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Fuga B, Sellera FP, Esposito F, Moura Q, Pillonetto M, Lincopan N. Hybrid genome assembly of colistin-resistant mcr-1.5-producing Escherichia coli ST354 reveals phylogenomic pattern associated with urinary tract infections in Brazil. J Glob Antimicrob Resist 2024; 37:37-41. [PMID: 38408561 DOI: 10.1016/j.jgar.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/05/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The rapid and global spread of Escherichia coli carrying mcr-type genes at the human-animal-environmental interface has become a serious global public health problem. OBJECTIVE To perform a genomic investigation of a colistin-resistant E. coli strain (14005RM) causing urinary tract infection, using a hybrid de novo assembly of Illumina/Nanopore sequence data, presenting phylogenomic insights into the relationship with mcr-1-positive strains circulating at the human-animal-environmental interface, in Brazil. METHODS Genomic DNA was sequenced using both the Illumina NexSeq and Nanopore MinION platforms. De novo hybrid assembly was performed by Unicycler. Genomic data were assessed by in silico prediction and bioinformatic tools. RESULTS The genome assembly size was 5 333 039 bp. The mcr-1.5-positive E. coli strain 14005RM belongs to the sequence type ST354 and presented a broad resistome (antibiotics, heavy metals, disinfectants, and glyphosate) and virulome. The mcr-1.5 gene was carried by an IncI2 plasmid (p14005RM, sizing 65,458 kb). Full genome SNP-based phylogenetic analysis reveals that mcr-1.5-producing E. coli strain 14005RM is highly related (> 98% identity) to colistin-resistant mcr-1.1-positive ST354 lineages associated with urinary tract infections in Brazil since 2015. CONCLUSION Mobile colistin resistance within the Brazilian One Health microbiosphere is mediated by mcr gene variants propagated by IncX4, IncHI2, and IncI2 plasmids, circulating among global clones of E. coli.
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Affiliation(s)
- Bruna Fuga
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil.
| | - Fábio P Sellera
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Quézia Moura
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Federal Institute of Espírito Santo, Vila Velha, Brazil; Postgraduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
| | - Marcelo Pillonetto
- State Public Health Laboratory of Paraná, São José dos Pinhais, Brazil; Pontifical Catholic University of Paraná, Curitiba, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
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2
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Moura Q, Fernandes MR, Sellera FP, Cardoso B, Nascimento CL, Dutra GHP, Lincopan N. Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In 229/ blaCTX-M-2 Array Isolated from a Migratory Black Skimmer. Pathogens 2024; 13:63. [PMID: 38251370 PMCID: PMC10821149 DOI: 10.3390/pathogens13010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024] Open
Abstract
Migratory birds have contributed to the dissemination of multidrug-resistant (MDR) bacteria across the continents. A CTX-M-2-producing Escherichia coli was isolated from a black skimmer (Rynchops niger) in Southeast Brazil. The whole genome was sequenced using the Illumina NextSeq platform and de novo assembled by CLC. Bioinformatic analyses were carried out using tools from the Center for Genomic Epidemiology. The genome size was estimated at 4.9 Mb, with 4790 coding sequences. A wide resistome was detected, with genes encoding resistance to several clinically significant antimicrobials, heavy metals, and biocides. The blaCTX-M-2 gene was inserted in an In229 class 1 integron inside a ∆TnAs3 transposon located in an IncHI2/ST2 plasmid. The strain was assigned to ST5506, CH type fumC19/fimH32, serotype O8:K87, and phylogroup B1. Virulence genes associated with survival in acid conditions, increased serum survival, and adherence were also identified. These data highlight the role of migratory seabirds as reservoirs and carriers of antimicrobial resistance determinants and can help to elucidate the antimicrobial resistance dynamics under a One Health perspective.
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Affiliation(s)
- Quézia Moura
- Federal Institute of Espírito Santo, Vila Velha 29106-010, Brazil
- Postgraduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória 29047-105, Brazil
| | - Miriam R. Fernandes
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-9760, USA;
| | - Fábio P. Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, Brazil;
- School of Veterinary Medicine, Metropolitan University of Santos, Santos 11045-002, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil;
- One Health Brazilian Resistance Project (OneBR), São Paulo 05508-000, Brazil
| | | | - Gustavo H. P. Dutra
- Veterinary Unit of Santos Aquarium, Santos 11030-600, Brazil; (C.L.N.); (G.H.P.D.)
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil;
- One Health Brazilian Resistance Project (OneBR), São Paulo 05508-000, Brazil
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil
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3
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Esposito F, Cardoso B, Sellera FP, Sano E, Fuentes-Castillo D, Fontana H, Fuga B, Moura Q, Sato MI, Brandão CJ, Lincopan N. Expansion of healthcare-associated hypervirulent KPC-2-producing Klebsiella pneumoniae ST11/KL64 beyond hospital settings. One Health 2023; 17:100594. [PMID: 37448770 PMCID: PMC10336671 DOI: 10.1016/j.onehlt.2023.100594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
The spread of carbapenemase-producing Klebsiella pneumoniae beyond hospital settings is a global critical issue within a public health and One Health perspective. Another worrisome concern is the convergence of virulence and resistance in healthcare-associated lineages of K. pneumoniae leading to unfavorable clinical outcomes. During a surveillance study of WHO critical priority pathogens circulating in an impacted urban river in São Paulo, Brazil, we isolate two hypermucoviscous and multidrug-resistant K. pneumoniae strains (PINH-4250 and PINH-4900) from two different locations near to medical centers. Genomic investigation revealed that both strains belonged to the global high-risk sequence type (ST) ST11, carrying the blaKPC-2 carbapenemase gene, besides other medically important antimicrobial resistance determinants. A broad virulome was predicted and associated with hypervirulent behavior in the Galleria mellonella infection model. Comparative phylogenomic analysis of PINH-4250 and PINH-4900 along to an international collection of publicly available genomes of K. pneumoniae ST11 revealed that both environmental strains were closely related to hospital-associated K. pneumoniae strains recovered from clinical samples between 2006 and 2018, in São Paulo city. Our findings support that healthcare-associated KPC-2-positive K. pneumoniae of ST11 clone has successfully expanded beyond hospital settings. In summary, aquatic environments can become potential sources of international clones of K. pneumoniae displaying carbapenem resistance and hypervirulent behaviors, which is a critical issue within a One Health perspective.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P. Sellera
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), Brazil
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Maria I.Z. Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Carlos J. Brandão
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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4
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Gaeta NC, de Carvalho DU, Fontana H, Sano E, Moura Q, Fuga B, Munoz PM, Gregory L, Lincopan N. Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America. Sci Total Environ 2022; 823:153590. [PMID: 35122850 PMCID: PMC8994849 DOI: 10.1016/j.scitotenv.2022.153590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 05/03/2023]
Abstract
Mining dam disasters contribute to the contamination of aquatic environments, impacting associated ecosystems and wildlife. A multidrug-resistant Escherichia coli strain (B2C) was isolated from a river water sample in Brazil after the Mariana mining dam disaster. The genome was sequenced using the Illumina MiSeq platform, and de novo assembled using Unicycler. Resistome, virulome, and plasmidome were predicted using bioinformatics tools. Data analysis revealed that E. coli B2C belonged to sequence type ST219 and phylogroup E. Strikingly, a broad resistome (antibiotics, hazardous heavy metals, and biocides) was predicted, including the presence of the clinically relevant blaCTX-M-2 extended-spectrum β-lactamase (ESBL) gene, qacE∆1 efflux pump gene, and the mer (mercury resistance) operon. SNP-based analysis revealed that environmental E. coli B2C was clustered along to ESBL-negative E. coli strains of ST219 isolated between 1980 and 2021 from livestock in the United States of America. Acquisition of clinically relevant genes by ST219 seems to be a recent genetic event related to anthropogenic activities, where polluted water environments may contribute to its dissemination at the human-animal-environment interface. In addition, the presence of genes conferring resistance to heavy metals could be related to environmental pollution from mining activities. Antimicrobial resistance genes could be essential biomarkers of environmental exposure to human and mining pollution.
