1
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Foo A, Cerdeira L, Hughes GL, Heinz E. Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR. Wellcome Open Res 2023; 8:131. [PMID: 37577055 PMCID: PMC10412942 DOI: 10.12688/wellcomeopenres.19155.2] [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] [Accepted: 05/18/2023] [Indexed: 08/15/2023] Open
Abstract
Background: Ongoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects. Methods: To analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths. Results: We demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs. Conclusions: Our metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.
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Affiliation(s)
- Aidan Foo
- Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Louise Cerdeira
- Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Grant L. Hughes
- Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Eva Heinz
- Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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2
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Carey ME, Dyson ZA, Argimón S, Cerdeira L, Yeats C, Aanensen D, Mboowa G, Baker S, Tessema SK, Smith AM, Okeke IN, Holt KE. Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open Forum Infect Dis 2023; 10:S38-S46. [PMID: 37274533 PMCID: PMC10236510 DOI: 10.1093/ofid/ofad044] [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] [Indexed: 06/06/2023] Open
Abstract
The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.
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Affiliation(s)
- Megan E Carey
- Correspondence: Megan E. Carey, PhD, MSPH, Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK ()
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Louise Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- IAVI, Chelsea & Westminster Hospital, London, United Kingdom
| | - Sofonias K Tessema
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Anthony M Smith
- Division of the National Health Laboratory Service, Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
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3
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Dias JB, Soncini JGM, Cerdeira L, Lincopan N, Vespero EC. MDR Escherichia coli carrying CTX-M-24 (IncF[F-:A1:B32]) and KPC-2 (IncX3/IncU) plasmids isolated from community-acquired urinary trainfection in Brazil. Braz J Infect Dis 2022; 26:102706. [PMID: 36228665 PMCID: PMC9646818 DOI: 10.1016/j.bjid.2022.102706] [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: 05/21/2022] [Revised: 08/28/2022] [Accepted: 09/17/2022] [Indexed: 11/05/2022] Open
Abstract
Acquired antibiotic resistance in bacteria has become an important worldwide challenge. Currently, several bacteria, including Escherichia coli, have multidrug resistance profiles. Genes such as bla CTX-M-24 and bla KPC-2 (carbapenemase) are widespread. This research letter reports about a genomic surveillance study where multidrug-resistant E. coli containing CTX-M-24(IncF [F-:A1:B32]) and KPC-2(IncX3/IncU) plasmids were obtained from community- acquired urinary tract infection in Brazil.
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Affiliation(s)
- Juliana Buck Dias
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de Patologia, Análises Clínicas e Toxicológicas, Laboratório de Microbiologia Clínica, Londrina, PR, Brazil
| | - João Gabriel Material Soncini
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de Patologia, Análises Clínicas e Toxicológicas, Laboratório de Microbiologia Clínica, Londrina, PR, Brazil,Corresponding author.
| | - Louise Cerdeira
- Liverpool School of Tropical Medicine, Department of Vector Biology, Liverpool, United Kingdom,Monash University, Central Clinical School, Department of Infectious Diseases, Melbourne, Australia
| | - Nilton Lincopan
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Eliana Carolina Vespero
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de Patologia, Análises Clínicas e Toxicológicas, Laboratório de Microbiologia Clínica, Londrina, PR, Brazil
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4
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Quek S, Cerdeira L, Jeffries CL, Tomlinson S, Walker T, Hughes GL, Heinz E. Wolbachia endosymbionts in two Anopheles species indicates independent acquisitions and lack of prophage elements. Microb Genom 2022; 8. [PMID: 35446252 PMCID: PMC9453072 DOI: 10.1099/mgen.0.000805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/20/2022] Open
Abstract
Wolbachia is a genus of obligate bacterial endosymbionts that infect a diverse range of arthropod species as well as filarial nematodes, with its single described species, Wolbachia pipientis, divided into several ‘supergroups’ based on multilocus sequence typing. Wolbachia strains in mosquitoes have been shown to inhibit the transmission of human pathogens, including Plasmodium malaria parasites and arboviruses. Despite their large host range, Wolbachia strains within the major malaria vectors of the Anopheles gambiae and Anopheles funestus complexes appear at low density, established solely on PCR-based methods. Questions have been raised as to whether this represents a true endosymbiotic relationship. However, recent definitive evidence for two distinct, high-density strains of supergroup B Wolbachia within Anopheles demeilloni and Anopheles moucheti has opened exciting possibilities to explore naturally occurring Wolbachia endosymbionts in Anopheles for biocontrol strategies to block Plasmodium transmission. Here, we utilize genomic analyses to demonstrate that both Wolbachia strains have retained all key metabolic and transport pathways despite their smaller genome size, with this reduction potentially attributable to degenerated prophage regions. Even with this reduction, we confirmed the presence of cytoplasmic incompatibility (CI) factor genes within both strains, with wAnD maintaining intact copies of these genes while the cifB gene was interrupted in wAnM, so functional analysis is required to determine whether wAnM can induce CI. Additionally, phylogenetic analysis indicates that these Wolbachia strains may have been introduced into these two Anopheles species via horizontal transmission events, rather than by ancestral acquisition and subsequent loss events in the Anopheles gambiae species complex. These are the first Wolbachia genomes, to our knowledge, that enable us to study the relationship between natural strain Plasmodium malaria parasites and their anopheline hosts.
