Brenda Cardoso

Universidade de São Paulo

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Nilton Lincopán

Universidade de São Paulo

Fernanda Esposito

Universidade de São Paulo

Herrison Fontana

Universidade de São Paulo

Bruna Fuga

Universidade de São Paulo

Fábio P. Sellera

Universidade de São Paulo

Elder Sano

Universidade de São Paulo

Quézia Moura

Instituto Federal do Espírito Santo

Danny Fuentes‐Castillo

University of Concepción

Louise Cerdeira

Liverpool School of Tropical Medicine

Adriana Cardenas-Arias

Universidade de São Paulo

Cooperative Institutions

Universidade de São Paulo

Hospital Universitário da Universidade de São Paulo

Centro Universitário de Patos de Minas

Universidade Federal de São Paulo

Universidade Brasil

Universidade Federal de Uberlândia

Hospital São Paulo

Universidade Estadual de Campinas (UNICAMP)

Instituto Butantan

Universidade da Região de Joinville

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Genomic features of a carbapenem-resistant OXA-219-positive Acinetobacter baumannii of international ST15 (CC15) from a patient with community-onset urinary tract infection in Chilean Patagonia

Journal of Global Antimicrobial Resistance (2020)

Sebastián Cifuentes Quézia Moura Brenda Cardoso Fernanda Esposito Louise Cerdeira

Carbapenemase-producing Acinetobacter baumannii has been recognized as a critical priority pathogen by the World Health Organization. We hereby report the identification and the draft genome sequence of a carbapenem-resistant A. baumannii isolated from a patient with community-onset urinary tract infection, in a Chilean Patagonian city. The whole genome was sequenced on an Illumina NextSeq platform and de novo assembled using Unicycler v.0.4. Resistome analysis and epidemiological investigation (based on MLST data and Pasteur scheme) were performed using bioinformatics tools available from the Center for Genomic Epidemiology. The genome size was calculated at 3 890 824 bp, with a GC content of 39.1%, comprising 3864 total genes, 30 tRNAs, 3 rRNAs, 4 ncRNAs, and 109 pseudogenes. Carbapenem-resistant A. baumannii Ab3_Ch strain belonged to the international sequence type ST15 (clonal complex, CC15), and harboured the ISAba-1-blaOXA-219 gene array, along to blaTEM-1B and blaADC-6 β-lactamase genes, and aac(3)-IIa and aph(3′)-VIa aminoglycoside resistance genes. Additionally, efflux pump encoding genes (abaF, abaQ, abeS, adeI, adeK, adeL, adeN, adeR, adeS, and amvA) were identified, and mutations in the quinolone resistance-determining region of gyrA (Ser81Leu) and parC (Ser84Leu) were considered responsible for fluoroquinolone resistance. This genome sequence data could be used for comparative genomic studies of critical priority A. baumannii strains, as well as to understand the specific features of hospital-associated A. baumannii lineages of international clonal complexes emerging in community settings.

Acinetobacter baumannii

Multilocus sequence typing

Resistome

Carbapenem

10.1016/j.jgar.2020.07.011

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Citations (9)

Healthcare-associated NDM-1-producing Enterobacter hormaechei subsp. xiangfangensis clone ST136 emerging as pathogen of companion animals in Brazil

Journal of Antimicrobial Chemotherapy (2023)

Vanessa Cristine Kobs Francielle de Medeiros Patrícia P. Fernandes Roseneide Campos Deglmann Herrison Fontana

Journal Article Healthcare-associated NDM-1-producing Enterobacter hormaechei subsp. xiangfangensis clone ST136 emerging as pathogen of companion animals in Brazil Get access Vanessa C Kobs, Vanessa C Kobs Post-Graduation Program on Health and Environment, Universidade da Região de Joinville (Univille), Joinville, Brazil Corresponding author. E-mail: v.kobs@univille.br https://orcid.org/0000-0001-6346-2278 Search for other works by this author on: Oxford Academic PubMed Google Scholar Francielle de Medeiros, Francielle de Medeiros Laboratório Medivet Diagnósticos Veterinários, Joinville, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Patrícia P Fernandes, Patrícia P Fernandes Laboratório Medivet Diagnósticos Veterinários, Joinville, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Roseneide C Deglmann, Roseneide C Deglmann Post-Graduation Program on Health and Environment, Universidade da Região de Joinville (Univille), Joinville, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Herrison Fontana, Herrison Fontana One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilDepartment of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Brenda Cardoso, Brenda Cardoso One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilDepartment of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Elder Sano, Elder Sano One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilDepartment of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil https://orcid.org/0000-0002-9615-2281 Search for other works by this author on: Oxford Academic PubMed Google Scholar Fernanda Esposito, Fernanda Esposito One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilDepartment of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Fábio P Sellera, Fábio P Sellera One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilSchool of Veterinary Medicine, Metropolitan University of Santos, Santos, BrazilDepartment of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Nilton Lincopan, Nilton Lincopan One Health Brazilian Resistance Project (OneBR), São Paulo, BrazilDepartment of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, BrazilDepartment of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil https://orcid.org/0000-0003-0161-5800 Search for other works by this author on: Oxford Academic PubMed Google Scholar ... Show more Paulo H C de França Paulo H C de França Post-Graduation Program on Health and Environment, Universidade da Região de Joinville (Univille), Joinville, Brazil Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Antimicrobial Chemotherapy, Volume 78, Issue 6, June 2023, Pages 1553–1556, https://doi.org/10.1093/jac/dkad124 Published: 05 May 2023