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Affiliation(s)
- Natália C Gaeta
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.
| | - Daniel U de Carvalho
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Lilian Gregory
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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5
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Bueris V, Sellera FP, Fuga B, Sano E, Carvalho MPN, Couto SCF, Moura Q, Lincopan N. Convergence of virulence and resistance in international clones of WHO critical priority enterobacterales isolated from Marine Bivalves. Sci Rep 2022; 12:5707. [PMID: 35383231 PMCID: PMC8983722 DOI: 10.1038/s41598-022-09598-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022] Open
Abstract
The global spread of critical-priority antimicrobial-resistant Enterobacterales by food is a public health problem. Wild-caught seafood are broadly consumed worldwide, but exposure to land-based pollution can favor their contamination by clinically relevant antimicrobial-resistant bacteria. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we performed genomic surveillance and cell culture-based virulence investigation of WHO critical priority Enterobacterales isolated from marine bivalves collected in the Atlantic Coast of South America. Broad-spectrum cephalosporin-resistant Klebsiella pneumoniae and Escherichia coli isolates were recovered from eight distinct geographical locations. These strains harbored blaCTX-M-type or blaCMY-type genes. Most of the surveyed genomes confirmed the convergence of wide virulome and resistome (i.e., antimicrobials, heavy metals, biocides, and pesticides resistance). We identified strains belonging to the international high-risk clones K. pneumoniae ST307 and E. coli ST131 carrying important virulence genes, whereas in vitro experiments confirmed the high virulence potential of these strains. Thermolabile and thermostable toxins were identified in some strains, and all of them were biofilm producers. These data point to an alarming presence of resistance and virulence genes in marine environments, which may favor horizontal gene transfer and the spread of these traits to other bacterial species.
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Affiliation(s)
- Vanessa Bueris
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil. .,Laboratory of Genetics, Butantan Institute, São Paulo, Brazil.
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.,School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Elder Sano
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Marcelo P N Carvalho
- Department of Veterinary Clinic and Surgery, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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6
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Cardoso B, Esposito F, Fontana H, Fuga B, Moura Q, Sano E, Sato MIZ, Brandão CJ, Oliveira FA, Levy CE, Lincopan N. Genomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in Brazil. Genomics 2021; 114:378-383. [PMID: 34923088 DOI: 10.1016/j.ygeno.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/27/2021] [Accepted: 12/14/2021] [Indexed: 11/04/2022]
Abstract
Convergence of resistance and virulence in Klebsiella pneumoniae is a critical public health issue worldwide. A multidrug-resistant CTX-M-15-producing K. pneumoniae (TIES-4900 strain) was isolated from a highly impacted urban river, in Brazil. The genome was sequenced by MiSeq Illumina platform and de novo assembled using Unicycler. In silico prediction was accomplished by bioinformatics tools. The size of the genome is 5.4 Mb with 5145 protein-coding genes. TIES-4900 strain belonged to the sequence type ST15, yersiniabactin sequence type YbST10, ICEKp4, KL24 (wzi-24) and O1v1 locus. Phylogenomics confirmed genomic relatedness with ST15 clones from human and animal hosts. Convergence of broad resistome (antibiotics, heavy-metals and biocides) and virulome, including the Kpi pilus system involved in host-pathogen interaction and persistence of ST15 clone to hospital environments, were predicted. Virulent behavior was confirmed in the Galleria mellonella infection model. This study may give genomic insights on the spread of critical-priority WHO pathogens beyond hospital settings.
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Affiliation(s)
- Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Mato Grosso do Sul, Brazil
| | - Elder Sano
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Maria I Z Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Carlos J Brandão
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | | | - Carlos E Levy
- Hospital de Clínicas, Universidade Estadual de Campinas, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil.
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7
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Cerdeira L, Nakamura-Silva R, Oliveira-Silva M, Sano E, Esposito F, Fuga B, Moura Q, Miranda CES, Wyres K, Lincopan N, Pitondo-Silva A. A novel hypermucoviscous Klebsiella pneumoniae ST3994-K2 clone belonging to Clonal Group 86. Pathog Dis 2021; 79:6373921. [PMID: 34550351 DOI: 10.1093/femspd/ftab047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Emergent hypervirulent Klebsiella pneumoniae has been responsible for severe diseases, representing a serious threat to public health. We report the whole-genome sequencing of a novel ST3994-K2 clone, a single locus variant of ST86 K2, which is considered a worrying hypervirulent clone that emerged in several parts of the world. The strain K. pneumonia Kpi144 was isolated in 2013 from a blood culture of a 69-year-old male patient admitted to a tertiary hospital in Teresina, state of Piauí, northeastern Brazil. The strain was susceptible to 41 antibiotics tested, presented hypermucoviscous phenotype and a virulent behavior was observed in the Galleria mellonella infection model. Moreover, the virulome showed several virulence genes. To the best of our knowledge, this is the first worldwide report of a novel ST3994-K2 K. pneumoniae clone, an SLV of ST86 K2, which is considered a worrying virulent clone that has emerged in several parts of the world, including South America and Brazil.
