum beta-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?. MSYSTEMS, v. 6, n. 1, JAN-FEB 2021. (16/08593-9, 15/21325-0)

SELLERA, ABIO P.; FERNANDES, MIRIAM R.; RUIZ, REGINA; FALLEIROS, ANA C. M.; RODRIGUES, FERNANDA P.; CERDEIRA, LOUISE; LINCOPAN, NILTON. Identification of KPC-2-producing Escherichia coli in a companion animal: a new challenge for veterinary clinicians. Journal of Antimicrobial Chemotherapy, v. 73, n. 8, p. 2259-2261, AUG 2018. (16/08593-9, 15/21325-0, 15/13527-2)

FUGA, BRUNA; FERREIRA, MELINA LORRAINE; CERDEIRA, LOUISE TEIXEIRA; DE CAMPOS, PAOLA AMARAL; DIAS, VINICIUS LOPES; ROSSI, IARA; MACHADO, LUIZ GUSTAVO; LINCOPAN, NILTON; GONTIJO-FILHO, PAULO PINTO; RIBAS, ROSINEIDE MARQUES. Novel small IncX3 plasmid carrying the bla(KPC-2) gene in high-risk Klebsiella pneumoniae ST11/CG258. DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, v. 96, n. 2, FEB 2020. (15/21325-0)

CUNHA, MARCOS P. V.; LINCOPAN, NILTON; CERDEIRA, LOUISE; ESPOSITO, FERNANDA; DROPA, MILENA; FRANCO, LETICIA S.; MORENO, ANDREA M.; KNOEBL, TEREZINHA. Coexistence of CTX-M-2, CTX-M-55, CMY-2, FosA3, and QnrB19 in Extraintestinal Pathogenic Escherichia coli from Poultry in Brazil. Antimicrobial Agents and Chemotherapy, v. 61, n. 4, APR 2017. (14/11523-7, 16/12641-9, 15/21325-0)

CERDEIRA, LOUISE T.; LAM, MARGARET M. C.; WYRES, KELLY L.; WICK, RYAN R.; JUDD, LOUISE M.; LOPES, RALF; RIBAS, ROSINEIDE M.; MORAIS, MARCIA M.; HOLT, KATHRYN E.; LINCOPAN, NILTON. Small IncQ1 and Col-Like Plasmids Harboring bla(KPC-2) and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258. Antimicrobial Agents and Chemotherapy, v. 63, n. 3, MAR 2019. (16/08593-9, 15/21325-0, 17/25909-2)

MARTINS, EVELIN RODRIGUES; CAMPAGNARI BUENO, MARIA FERNANDA; FRANCISCO, GABRIELA RODRIGUES; CASELLA, TIAGO; GARCIA, DOROTI DE OLIVEIRA; CERDEIRA, LOUISE TEIXEIRA; GERBER, ALEXANDRA LEHMKUHL; PAULA DE ALMEIDA, LUIZ GONZAGA; LINCOPAN, NILTON; RIBEIRO DE VASCONCELOS, ANA TEREZA; et al. Genome and plasmid context of two rmtG-carrying Enterobacter hormaechei isolated from urinary tract infections in Brazil. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 20, p. 36-40, MAR 2020. (14/17184-0, 15/21325-0)

CUNHA, MARCOS P. V.; DAVIES, YAME M.; CERDEIRA, LOUISE; DROPA, MILENA; LINCOPAN, NILTON; KNOBL, TEREZINHA. Complete DNA Sequence of an IncM1 Plasmid Bearing the Novel qnrE1 Plasmid-Mediated Quinolone Resistance Variant and bla(CTX-M-8) from Klebsiella pneumoniae Sequence Type 147. Antimicrobial Agents and Chemotherapy, v. 61, n. 9, SEP 2017. (16/12641-9, 15/21325-0, 14/11523-7)

MARTINS, EVELIN RODRIGUES; CASELLA, TIAGO; CAMPAGNARI BUENO, MARIA FERNANDA; FRANCISCO, GABRIELA RODRIGUES; TOLENTINO, FERNANDA MODESTO; TEGON DE FREITAS, ANA CAROLINA; CERDEIRA, LOUISE; COSTA, MONALISA NOGUEIRA; CEVADA, CARLA; LINCOPAN, NILTON; et al. Draft genome sequence of an aminoglycoside-resistant RmtD2-producing Enterobacter cloacae subsp cloacae ST395 in Brazil. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 10, p. 308-309, SEP 2017. (15/21325-0, 14/17184-0)

CASELLA, TIAGO; CERDEIRA, LOUISE T.; FERNANDES, MIRIAM R.; SOUZA, TIAGO A.; HAENNI, MARISA; MADEC, JEAN-YVES; LINCOPAN, NILTON; NOGUEIRA, MARA C. L.. Draft genome sequence of a CTX-M-15-producing Escherichia coli ST345 from commercial chicken meat in Brazil. JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE, v. 9, p. 2-pg., 2017-06-01. (14/17184-0, 15/21325-0)