Graduation (instrument)

10.1093/jac/dkad124

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Emergent Escherichia coli of the highly virulent B2-ST1193 clone producing KPC-2 carbapenemase in ready-to-eat vegetable

Journal of Global Antimicrobial Resistance (2024)

Karine Dantas Gregory Melocco Fernanda Esposito Herisson Fontana Brenda Cardoso

Critical priority carbapenem-resistant pathogens constitute a worldwide public health problem. Escherichia coli ST1193 is an emerging high-risk clone that demonstrates prolonged gut persistence, and association with community-onset urinary and bloodstream infections. The purpose of this study is to report microbiological and genomic data on the emergence of KPC-2-producing E. coli ST1193 in ready-to-eat (RTE) vegetable.

clone (Java method)

Persistence (discontinuity)

10.1016/j.jgar.2024.11.020

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Citations (0)

Data set 1 - uidA gene multifasta file

Figshare (2021)

Ana Carolina de Mello Santos Bruna Fuga Fernanda Esposito Brenda Cardoso Fernanda Fernandes Santos

Multi-FASTA file containing the uidA gene of all the E. coli strains used in the study.

Data set

10.6084/m9.figshare.14403800

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli survey in wild seabirds at a pristine atoll in the southern Atlantic Ocean, Brazil: First report of the O25b-ST131 clone harboring blaCTX-M-8

The Science of The Total Environment (2021)

Ana Carolina Ewbank Danny Fuentes‐Castillo Carlos Sacristán Brenda Cardoso Fernanda Esposito

Atoll

10.1016/j.scitotenv.2021.150539

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Citations (17)

World Health Organization critical priority Escherichia coli clone ST648 in magnificent frigatebird (Fregata magnificens) of an uninhabited insular environment

Frontiers in Microbiology (2022)

Ana Carolina Ewbank Danny Fuentes‐Castillo Carlos Sacristán Fernanda Esposito Bruna Fuga

Antimicrobial resistance is an ancient natural phenomenon increasingly pressured by anthropogenic activities. Escherichia coli has been used as markers of environmental contamination and human-related activity. Seabirds may be bioindicators of clinically relevant bacterial pathogens and their antimicrobial resistance genes, including extended-spectrum-beta-lactamase (ESBL) and/or plasmid-encoded AmpC (pAmpC), in anthropized and remote areas. We evaluated cloacal swabs of 20 wild magnificent frigatebirds ( Fregata magnificens ) of the Alcatrazes Archipelago, the biggest breeding colony of magnificent frigatebirds in the southern Atlantic and a natural protected area with no history of human occupation, located in the anthropized southeastern Brazilian coast. We characterized a highly virulent multidrug-resistant ST648 (O153:H9) pandemic clone, harboring bla CTX – M –2 , bla CMY –2 , qnrB, tetB, sul1, sul2, aadA1, aac(3)-VIa and mdfA , and virulence genes characteristic of avian pathogenic (APEC) ( hlyF, iroN, iss, iutA , and ompT ) and other extraintestinal E. coli (ExPEC) ( chuA, kpsMII , and papC ). To our knowledge, this is the first report of ST648 E. coli co-producing ESBL and pAmpC in wild birds inhabiting insular environments. We suggest this potentially zoonotic and pathogenic lineage was likely acquired through indirect anthropogenic contamination of the marine environment, ingestion of contaminated seafood, or by intra and/or interspecific contact. Our findings reinforce the role of wild birds as anthropization sentinels in insular environments and the importance of wildlife surveillance studies on pathogens of critical priority classified by the World Health Organization.

clone (Java method)

10.3389/fmicb.2022.940600

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Citations (12)

Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital

Frontiers in Microbiology (2021)

Fernanda Esposito Brenda Cardoso Herrison Fontana Bruna Fuga Adriana Cardenas-Arias

The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.