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Affiliation(s)
- Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, United Kingdom
| | - Rafael Nakamura-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, CEP 14096-900, São Paulo, Brazil
| | - Mariana Oliveira-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, CEP 14096-900, São Paulo, Brazil
| | - Elder Sano
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil.,One Health Brazilian Resistance Project (OneBR), University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), University of São Paulo, São Paulo, CEP 05508-000, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Bruna Fuga
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil.,One Health Brazilian Resistance Project (OneBR), University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, CEP 29106-010, Brazil
| | | | - Kelly Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Nilton Lincopan
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil.,One Health Brazilian Resistance Project (OneBR), University of São Paulo, São Paulo, CEP 05508-000, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - André Pitondo-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, CEP 14096-900, São Paulo, Brazil.,Postgraduate Program in Dentistry, University of Ribeirão Preto, Ribeirão Preto, CEP 14096-900, São Paulo, Brazil
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8
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Esposito F, Cardoso B, Fontana H, Fuga B, Cardenas-Arias A, Moura Q, Fuentes-Castillo D, Lincopan N. 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. Front Microbiol 2021; 12:701921. [PMID: 34539602 PMCID: PMC8446631 DOI: 10.3389/fmicb.2021.701921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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9
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Vianello MA, Cardoso B, Fuentes-Castillo D, Moura Q, Esposito F, Fuga B, Lincopan N, Egito EST. International high-risk clone of fluoroquinolone-resistant Escherichia coli O15:H1-D-ST393 in remote communities of Brazilian Amazon. Infect Genet Evol 2021; 91:104808. [PMID: 33737229 DOI: 10.1016/j.meegid.2021.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/07/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
The global dissemination of multidrug-resistant Escherichia coli lineages belonging to high- risk clones poses a significant public health threat. Herein we report the identification and genomic profiling of two multidrug-resistant E. coli strains [BL-II-03(2) and BL-II-11(3)] belonging to the O15:H1-D-ST393 (clonal complex 31) worldwide spread clone, isolated from fecal samples of indigenous peoples belonging to two different ethnic groups of remote communities of Brazilian Amazon. Genomic analysis revealed genes and mutations conferring resistance to β-lactams [blaTEM-1], aminoglycosides [aadA5, aph(3″)-Ib, aph(6)-Id], tetracyclines [tetB], sulfamethoxazole/trimethoprim [sul1, sul2, dfrA17], and fluoroquinolones [gyrA (D87N, S83L), parC (S80I, S57T), parE (L416F)]; and presence of IncQ1, IncFIA, and IncFIB(pB171) plasmids. On the other hand, phylogenomics of globally reported E. coli ST393 assigned E. coli strains BL-II-03(2) and BL-II-11(3) to a cluster comprising human isolates from Australia, Canada, China, Sweden, and United States of America. These results might provide valuable information for understanding dissemination of intercontinental multidrug-resistant clones in remote communities with low levels of antibiotic exposure.
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Affiliation(s)
- Marco Aurelio Vianello
- Graduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Brenda Cardoso
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil.
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Fuga B, Cerdeira L, Moura Q, Fontana H, Fuentes-Castillo D, Carvalho AC, Lincopan N. Genomic data reveals the emergence of an IncQ1 small plasmid carrying bla KPC-2 in Escherichia coli of the pandemic sequence type 648. J Glob Antimicrob Resist 2021; 25:8-13. [PMID: 33662640 PMCID: PMC8213540 DOI: 10.1016/j.jgar.2021.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022] Open
Abstract
Epidemiological success of KPC has been linked to plasmids carrying blaKPC genes. An IncQ1 small plasmid carrying blaKPC-2 was found in pandemic Escherichia coli ST648. Plasmid analysis revealed blaKPC-2 on an NTEKPC-IId element with the aph(3')-VIa gene. Plasmid phylogeny confirmed >99% identity with IncQ/blaKPC-2 from Klebsiella pneumoniae. The emergence and rapid expansion of IncQ1/blaKPC-2 to novel hosts is discussed.
Objectives The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying blaKPC genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis based on single nucleotide polymorphisms (SNPs) as well as the comparative resistome and plasmidome of globally disseminated blaKPC-2-positive E. coli strains with identical sequence type (ST) were further investigated. Methods Total DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using Unicycler. Genomic data were evaluated through bioinformatics tools available from the Center of Genomic Epidemiology and by in silico analysis. Results Genomic analysis revealed the convergence of a wide resistome and virulome in E. coli ST648, showing a high-level phylogenetic relationship with a KPC-2-positive ST648 cluster identified in the USA and association with international clade 2. Additionally, the emergence of an IncQ1 small plasmid (pEc351) carrying blaKPC-2 (on an NTEKPC-IId element), aph(3')-VIa, and plasmid regulatory and replication genes in the pandemic clone ST648 is reported. Conclusion Identification of a blaKPC-2-positive IncQ1 plasmid in a high-risk E. coli clone represents rapid adaptation and expansion of these small plasmids encoding carbapenemases to novel bacterial hosts with global distribution, which deserves continued monitoring.
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Affiliation(s)
- Bruna Fuga
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil.
| | - Louise Cerdeira
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Quézia Moura
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Faculty of Health Sciences, Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Pathology, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Albalúcia C Carvalho
- Clinical Laboratory, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Nilton Lincopan
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil.
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11
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Cerdeira L, Nakamura-Silva R, Oliveira-Silva M, Fuga B, Moura Q, Vespero EC, Lincopan N, Pitondo-Silva A. Draft genome sequences of PDR and XDR Klebsiella pneumoniae belonging to high-risk CG258 isolated from a Brazilian tertiary hospital. Infect Genet Evol 2020; 87:104643. [PMID: 33246084 DOI: 10.1016/j.meegid.2020.104643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Affiliation(s)
- Louise Cerdeira
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Rafael Nakamura-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Mariana Oliveira-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Bruna Fuga
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Clinical and Toxicological Analysis, State University of Londrina, Londrina, Paraná, Brazil
| | - Nilton Lincopan
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - André Pitondo-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil; Postgraduate Program in Dentistry, University of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil.
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Fuentes-Castillo D, Power P, Cerdeira L, Cardenas-Arias A, Moura Q, Oliveira FA, Levy CE, Gutkind G, Catão-Dias JL, Lincopan N. FONA-7, a Novel Extended-Spectrum β-Lactamase Variant of the FONA Family Identified in Serratia fonticola. Microb Drug Resist 2020; 27:585-589. [PMID: 32991273 DOI: 10.1089/mdr.2020.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Serratia fonticola is a human pathogen widely found in the environment, with birds being reported as possible natural hosts. During an epidemiological and genomic surveillance study conducted to monitor the occurrence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in South American wild birds, we identified an ESBL-positive S. fonticola in a fecal sample collected from a Hudsonian Whimbrel, during its non-breeding range on the Pacific Coast of Chile. Whole genome sequencing analysis and "in silico" modeling revealed a novel variant of the class A ESBLs FONA family, designated FONA-7, which shows 96.28% amino acid identity with FONA-6; with amino acid substitutions occurring in the signal peptide sequence (Thr22→Ser), and in the mature protein (Ser39→Asn and Thr227→Ile). This finding denotes that migratory birds can be potential vectors for the transboundary spread of ESBL-producing bacteria, creating a further theoretical risk for the origin of novel plasmid-encoded β-lactamases.