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Affiliation(s)
- Shannon Quek
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Louise Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claire L Jeffries
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Sean Tomlinson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Walker
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Grant L Hughes
- Department of Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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5
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Hawkey J, Cottingham H, Tokolyi A, Wick RR, Judd LM, Cerdeira L, de Oliveira Garcia D, Wyres KL, Holt KE. Linear plasmids in Klebsiella and other Enterobacteriaceae. Microb Genom 2022; 8. [PMID: 35416146 PMCID: PMC9453081 DOI: 10.1099/mgen.0.000807] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family Enterobacteriaceae belong to Salmonella, first found in Salmonella enterica Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. Screening of assembly graphs assembled from public read sets identified linear plasmid structures in a further 13 K. pneumoniae species complex genomes. We used these 25 linear plasmid sequences to query all bacterial genome assemblies in the National Center for Biotechnology Information database, and discovered an additional 61 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function; however, each phylogroup carried its own unique toxin–antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug-resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Alex Tokolyi
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | | | | | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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6
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Fedrigo NH, Xavier DE, Cerdeira L, Fuga B, Marini PVB, Shinohara DR, Carrara-Marroni FE, Lincopan N, Tognim MCB. Genomic insights of Acinetobacter baumannii ST374 reveal wide and increasing resistome and virulome. Infect Genet Evol 2022; 97:105148. [PMID: 34801753 DOI: 10.1016/j.meegid.2021.105148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/17/2021] [Revised: 09/23/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
WGS-based surveillance has significantly improved the ability to track global spread and emergence of multidrug-resistant clones of clinically relevant pathogens. In this study, we performed the genomic characterization and comparative analysis of an Acinetobacter baumannii (strain Ac56) belonging to the sequence type ST374, which was isolated for the first time in Brazil, in 1996. Genomic analysis of Ac56 predicted a total of 5373 genes, with 3012 being identical across nine genomes of A. baumannii isolates of ST374 from European, Asian, North and South American countries. GoeBURST analysis grouped ST374 lineages into clonal complex CC3 (international clone IC-III). Resistome analysis of ST374 clone predicted genes associated with resistance to heavy metals and clinically relevant beta-lactams and aminoglycosides antibiotics. In this regard, in two closely related A. baumannii strains, the intrinsic blaADC gene was linked to the insertion sequence ISAba1; including the Ac56 strain, where it has been possibly associated with intermediate susceptibility to meropenem. Other four carbapenem-resistant A. baumannii strains carried the ISAba1/blaOXA-23 gene array, which was associated with the transposon Tn2008 or with Tn2006 in an AbaR4-type resistance island. While most virulence genes were shared for A. baumannii strains of ST374, three isolates from Thailand harbored KL49 capsular loci, previously identified in the hypervirulent A. baumannii LAC-4 strain. Analysis of thirty-four predicted plasmids showed eight major groups, of which GR-6 (LN-1) and GR-2 (LN-2) were prevalent. All strains, including the earliest isolate Ac56 harbored at least one complete prophage, whereas none CRISPR-associated (cas) gene was detected. In summary, genomic data of A. baumannii ST374 reveal a potential of this lineage to become a successful clone.
