Draft genome sequences of KPC-2- and CTX-M-15-producing Klebsiella pneumoniae ST437 isolated from a clinical sample and urban rivers in Sao Paulo, Brazil

Gabriela Rodrigues Francisco; Maria Fernanda C Bueno; Louise Cerdeira; Nilton Lincopan; Susan Ienne; Tiago A Souza; Doroti de Oliveira Garcia

doi:10.1016/j.jgar.2018.12.003

Draft genome sequences of KPC-2- and CTX-M-15-producing Klebsiella pneumoniae ST437 isolated from a clinical sample and urban rivers in Sao Paulo, Brazil

J Glob Antimicrob Resist. 2019 Mar:16:74-75. doi: 10.1016/j.jgar.2018.12.003. Epub 2018 Dec 19.

Authors

Gabriela Rodrigues Francisco¹, Maria Fernanda C Bueno¹, Louise Cerdeira², Nilton Lincopan³, Susan Ienne⁴, Tiago A Souza⁴, Doroti de Oliveira Garcia⁵

Affiliations

¹ Center of Bacteriology, Instituto Adolfo Lutz, Sao Paulo, Brazil.
² Department of Clinical Analysis, School of Pharmacy, Universidade de Sao Paulo, Sao Paulo, Brazil.
³ Department of Clinical Analysis, School of Pharmacy, Universidade de Sao Paulo, Sao Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, Universidade de Sao Paulo, Sao Paulo, Brazil.
⁴ Core Facility for Scientific Research-Universidade de Sao Paulo (CEFAP-USP/GENIAL), Sao Paulo, Brazil.
⁵ Center of Bacteriology, Instituto Adolfo Lutz, Sao Paulo, Brazil. Electronic address: [email protected].

PMID: 30578976
DOI: 10.1016/j.jgar.2018.12.003

Abstract

Objectives: KPC-producing Klebsiella pneumoniae is considered one of the most worrisome multidrug-resistant micro-organisms in nosocomial infections. It has also been reported in wastewater and urban rivers in the city of Sao Paulo, Brazil. Here we report the draft genome sequences of three KPC-2- and CTX-M-15-producing K. pneumoniae sequence type 437 (ST437) isolates obtained from two urban rivers and from a clinical sample of a patient in Sao Paulo.

Methods: A genomic library was constructed using a Nextera XT Kit. An Illumina platform was used to perform whole-genome sequencing (WGS).

Results: WGS of environmental isolates Kp148/PINH-4900 and Kp196/TIET-4200 and clinical isolate Kp314/11 resulted in estimated genome sizes of 5464058, 5437723 and 5319218bp, respectively. Resistome analysis of the environmental and clinical strains revealed the presence of resistance genes to the following antimicrobials in all strains: aminoglycosides [aac(6')-Ib-cr]; β-lactams (bla_OXA-1, bla_SHV-11, bla_CTX-M-15 and bla_KPC-2); fluoroquinolones [aac(6')-Ib-cr, oqxA and oqxB]; fosfomycin (fosA^KP); macrolides [mph(A)]; phenicols (catB4); sulfonamides (sul1); and trimethoprim (dfrA30). The tetracycline resistance gene tetA was identified in Kp148/PINH-4900 and Kp314/11 only; the aminoglycoside resistance gene aph(3')-Ia was found only in environmental isolates, and aadA2 only in Kp314/11; and the phenicol resistance gene catA1 was identified only in Kp148/PINH-4900.

Conclusions: The draft genome sequences of these strains help us to elucidate the dissemination of resistance genes in micro-organisms inside and outside the hospital and are useful for further comparisons between clinical and environmental strains.

Keywords: CTX-M-15; Clinical sample; KPC; Klebsiella pneumoniae; ST437; Urban river.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Bacterial Typing Techniques
Brazil
Drug Resistance, Multiple, Bacterial
Genome, Bacterial*
Humans
Klebsiella Infections / microbiology*
Klebsiella pneumoniae / classification
Klebsiella pneumoniae / drug effects
Klebsiella pneumoniae / enzymology
Klebsiella pneumoniae / genetics*
Microbial Sensitivity Tests
Multilocus Sequence Typing
Parks, Recreational*
Rivers / microbiology*
Sequence Analysis, DNA
Whole Genome Sequencing
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
beta-lactamase CTX-M-15
beta-Lactamases
beta-lactamase KPC-2, Klebsiella pneumoniae