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Affiliation(s)
- Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Pablo Power
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Flavio A Oliveira
- Hospital de Clínicas, Universidade Estadual de Campinas, Campinas, Brazil
| | - Carlos E Levy
- Hospital de Clínicas, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gabriel Gutkind
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José L Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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13
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Cifuentes S, Moura Q, Cardoso B, Esposito F, Cerdeira L, Álvarez E, Barrera E, Opazo-Capurro A, Gonzalez-Rocha G, Lincopan N. 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. J Glob Antimicrob Resist 2020; 22:756-758. [DOI: 10.1016/j.jgar.2020.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/16/2020] [Accepted: 07/12/2020] [Indexed: 11/26/2022] Open
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Fuentes-Castillo D, Esposito F, Cardoso B, Dalazen G, Moura Q, Fuga B, Fontana H, Cerdeira L, Dropa M, Rottmann J, González-Acuña D, Catão-Dias JL, Lincopan N. Genomic data reveal international lineages of critical priority Escherichia coli harbouring wide resistome in Andean condors (Vultur gryphus Linnaeus, 1758). Mol Ecol 2020; 29:1919-1935. [PMID: 32335957 DOI: 10.1111/mec.15455] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/01/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Critical priority pathogens have globally disseminated beyond clinical settings, thereby threatening wildlife. Andean Condors (Vultur gryphus) are essential for ecosystem health and functioning, but their populations are globally near threatened and declining due to anthropogenic activities. During a microbiological and genomic surveillance study of critical priority antibiotic-resistant pathogens, we identified pandemic lineages of multidrug-resistant extended-spectrum β-lactamase (ESBL)-producing Escherichia coli colonizing Andean Condors admitted at two wildlife rehabilitation centres in South America. Genomic analysis revealed the presence of genes encoding resistance to hospital and healthcare agents among international E. coli clones belonging to sequence types (STs) ST162, ST602, ST1196 and ST1485. In this regard, the resistome included genes conferring resistance to clinically important cephalosporins (i.e., CTX-M-14, CTX-M-55 and CTX-M-65 ESBL genes), heavy metals (arsenic, mercury, lead, cadmium, copper, silver), pesticides (glyphosate) and domestic/hospital disinfectants, suggesting a link with anthropogenic environmental pollution. On the other hand, the presence of virulence factors, including the astA gene associated with outbreak of childhood diarrhoea and extra-intestinal disease in animals, was identified, whereas virulent behaviour was confirmed using the Galleria mellonella infection model. E. coli ST162, ST602, ST1196 and ST1485 have been previously identified in humans and food-producing animals worldwide, indicating that a wide resistome could contribute to rapid adaptation and dissemination of these clones at the human-animal-environment interface. Therefore, these results highlight that Andean Condors have been colonized by critical priority pathogens, becoming potential environmental reservoirs and/or vectors for dissemination of virulent and antimicrobial-resistant bacteria and/or their genes, in associated ecosystems and wildlife.
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Affiliation(s)
- Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, Sao Paulo, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Gislaine Dalazen
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Herrison Fontana
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Louise Cerdeira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Milena Dropa
- School of Public Health, University of São Paulo, Sao Paulo, Brazil
| | | | - Daniel González-Acuña
- Department of Animal Sciences, Faculty of Veterinary Sciences, University of Concepción, Chillán, Chile
| | - José L Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, Sao Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
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15
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Sartori L, Sellera FP, Moura Q, Cardoso B, Fontana H, Côrtes LA, Cerdeira L, Lincopan N. Genomic features of a polymyxin-resistant Klebsiella pneumoniae ST491 isolate co-harbouring bla CTX-M-8 and qnrE1 genes from a hospitalised cat in São Paulo, Brazil. J Glob Antimicrob Resist 2020; 21:186-187. [PMID: 32224265 DOI: 10.1016/j.jgar.2020.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/09/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES Klebsiella pneumoniae has emerged as one of the major pathogens of humans and companion animals. Moreover, polymyxin resistance in K. pneumoniae is increasingly reported worldwide, mainly among extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing isolates. The aim of this study was to report the draft genome sequence of a polymyxin-resistant, ESBL-producing K. pneumoniae isolate (14CSI) from a hospitalised domestic cat in Brazil. METHODS Whole-genome sequencing of strain 14CSI was performed on an Illumina NextSeq platform and the genome was de novo assembled using Velvet v.1.2.10. Data analysis was performed using bioinformatics tools available from the Center for Genomic Epidemiology and the Institut Pasteur database. RESULTS The genome size of strain 14CSI was calculated at 5 260 459 bp, with a GC content of 57.3% and comprising 5294 total genes, 28 tRNAs, 7 rRNAs, 8 ncRNAs and 237 pseudogenes. Klebsiella pneumoniae strain 14CSI belongs to sequence type 491 (ST491), presents a mutation (A14S) in the mgrB gene and co-harbours blaCTX-M-8 and qnrE1 genes. Genes conferring resistance to heavy metals were further identified. CONCLUSION This draft genome could be used as a reference sequence for comparative analysis of polymyxin-resistant and/or CTX-M-8-producing K. pneumoniae strains circulating at the human-animal interface.
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Affiliation(s)
- Luciana Sartori
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Mato Grosso do Sul, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Louise Cerdeira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Zamparette CP, Schorner M, Campos E, Moura Q, Cerdeira L, Tartari DC, Sereia AFR, Cunha P, Fontana H, de Oliveira LFV, Grisard EC, Lincopan N, Bazzo ML, Sincero TCM. IncX4 Plasmid-Mediated mcr-1.1 in Polymyxin-Resistant Escherichia coli from Outpatients in Santa Catarina, Southern Brazil. Microb Drug Resist 2020; 26:1326-1333. [PMID: 32004096 DOI: 10.1089/mdr.2019.0203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasmid-mediated polymyxin resistance has become a global health concern, not only because its dissemination has occurred drastically but also because it has begun to be reported in multidrug-resistant (MDR) pathogens. We hereby report microbiological and genomic characteristics of two mcr-1.1-positive polymyxin-resistant Escherichia coli isolates identified for the first time in community patients, in Santa Catarina, Southern Brazil. E. coli strains belonging to ST206 and ST354 and the resistome analysis revealed the presence of clinically important genes responsible for MDR profile. Interestingly, in both polymyxin-resistant E. coli strains, mcr-1.1 genes were carried by IncX4 plasmids, responsible for the worldwide dissemination of mcr-type genes. In this regard, plasmid backbones were almost identical to the first IncX4 plasmid reported in Brazil and sharing more than 99.9% identity to IncX4 plasmids from China, also lacking the ISApl1 insertion sequence upstream of mcr-1. In conclusion, these data confirm the presence of international ST206 and ST354 carrying mcr-1.1 genes and that the IncX4 plasmids have been key vectors contributing to the endemic status of mcr-1.1-positive polymyxin-resistant E. coli in Brazil. Also, we described the first known clinical isolate with the mrc1.1 gene in Santa Catarina state, Brazil, showing that plasmid-mediated polymyxin resistance has been affecting humans earlier than has been known so far.