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Affiliation(s)
| | | | - Louise Cerdeira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | - Floristher Elaine Carrara-Marroni
- Department of Pathology, Clinical and Toxicological Analysis, University Hospital, State University of Londrina, Londrina, Paraná, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Science, 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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7
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Gonzales-Escalante E, Ruggiero M, Cerdeira L, Esposito F, Fontana H, Lincopan N, Gutkind G, Di Conza J. Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST147 Carrying Both mcr-1 and blaNDM-1 Genes in Peru. Microb Drug Resist 2021; 28:171-179. [PMID: 34698586 DOI: 10.1089/mdr.2021.0128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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
The increasing prevalence and dissemination of carbapenemase-producing Enterobacterales represent a serious concern for public health. We studied the genetic features of a multidrug-resistant isolate of high-risk clone ST147 Klebsiella pneumoniae coharboring mcr-1 and blaNDM-1 recovered from a human clinical urine sample in 2017 in Peru. Whole-genome sequencing and conjugation assays identified mcr-1 and blaNDM-1 genes on two different conjugative plasmids, which belong to IncI2 and IncFIB/HI1B incompatibility groups, respectively. The presence of blaCTX-M-15 (in the studied isolate, located on the chromosome) and mutations in GyrA S83I and ParC S80I were detected, as expected for ST147. In addition, other β-lactamases (blaTEM-26 and blaOXA-1) and PMQR (qnrE2 and aac(6')-Ib-cr) among several resistance determinants were identified. The coexistence not previously described of these genes in the same high-risk clone is a cause for serious concern that supports the need for implementation of genomic surveillance studies.
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Affiliation(s)
- Edgar Gonzales-Escalante
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales - CITBM, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Melina Ruggiero
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
| | - Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Fernanda Esposito
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Herrison Fontana
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Gabriel Gutkind
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
| | - Jose Di Conza
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
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8
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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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9
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Fernandes MR, Sellera FP, Cunha MPV, Lopes R, Cerdeira L, Lincopan N. Emergence of CTX-M-27-producing Escherichia coli of ST131 and clade C1-M27 in an impacted ecosystem with international maritime traffic in South America. J Antimicrob Chemother 2021; 75:1647-1649. [PMID: 32167559 PMCID: PMC7225873 DOI: 10.1093/jac/dkaa069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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
| | - Marcos P V Cunha
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Ralf Lopes
- 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
| | - 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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10
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Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nat Commun 2021; 12:2684. [PMID: 33976138 PMCID: PMC8113504 DOI: 10.1038/s41467-021-22700-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/23/2021] [Indexed: 01/20/2023] Open
Abstract
Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Kalani Paranagama
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Ecological and Veterinary Sciences, University of Liverpool, Liverpool, UK
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Dept Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Zamin Iqbal
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Martin Hunt
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | | | - Claire Jenkins
- National Infection Service, Public Health England, London, UK
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Dept Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
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11
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de Campos TA, de Almeida FM, de Almeida APC, Nakamura-Silva R, Oliveira-Silva M, de Sousa IFA, Cerdeira L, Lincopan N, Pappas GJ, Pitondo-Silva A. Multidrug-Resistant (MDR) Klebsiella variicola Strains Isolated in a Brazilian Hospital Belong to New Clones. Front Microbiol 2021; 12:604031. [PMID: 33935984 PMCID: PMC8085564 DOI: 10.3389/fmicb.2021.604031] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/25/2021] [Indexed: 01/18/2023] Open
Abstract
Klebsiella variicola is mainly associated with opportunistic infections and frequently identified as Klebsiella pneumoniae. This misidentification implies a wrong epidemiology result as well as incorrect attribution to K. pneumoniae as the etiology of some severe infections. Recently, huge efforts have been made to study K. variicola, however, the biological aspects of this species are still unclear. Here we characterized five K. variicola strains initially identified as K. pneumoniae, with a Vitek-2 System and 16S rRNA sequencing. One-step multiplex polymerase chain reaction and Whole Genome Sequencing (WGS) identified them as K. variicola. Additionally, WGS analysis showed that all the strains are closely related with K. variicola genomes, forming a clustered group, apart from K. pneumoniae and K. quasipneumoniae. Multilocus sequence typing analysis showed four different sequence types (STs) among the strains and for two of them (Kv97 and Kv104) the same ST was assigned. All strains were multidrug-resistant (MDR) and three showed virulence phenotypes including invasion capacity to epithelial cells, and survival in human blood and serum. These results showed the emergence of new K. variicola clones with pathogenic potential to colonize and cause infection in different tissues. These characteristics associated with MDR strains raise great concern for human health.