Resistome

Fosfomycin

Multilocus sequence typing

10.3389/fmicb.2021.701921

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Genomic analysis of multidrug-resistant CTX-M-15-positive Klebsiella pneumoniae belonging to the highly successful ST15 clone isolated from a dog with chronic otitis

Journal of Global Antimicrobial Resistance (2020)

Fábio P. Sellera Ralf Lopes Daniel F. M. Monte Brenda Cardoso Fernanda Esposito

Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae have been increasingly reported worldwide as a frequent cause of human and animal infections. K. pneumoniae belonging to the K24 capsular serotype and sequence type (ST) ST15 has been considered a global successful clone responsible for the spread of the blaCTX-M-15 gene. To report the draft genome sequence of a multidrug-resistant CTX-M-15-positive K. pneumoniae K24-ST15 strain (L3KP1), which was isolated from a dog with chronic otitis. Genomic DNA was extracted and sequenced using Illumina NextSeq platform. De novo assembly was performed by SPAdes and in silico prediction accomplished by curated bioinformatics tools. The genome size was calculated at 5 642 348 bp, with a GC content of 57.11%, and comprising 5601 total genes, 52 tRNAs, 8 rRNAs, 9 ncRNAs and 105 pseudogenes. The K. pneumoniae L3KP1 strain belonged to ST15 and carried the yersiniabactin biosynthetic gene cluster [ybt 10 (YbST28) in the integrative conjugative element ICEKp4], and the KL24 locus encoding capsular serotype K24. Besides the blaCTX-M-15 ESBL gene, other clinically important resistance genes to β-lactams, aminoglycosides, fosfomycin, macrolides, phenicol, quinolones, sulfonamides, tetracyclines and trimethoprim were detected. Additionally, heavy metals and disinfectant resistance genes were also identified. This draft genome might be useful for comparative genomic analyses of the international clone of K. pneumoniae K24-ST15-CTX-M-15. In addition, information presented in this study also shed light on the urgent need to monitor ESBL-producing K. pneumoniae in veterinary hospitals.

Multilocus sequence typing

Klebsiella pneumonia

genomic DNA

10.1016/j.jgar.2020.06.017

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Citations (6)

Phylogenomic analysis of CTX-M-15–producing Enterobacter hormaechei belonging to the high-risk ST78 from animal infection: another successful One Health clone?

Journal of Global Antimicrobial Resistance (2022)

Brenda Cardoso Fábio P. Sellera Elder Sano Fernanda Esposito Lourdes A. V. Seabra

Extended-spectrum β-lactamase (ESBL)–producing Enterobacter cloacae complex (ECC) members have been a leading cause of severe infections in hospital setting and have lately been recognized as important pathogens for animals. In this article, we report phylogenomic data of a multidrug-resistant and CTX-M-15–positive E. hormaechei belonging to ST78 isolated from a calf with omphalitis. Genomic DNA was extracted and sequenced using the Illumina NextSeq platform. De novo assembly was performed by Unicycler and in silico prediction accomplished by curated bioinformatics tools. Single nucleotide polymorphism (SNP)-based comparative phylogenomic analysis was conducted by using publicly available ECC genomes belonging to ST78. The genome size was calculated at 3 8465 40 bp, comprising 4717 total genes, 3 rRNAs, 43 tRNAs, 7 ncRNAs, and 74 pseudogenes. The animal-associated E. hormaechei (ECBEZ strain) ST78 harboured the blaCTX-M-15 ESBL gene in addition to other critically important resistance genes conferring resistance to β-lactams, aminoglycosides, fosfomycin, phenicol, quinolones, sulphonamides, tetracyclines, and trimethoprim. Phylogenetic analysis revealed that ECBEZ is closely related to human-isolated strains from Asian and African countries. Phylogenomic analysis of CTX-M-15-producing E. hormaechei from animal infection reveals that ST78 is a successful One Health clone among ECC members. Furthermore, data presented in this study reinforce the urgent need to monitor ESBL-producing ECC members in veterinary settings.

Indel

Enterobacteriaceae Infections

10.1016/j.jgar.2022.02.010

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Citations (6)

Detection and Whole-Genome Analysis of a High-Risk Clone ofKlebsiella pneumoniaeST340/CG258 Producing CTX-M-15 in a Companion Animal

Microbial Drug Resistance (2019)

Juan D. Valencia-Bacca Meire M. Silva Louise Cerdeira Fernanda Esposito Brenda Cardoso

The emergence and dissemination of high-risk clones of Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) in animal infections is a critical issue. We report the detection and genomic features of a multidrug-resistant (MDR) ESBL (CTX-M-15)-producing K. pneumoniae infecting a domestic cat. Whole-genome sequencing analysis identified the international ST340 (clonal group CG258), and genes and mutations conferring resistance to β-lactams, aminoglycosides, macrolides, phenicols, fosfomycin, sulfonamides, tetracycline, trimethoprim, and fluoroquinolones. In addition, the presence of genes encoding resistance to disinfectant and heavy metals hazardous to humans was also confirmed. The MDR profile exhibited by the strain contributed to treatment failure and death of the companion animal. Therefore, active surveillance of critical priority lineages of K. pneumoniae should not only focus on human infections but also on veterinary infections.

Fosfomycin

Trimethoprim

clone (Java method)

10.1089/mdr.2019.0190

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Citations (10)