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Affiliation(s)
- Caetana P Zamparette
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Marcos Schorner
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Elizandra Campos
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniela C Tartari
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | | | - Patricia Cunha
- Neoprospecta Microbiome Technologies, Florianopolis, Brazil
| | - Herrison Fontana
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Edmundo C Grisard
- Department of Microbiology, Imunology and Parasitology, Biological Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Luiza Bazzo
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Thaís C M Sincero
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianopolis, Brazil
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Fernandes MR, Sellera FP, Moura Q, Esposito F, Sabino CP, Lincopan N. Identification and genomic features of halotolerant extended-spectrum-β-lactamase (CTX-M)-producing Escherichia coli in urban-impacted coastal waters, Southeast Brazil. Mar Pollut Bull 2020; 150:110689. [PMID: 31733900 DOI: 10.1016/j.marpolbul.2019.110689] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
We report the occurrence and genomic analysis of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in anthropogenically polluted coastal waters of Southeast Brazil. E. coli strains belonging to sequence types (STs) ST10, ST38, ST155 and ST1284 exhibited a wide resistome, with genes conferring resistance to medically relevant antimicrobials and heavy metals, and a halophilic behavior (tolerance to 9-10% NaCl). These findings suggest a heavy contamination in this area by critical priority bacteria adapted to marine environments, which might have negative impacts on human and ocean health.
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Affiliation(s)
- Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Mato Grosso do Sul, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Caetano P Sabino
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Melo LC, Haenni M, Saras E, Cerdeira L, Moura Q, Boulouis HJ, Madec JY, Lincopan N. Genomic characterisation of a multidrug-resistant TEM-52b extended-spectrum β-lactamase-positive Escherichia coli ST219 isolated from a cat in France. J Glob Antimicrob Resist 2019; 18:223-224. [PMID: 31325616 DOI: 10.1016/j.jgar.2019.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. Here we report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coli isolated from a companion animal in France. METHODS Whole genomic DNA from E. coli 39590 was extracted and was sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Velvet v.1.2.10 and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v.3.2. Genomic analyses were performed through bioinformatics tools from the Center for Genomic Epidemiology. RESULTS The genome size was calculated as 5362108bp, with 5268 protein-coding sequences and a GC content of 50.5%. E. coli strain 39590 belonged to ST219, serotype O4:H34 and phylogroup E. The antimicrobial resistome consisted of genes encoding resistance to β-lactams (blaTEM-52b), aminoglycosides [aph(3″)-Ib, aph(6)-Id, aadA2, aadA24], phenicols (catA1), sulfonamides (sul1, sul2), trimethoprim (dfrA1, dfrA14), lincosamides (lnuG) and tetracycline (tetA) as well as mutations in gyrA (Ser83Leu, Asp87Asn) and parC (Ser80Ile) conferring resistance to quinolones. Virulome analysis revealed iss, astA and eilA genes, and IncQ1, IncX4, IncX1, IncFIB and IncFIC plasmid incompatibility groups were identified. CONCLUSION This draft genome can be used as a reference sequence for comparative studies using human and non-human E. coli isolates to identify genetic events that have contributed to pathogenicity and adaptation of TEM-52-producing E. coli clones at the human-animal interface as well as to elucidate dynamics of the spread of blaTEM-52 ESBL genes.
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Affiliation(s)
- Luana C Melo
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
| | - Marisa Haenni
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Estelle Saras
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Henri-Jean Boulouis
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Centre Hospitalier Universitaire Vétérinaire d'Alfort (CHUVA), Maisons-Alfort, France
| | - Jean-Yves Madec
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.
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19
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Fuentes-Castillo D, Farfán-López M, Esposito F, Moura Q, Fernandes MR, Lopes R, Cardoso B, Muñoz ME, Cerdeira L, Najle I, Muñoz PM, Catão-Dias JL, González-Acuña D, Lincopan N. Wild owls colonized by international clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli and Salmonella Infantis in the Southern Cone of America. Sci Total Environ 2019; 674:554-562. [PMID: 31022545 DOI: 10.1016/j.scitotenv.2019.04.149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/24/2019] [Accepted: 04/09/2019] [Indexed: 05/28/2023]
Abstract
Extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae have been classified as critical priority pathogens by the World Health Organization (WHO). We have conducted a microbiological and genomic surveillance study, in order to investigate the occurrence and features of antibiotic-resistant bacteria in wild birds admitted to a wildlife rescue and rehabilitation centre in Chile. This study reports for the first time the occurrence of highly virulent ESBL-producing Escherichia coli and Salmonella enterica serovar Infantis in wild owls inhabiting the Southern Cone of America. Genomic analysis revealed a wide resistome (for antibiotics, heavy metals and disinfectants) among international lineages of E. coli belonging to ST345 and ST2705, and S. Infantis ST32, producing CTX-M-8 or CTX-M-65 ESBLs. On the other hand, wide virulome was associated with a highly virulent behaviour in the Galleria mellonella infection model. Worryingly, all these lineages have been previously reported in humans, supporting that wide resistome and virulome could be contributing to rapid adaptation and dissemination of these clones at the human-animal-environment interface. In summary, wild owls can constitute environmental reservoirs of international clones of ESBL (CTX-M)-producing E. coli and S. Infantis carrying a wide resistome and virulome, in the Southern Cone of America, with potential risks to human, animal and environmental health.
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Affiliation(s)
- Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Mariella Farfán-López
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Ralf Lopes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria E Muñoz
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Ignacia Najle
- Department of Animal Sciences, Faculty of Veterinary Sciences, University of Concepción, Chillán, Chile
| | - Patricio M Muñoz
- Department of Mineralogy and Geotectonics, Institute of Geosciences, University of São Paulo, São Paulo, Brazil
| | - José L Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel González-Acuña
- Department of Animal Sciences, Faculty of Veterinary Sciences, University of Concepción, Chillán, Chile
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil.
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20
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Fernandes MR, Sellera FP, Moura Q, Carvalho MPN, Rosato PN, Cerdeira L, Lincopan N. Zooanthroponotic Transmission of Drug-Resistant Pseudomonas aeruginosa, Brazil. Emerg Infect Dis 2019; 24:1160-1162. [PMID: 29774849 PMCID: PMC6004847 DOI: 10.3201/eid2406.180335] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We recovered VIM-2 carbapenemase-producing Pseudomonas aeruginosa isolates from an infected dog, its owner, and the domestic environment. Genomic investigation revealed household transmission of the high-risk hospital clone sequence type 233 in the human–animal–environment interface. Results suggest zooanthroponotic transmission of VIM-2–producing P. aeruginosa in the household following the patient's hospital discharge.
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21
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Rueda Furlan JP, Moura Q, Lima Gonzalez IH, Locosque Ramos P, Lincopan N, Guedes Stehling E. Draft genome sequence of a multidrug-resistant CTX-M-65-producing Escherichia coli ST156 colonizing a giant anteater (Myrmecophaga tridactyla) in a Zoo. J Glob Antimicrob Resist 2019; 17:19-20. [PMID: 30877057 DOI: 10.1016/j.jgar.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES This study aimed to report the draft genome sequence of a multidrug-resistant (MDR) Escherichia coli colonizing a giant anteater (Myrmecophaga tridactyla) in a Brazilian Zoo. METHODS The genome was sequenced using the Illumina MiSeq Platform and de novo genome assembly was performed using SPAdes v. 3.9. The draft genome sequence was annotated using NCBI Prokaryotic Genome Annotation Pipeline. Antibiotic resistance genes, virulence genes, sequence type, serotype and plasmid incompatibility groups were identified using tools from the Center for Genomic Epidemiology. RESULTS The genome presented 4970 coding sequences and a GC content of 50.2%. Several antimicrobial resistance genes associated with resistance to β-lactams (blaTEM-1A and blaCTX-M-65), aminoglycosides [aph(6)-ld, aph(3″)-lb, aph(4)-la, aac(3)-lVa, aadA1 and aadA2], tetracyclines (tetB), sulphonamides (sul2 and sul3), trimethoprim (dfrA8 and dfrA12) and phenicols (floR and cmlA1) were identified. Moreover, mutations in quinolone resistance-determining regions (QRDR) were found. This E. coli isolate also presented virulence genes and belonged to serotype ONT:H25 and ST156 (CC156). CONCLUSION This is the first report of a draft genome sequence of a CTX-M-65-producing E. coli ST156 obtained from a zoo animal, which can be used by genomic surveillance platforms, in order to track transmission dynamics of extended-spectrum β-lactamase (ESBL)-producing E. coli at the human-animal interface.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.