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Affiliation(s)
- Tatiana Amabile de Campos
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Brasília, Brazil
| | | | | | - Rafael Nakamura-Silva
- Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Mariana Oliveira-Silva
- Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil
| | | | - Louise Cerdeira
- Instituto de Ciências Biológicas, Universidade de São Paulo, São Paulo, Brazil.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Nilton Lincopan
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Georgios Joannis Pappas
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Biologia Molecular, Universidade de Brasília, Brasília, Brazil
| | - André Pitondo-Silva
- Programa de Pós-graduação em Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil.,Programa de Pós-graduação em Odontologia, Universidade de Ribeirão Preto, Ribeirão Preto, Brazil
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12
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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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13
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Sellera FP, Fuga B, Fontana H, Esposito F, Cardoso B, Konno S, Berl C, Cappellanes MH, Cortez M, Ikeda M, de Souza CM, Cerdeira L, Lincopan N. Detection of IncN-pST15 one-health plasmid harbouring bla KPC-2 in a hypermucoviscous Klebsiella pneumoniae CG258 isolated from an infected dog, Brazil. Transbound Emerg Dis 2021; 68:3083-3088. [PMID: 33507616 PMCID: PMC9290030 DOI: 10.1111/tbed.14006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/27/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022]
Abstract
The emergence and rapid spread of carbapenemase‐producing Enterobacterales represents a serious public health concern. Critically, these global priority bacteria have begun to be reported in companion animals, implying a potential risk of cross‐transmission between humans and pets. Using long‐read (MinION) and short‐read (Illumina) sequencing technologies, we have identified and characterized a hypermucoviscous KPC‐2‐producing Klebsiella pneumoniae strain belonging to the high‐risk international clone ST11/CG258, in a dog with urinary tract infection. Strikingly, the blaKPC‐2 gene was carried by a 54‐kb IncN plasmid assignated to ST15, which shared 99.8 and 96.8% pairwise identity with IncN‐pST15 plasmids from human and environmental K. pneumoniae strains, respectively; all come from an area with high endemicity of KPC‐2. Our findings suggest that IncN‐pST15 plasmids conferring carbapenem resistance can play as important a role as clonal transmission of K. pneumoniae, representing another major challenge for One Health.
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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.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Carla Berl
- PetCare Veterinary Hospital, São Paulo, Brazil
| | | | | | | | - César M de Souza
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Clayton, Vic., Australia
| | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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14
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Cardoso B, Fontana H, Esposito F, Cerdeira L, Santos SR, Yoshioka CRM, da Silveira IR, Cassettari V, Lincopan N. Genomic insights of international clones of Haemophilus influenzae causing invasive infections in vaccinated and unvaccinated infants. Microb Pathog 2020; 150:104644. [PMID: 33259886 DOI: 10.1016/j.micpath.2020.104644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
The emergence of invasive Haemophilus influenzae infections in vaccinated patient is a public health concern. We have investigated the genomic basis of invasiveness and possible vaccine failure in H. influenzae causing invasive disease in vaccinated and unvaccinated children in Brazil. Three H. influenzae strains isolated from blood cultures of pediatric patients were sequenced. Serotype, MLST, resistome and virulome were predicted using bioinformatic tools, whereas single nucleotide polymorphisms (SNPs) analysis of cap loci and the presence of the putative virulence-enhancing IS1016-bexA partial deletion were predicted in silico. Infections were caused by H. influenzae type a (Hia), type b (Hib) and nontypeable (NTHi), belonging to international high-risk clones of sequence types ST23, ST6 and ST368, respectively, which have been identified in North American, European and Asian countries. Convergence of ampicillin resistance and virulence in Hib-ST6 was supported by blaTEM-1B and deletion in the bexA gene, whereas presence of SNPs in the cap-b locus was associated with antigenic modifications of the capsule structure. Hia-ST23 and NTHi-ST368 strains carried galU, lpsA, opsX, rfaF, iga1, lgtC and lic1/lic2 virulence genes, associated with colonization, adaptation and damage to the lung, or invasiveness. In summary, deletion in the bexA gene and presence of SNPs in the cap locus of Hib could be contributing to invasive disease and possible vaccine failure in pediatric patients, whereas serotype replacement of Hib with type "a" and NTHi strains denotes the ability of non-vaccine serotypes to re-colonize vaccinated patients. Finally, the dissemination of international high-risk clones of H. influenzae emphasizes the importance of monitoring changes in the molecular epidemiology of invasive H. influenzae disease.