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22
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de Carvalho MPN, Moura Q, Fernandes MR, Sellera FP, Pagotto AH, Stuginski DR, Castro RA, Sant'Anna SS, Grego KF, Lincopan N. Genomic features of a multidrug-resistant Enterobacter cloacae ST279 producing CTX-M-15 and AAC(6')-Ib-cr isolated from fatal infectious stomatitis in a crossed pit viper (Bothrops alternatus). J Glob Antimicrob Resist 2018; 15:290-291. [PMID: 30448520 DOI: 10.1016/j.jgar.2018.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/05/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The widespread dissemination of extended-spectrum β-lactamase-producing Enterobacteriaceae has become a major issue in veterinary medicine. However, until now, there has been no report of bacteria with such a phenotype in infected snakes. The aim of this study was to report the first draft genome sequence of an Enterobacter cloacae isolate (SERP1) recovered from a snake with infectious stomatitis. METHODS The whole genome of E. cloacae strain SERP1 was sequenced on an Illumina NextSeq platform and was de novo assembled using CLC NGS Cell v.10. Data analysis was performed using online tools from the Center of Genomic Epidemiology. RESULTS The genome size was calculated at 4966856bp, containing a total of 4796 protein-coding sequences. The strain was assigned to sequence type 279 (ST279) and, besides the clinically relevant blaCTX-M-15 and aac(6')-Ib-cr genes, it also presented resistance genes to β-lactams, aminoglycosides, phenicols, sulphonamides, tetracyclines, trimethoprim, quinolones and fosfomycin. CONCLUSION These data offer novel information regarding multidrug-resistant E. cloacae dissemination in wild animals and might contribute to further comparative genomic analysis.
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Affiliation(s)
- Marcelo P N de Carvalho
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | | | | | - Rafael A Castro
- Laboratory of Herpetology, Butantan Institute, São Paulo, Brazil
| | | | - Kathleen F Grego
- Laboratory of Herpetology, Butantan Institute, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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23
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Castelani L, Arcaro JRP, Braga JEP, Bosso AS, Moura Q, Esposito F, Sauter IP, Cortez M, Lincopan N. Short communication: Activity of nisin, lipid bilayer fragments and cationic nisin-lipid nanoparticles against multidrug-resistant Staphylococcus spp. isolated from bovine mastitis. J Dairy Sci 2018; 102:678-683. [PMID: 30415844 DOI: 10.3168/jds.2018-15171] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/19/2018] [Indexed: 11/19/2022]
Abstract
Staphylococci are the main etiological agents of bovine mastitis. Bacteriocins and nanoparticles have emerged as promising alternatives for the future development of antimicrobial agents. This study evaluated the activity of the bacteriocin nisin and bicelles of the synthetic cationic lipid dioctadecyldimethylammonium bromide, alone and in combination, against multidrug-resistant Staphylococcus spp. strains isolated from bovine mastitis. In summary, cationic nisin/dioctadecyldimethylammonium bromide nanoparticles are shown to be a promising alternative for the control of mastitis caused by multidrug-resistant Staphylococcus spp.
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Affiliation(s)
- L Castelani
- Institute of Animal Science, Dairy Cattle Center, Nova Odessa, São Paulo, Brazil 13380-011; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 05508-900.
| | - J R P Arcaro
- Institute of Animal Science, Dairy Cattle Center, Nova Odessa, São Paulo, Brazil 13380-011
| | - J E P Braga
- Institute of Animal Science, Dairy Cattle Center, Nova Odessa, São Paulo, Brazil 13380-011
| | - A S Bosso
- Institute of Animal Science, Dairy Cattle Center, Nova Odessa, São Paulo, Brazil 13380-011
| | - Q Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 05508-900
| | - F Esposito
- Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil 05508-900
| | - I P Sauter
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 05508-900
| | - M Cortez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 05508-900
| | - N Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil 05508-900; Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil 05508-900.
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24
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Silva MM, Sellera FP, Fernandes MR, Moura Q, Garino F, Azevedo SS, Lincopan N. Genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing Escherichia coli ST224 causing fatal infection in a domestic cat. J Glob Antimicrob Resist 2018; 15:252-253. [PMID: 30404045 DOI: 10.1016/j.jgar.2018.10.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVES Escherichia coli strains producing extended-spectrum β-lactamases (ESBLs), especially CTX-M-type, have been largely described in companion animals; however, genomic data are lacking to clarify the clinical impact of ESBL-producing isolates in these hosts. The aim of this study was to present the genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing E. coli isolate from a case of pneumonia in a domestic cat with fatal outcome. METHODS Genomic DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using CLC Genomic Workbench. Genomic data were analysed using online bioinformatics tools. RESULTS The genome size was evaluated at 5.1Mb, with 5334 protein-coding sequences. The strain was assigned to sequence type 224 (ST224) and presented genes conferring resistance to β-lactams (blaCTX-M-8), sulphonamides (sul2), tetracycline (tetA) and trimethoprim (dfrA14) as well as chromosomal point mutations in ParC (S80I), GyrA (S83L) and GyrB (D87N). In addition, the presence of the virulence genes cba, gad, ipfA, iroN, iss, mchF and tsh was detected. CONCLUSION This draft genome sequence might provide important data for a better understanding of genomic aspects regarding the dissemination of CTX-M-8-producing E. coli in the human-animal-environment interface.
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Affiliation(s)
- Meire M Silva
- Academic Veterinary Medicine Unit, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Felício Garino
- Academic Veterinary Medicine Unit, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Sérgio S Azevedo
- Academic Veterinary Medicine Unit, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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25
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Sellera FP, Fernandes MR, Moura Q, Carvalho MPN, Lincopan N. Extended-spectrum-β-lactamase (CTX-M)-producing Escherichia coli in wild fishes from a polluted area in the Atlantic Coast of South America. Mar Pollut Bull 2018; 135:183-186. [PMID: 30301029 DOI: 10.1016/j.marpolbul.2018.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/25/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
The presence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in oceanic ecosystems constitutes an emerging public health risks in the marine environment. In this study, we report for the first time the identification of ESBL (CTX-M)-producing E. coli in wild fishes from a polluted area in the South Atlantic coast of Brazil, where a genomic analysis confirm the presence of livestock and human E. coli lineages belonging to sequence types (STs) ST744 and ST746, which carried clinically relevant resistance genes for human and veterinary antibiotics, and heavy metals. These findings reveal the presence of multidrug-resistant (MDR) bacteria in the gut microbiota of wild fishes living in polluted coastal waters, alerting that microbial contamination by bacteria related directly and indirectly to human or animal activities could affect the safety of the seafood supply, as well as the commercial and recreational use of coastal marine waters.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo P N Carvalho
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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26
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Fernandes MR, Sellera FP, Moura Q, Gaspar VC, Cerdeira L, Lincopan N. International high-risk clonal lineages of CTX-M-producing Escherichia coli F-ST648 in free-roaming cats, South America. Infect Genet Evol 2018; 66:48-51. [PMID: 30227226 DOI: 10.1016/j.meegid.2018.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022]
Abstract
The dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli belonging to high-virulent pandemic lineages has become a global problem with serious consequences for public health worldwide. In this regard, E. coli lineages belonging to the sequence type ST648, which are mostly associated with human infections, have begun to be reported in animals. In this study, we report the identification and genomic characterization of international CTX-M-producing E. coli ST648/F lineages in free-roaming cats from an urban slum, in Brazil. Moreover, we have performed a comparative genomic analysis of worldwide reported E. coli ST648 strains, highlighting an epidemiologic linkage between human and companion animals.
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Affiliation(s)
- Miriam R Fernandes
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vitor C Gaspar
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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27
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Moura Q, Esposito F, Fernandes MR, Espinoza-Muñoz M, Souza TA, Santos SR, Cerdeira L, Cassettari V, Lincopan N. Genome sequence analysis of a hypermucoviscous/hypervirulent and MDR CTX-M-15/K19/ST29 Klebsiella pneumoniae isolated from human infection. Pathog Dis 2018; 75:4705889. [PMID: 29228178 DOI: 10.1093/femspd/ftx121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
The emergence of hypervirulent Klebsiella pneumoniae (hvKP) with multidrug resistance (MDR) profile is a worrisome public health issue. We report the first draft genome sequence of a hypermucoviscous (positive string test) and MDR K. pneumoniae serotype K19, belonging to ST29, isolated from human infection. This strain harboured multiple antimicrobial resistance genes, including blaCTX-M-15, besides yersiniabactin and type 3 fimbriae virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that K. pneumoniae K19/ST29 killed 100% of the larvae at 24 h post-infection, in a similar way to the known hypermucoviscous hvKP K1/ST23 lineage.
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Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Maria Espinoza-Muñoz
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Silvia R Santos
- Laboratory of Clinical Analysis, Hospital Universitário, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Valéria Cassettari
- Hospital Infection Control Committee, Hospital Universitário, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
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28
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Sellera FP, Fernandes MR, Moura Q, Lopes RB, Souza TA, Cerdeira L, Lincopan N. Draft genome sequence of a bla CMY-2/IncI1-harbouring Escherichia coli D:ST457 isolated from coastal benthic organisms. J Glob Antimicrob Resist 2018; 14:83-84. [PMID: 29944920 DOI: 10.1016/j.jgar.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/19/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Marine bivalves can act as bioindicators of marine environment pollution by multidrug-resistant (MDR) enteric bacteria of medical interest. The aim of this study was to report the draft genome sequence of a plasmid-encoded AmpC (pAmpC) (CMY-2)-carrying Escherichia coli isolate recovered from a marine bivalve sample in the coastal shore of Southeast Brazil. METHODS The whole genome was sequenced on an Illumina NextSeq platform and was assembled using Velvet v.1.2.10. Data analysis was carried out using tools available from the Center of Genomic Epidemiology and Geneious R10 software. RESULTS The genome size was calculated at 5198055bp, comprising a total of 5316 protein-coding sequences. The strain was assigned to ST457 and presented the blaCMY-2 pAmpC gene. In addition, the strain was clustered into the pathogenic phylogenetic group D. CONCLUSION The release of this draft genome sequence can provide valuable information to better understand the dissemination of MDR enteric bacteria in marine environments.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ralf B Lopes
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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29
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Moura Q, Cerdeira L, Fernandes MR, Vianello MA, Lincopan N. Novel class 1 integron (In1390) harboring bla GES-5 in a Morganella morganii strain recovered from a remote community. Diagn Microbiol Infect Dis 2018; 91:345-347. [PMID: 29628289 DOI: 10.1016/j.diagmicrobio.2018.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/16/2018] [Accepted: 03/05/2018] [Indexed: 11/25/2022]
Abstract
Antimicrobial resistance in Morganella morganii has been mainly acquired via plasmids and class 1 integrons. We hereby report acquisition of blaGES-5 by a M. morganii isolated in a remote community from the Amazon region. Genomic analysis revealed that blaGES-5 was harbored by a novel class 1 integron designated as In1390.
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Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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Fernandes MR, Sellera FP, Moura Q, Souza TA, Lincopan N. Draft genome sequence of a CTX-M-8, CTX-M-55 and FosA3 co-producing Escherichia coli ST117/B2 isolated from an asymptomatic carrier. J Glob Antimicrob Resist 2018; 12:183-184. [DOI: 10.1016/j.jgar.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 10/18/2022] Open
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Sellera FP, Fernandes MR, Moura Q, Souza TA, Nascimento CL, Cerdeira L, Lincopan N. Draft genome sequence of an extensively drug-resistant Pseudomonas aeruginosa isolate belonging to ST644 isolated from a footpad infection in a Magellanic penguin (Spheniscus magellanicus). J Glob Antimicrob Resist 2017; 12:88-89. [PMID: 29277728 DOI: 10.1016/j.jgar.2017.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES The incidence of multidrug-resistant bacteria in wildlife animals has been investigated to improve our knowledge of the spread of clinically relevant antimicrobial resistance genes. The aim of this study was to report the first draft genome sequence of an extensively drug-resistant (XDR) Pseudomonas aeruginosa ST644 isolate recovered from a Magellanic penguin with a footpad infection (bumblefoot) undergoing rehabilitation process. METHODS The genome was sequenced on an Illumina NextSeq® platform using 150-bp paired-end reads. De novo genome assembly was performed using Velvet v.1.2.10, and the whole genome sequence was evaluated using bioinformatics approaches from the Center of Genomic Epidemiology, whereas an in-house method (mapping of raw whole genome sequence reads) was used to identify chromosomal point mutations. RESULTS The genome size was calculated at 6436450bp, with 6357 protein-coding sequences and the presence of genes conferring resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracyclines, quinolones and fosfomycin; in addition, mutations in the genes gyrA (Thr83Ile), parC (Ser87Leu), phoQ (Arg61His) and pmrB (Tyr345His), conferring resistance to quinolones and polymyxins, respectively, were confirmed. CONCLUSION This draft genome sequence can provide useful information for comparative genomic analysis regarding the dissemination of clinically significant antibiotic resistance genes and XDR bacterial species at the human-animal interface.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Fernandes MR, Moura Q, Esposito F, Lincopan N. Authors' reply: Escherichia coli harbouring mcr-1 gene isolated from poultry not exposed to polymyxins in Brazil. ACTA ACUST UNITED AC 2017; 21:30268. [PMID: 27386795 DOI: 10.2807/1560-7917.es.2016.21.26.30268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/20/2022]
Affiliation(s)
- Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
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Sellera FP, Fernandes MR, Moura Q, Souza TA, Cerdeira L, Lincopan N. Draft genome sequence of Enterobacter cloacae ST520 harbouring bla KPC-2, bla CTX-M-15 and bla OXA-17 isolated from coastal waters of the South Atlantic Ocean. J Glob Antimicrob Resist 2017; 10:279-280. [PMID: 28827199 DOI: 10.1016/j.jgar.2017.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVES Aquatic environments have contributed to the dissemination of multidrug-resistant (MDR) bacteria, representing a risk for humans and animals. The aim of this study was to report the first draft genome sequence of a MDR Enterobacter cloacae strain recovered from seawater in a public beach in Brazil. METHODS The genome was sequenced on an Illumina MiSeq platform. De novo genome assembly was performed using SPAdes 3.10.1 and the whole genome sequence was analysed using bioinformatics tools from the Center of Genomic Epidemiology. RESULTS This draft genome resulted in 5 228 857bp with 5331 protein-coding sequences, revealing the presence of blaKPC-2, blaCTX-M-15 and blaOXA-17 genes, responsible for resistance to all β-lactam antibiotics. In addition, the strain was assigned to sequenced type 520 (ST520). CONCLUSION These data provide useful information for comparative genomic analysis regarding the dissemination of antibiotic resistance genes.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Moura Q, Fernandes MR, Cerdeira L, Nhambe LF, Ienne S, Souza TA, Lincopan N. Draft genome sequence of a multidrug-resistant KPC-2-producing Enterobacter aerogenes isolated from a hospitalised patient in Brazil. J Glob Antimicrob Resist 2017; 10:277-278. [PMID: 28764940 DOI: 10.1016/j.jgar.2017.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES Multidrug-resistant (MDR) Enterobacter aerogenes strains are frequently associated with nosocomial infections and high mortality rates, representing a serious public health problem. The aim of this study was to present the draft genome sequence of a MDR KPC-2-producing E. aerogenes isolated from a perineal swab of a hospitalised patient in Brazil. METHODS Genomic DNA was sequenced using an Illumina MiSeq platform. De novo genome assembly was carried out using the A5-Miseq pipeline, and whole-genome sequence analysis was performed using tools from the Center for Genomic Epidemiology. RESULTS The strain harboured resistance genes to β-lactams, aminoglycosides, sulphonamides and trimethoprim in addition to genes encoding multidrug efflux system proteins, a quaternary ammonium transporter and heavy metal efflux system proteins. In addition, the strain harboured genes encoding diverse virulence factors. CONCLUSION These data might allow a better understanding of the genetic basis of antimicrobial resistance and virulence in E. aerogenes strains.
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Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Lúcia F Nhambe
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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Moura Q, Fernandes MR, Cerdeira L, Santos ACM, de Souza TA, Ienne S, Pignatari ACC, Gales AC, Silva RM, Lincopan N. Draft genome sequence of a multidrug-resistant Aeromonas hydrophila ST508 strain carrying rmtD and bla CTX-M-131 isolated from a bloodstream infection. J Glob Antimicrob Resist 2017; 10:289-290. [PMID: 28739226 DOI: 10.1016/j.jgar.2017.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 11/29/2022] Open
Abstract
Here we report the draft genome sequence of a multidrug-resistant (MDR) Aeromonas hydrophila strain belonging to sequence type 508 (ST508) isolated from a human bloodstream infection. Assembly and annotation of this draft genome resulted in 5028498bp and revealed the presence of 16S rRNA methylase rmtD and blaCTX-M-131 genes encoding high-level resistance to aminoglycosides and cephalosporins, respectively, as well as multiple virulence genes. This draft genome can provide significant information for understanding mechanisms on the establishment and treatment of infections caused by this pathogen.
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Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Ana Carolina M Santos
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Tiago A de Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antonio Carlos C Pignatari
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Ana C Gales
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Rosa M Silva
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil.
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Moura Q, Fernandes MR, Silva KC, Monte DF, Esposito F, Dropa M, Noronha C, Moreno AM, Landgraf M, Negrão FJ, Lincopan N. Virulent nontyphoidal Salmonella producing CTX-M and CMY-2 β-lactamases from livestock, food and human infection, Brazil. Virulence 2017; 9:281-286. [PMID: 28102761 PMCID: PMC5955470 DOI: 10.1080/21505594.2017.1279779] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Quézia Moura
- a Department of Microbiology , Institute of Biomedical Sciences, Universidade de São Paulo , São Paulo , Brazil
| | - Miriam R Fernandes
- b Department of Clinical Analysis , School of Pharmacy, Universidade de São Paulo , São Paulo , Brazil
| | - Ketrin C Silva
- c School of Veterinary Medicine, Universidade de São Paulo , São Paulo , Brazil
| | - Daniel F Monte
- d Food and Experimental Nutrition Department , School of Pharmacy & Food Research Center, Universidade de São Paulo , São Paulo , Brazil
| | - Fernanda Esposito
- b Department of Clinical Analysis , School of Pharmacy, Universidade de São Paulo , São Paulo , Brazil
| | - Milena Dropa
- e Public Health Laboratory, School of Public Health, Universidade de São Paulo , São Paulo , Brazil
| | - César Noronha
- f State Center for Clinical Analysis , São Paulo, São Paulo , Brazil
| | - Andrea M Moreno
- c School of Veterinary Medicine, Universidade de São Paulo , São Paulo , Brazil
| | - Mariza Landgraf
- d Food and Experimental Nutrition Department , School of Pharmacy & Food Research Center, Universidade de São Paulo , São Paulo , Brazil
| | - Fábio J Negrão
- g Health Sciences Research Laboratory, School of Health Sciences, Universidade Federal da Grande Dourados , Dourados , Brazil
| | - Nilton Lincopan
- a Department of Microbiology , Institute of Biomedical Sciences, Universidade de São Paulo , São Paulo , Brazil.,b Department of Clinical Analysis , School of Pharmacy, Universidade de São Paulo , São Paulo , Brazil
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Moura Q, Fernandes MR, Cerdeira L, Ienne S, Souza TA, Negrão FJ, Lincopan N. Draft genome sequence of a multidrug-resistant CMY-2-producing Salmonella enterica subsp. enterica serovar Minnesota ST3088 isolated from chicken meat. J Glob Antimicrob Resist 2016; 8:67-69. [PMID: 28017672 DOI: 10.1016/j.jgar.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/20/2016] [Accepted: 10/31/2016] [Indexed: 11/19/2022] Open
Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Susan Ienne
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fábio Juliano Negrão
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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