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Affiliation(s)
- Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil.
| | - Herrison Fontana
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- 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
| | - Silvia R Santos
- University Hospital, Infection Control Committee, University of São Paulo, Brazil
| | | | - Isa R da Silveira
- University Hospital, Infection Control Committee, University of São Paulo, Brazil
| | - Valéria Cassettari
- University Hospital, Infection Control Committee, University of São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil.
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15
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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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16
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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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17
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Rossi I, Royer S, Ferreira M, Braga IA, Campos P, Batistão D, Fuga B, Cerdeira L, Lincopan N, Gontijo-Filho PP, Ribas RM. Novel ST1465/CC216 Nosocomial Lineage of Carbapenem-Resistant Acinetobacter baumannii Harboring an Unusual Plasmid Carrying blaNDM-1 Gene. Microb Drug Resist 2020; 27:471-475. [PMID: 32915684 DOI: 10.1089/mdr.2020.0219] [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: 11/13/2022] Open
Abstract
This study used whole-genome sequencing to analyze the first case of NDM-1-producing Acinetobacter baumannii belonging to the novel sequence type 1465/CC216 recovered in Brazil. The study identified an unusual plasmid carrying blaNDM-1 gene, in which some genes of the Tn125 transposon were lost. Besides, on the chromosome, the strain reported here presented blaOXA-106 gene, a variant of blaOXA-51 gene, and blaADC-25 with ISAba1 upstream. The isolation of new STs of A. baumannii carrying blaNDM-1 genes elicits our concerns about the possible spread of these genes among clinically relevant bacteria.
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Affiliation(s)
- Iara Rossi
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Sabrina Royer
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Melina Ferreira
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Iolanda A Braga
- Hospital das Clínicas and Federal University of Uberlândia, Uberlândia, Brazil
| | - Paola Campos
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Deivid Batistão
- School of Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bruna Fuga
- 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.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo P Gontijo-Filho
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rosineide M Ribas
- Laboratory of Molecular Microbiology, Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, Brazil
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18
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Cerdeira L, Monte DFM, Fuga B, Sellera FP, Neves I, Rodrigues L, Landgraf M, Lincopan N. Genomic insights of Klebsiella pneumoniae isolated from a native Amazonian fish reveal wide resistome against heavy metals, disinfectants, and clinically relevant antibiotics. Genomics 2020; 112:5143-5146. [PMID: 32916256 PMCID: PMC7758709 DOI: 10.1016/j.ygeno.2020.09.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/09/2020] [Revised: 09/01/2020] [Accepted: 09/05/2020] [Indexed: 12/05/2022]
Abstract
A multidrug-resistant CTX-M-15-producing Klebsiella pneumoniae (KpP1 strain) was isolated from a native Amazonian fish (Brachyplatystoma filamentosum) at the Brazilian Amazon. The strain was identified by MALDI-TOF. The genome was extracted, purified and a Nextera DNA Flex library was prepared and sequenced by Illumina platform. The sequenced genome was de novo assembled using Unicycler and in silico prediction accomplished by curated bioinformatics tools. The size of the genome is 5.6 Mb with 5715 genes. Whole-genome sequencing analysis revealed the presence of wide resistome, with genes conferring resistance to clinically relevant antibiotics, heavy metals and disinfectants. The KpP1 strain was assigned to the sequence type ST3827, KL111 (wzi113) and O3b locus. Native freshwater fish sold in wet markets of the Amazonian region could be an important vehicle for transmission of multidrug-resistant bacteria to humans. This study may give genomic insights on the spread of critical-priority WHO pathogens in a One Health context. A multidrug-resistant Klebsiella pneumoniae was isolated from a native Amazonian fish. Genomic analysis revealed that K. pneumoniae belonged to ST3827, KL111 and O3b locus. A wide resistome against heavy metals, disinfectants, and relevant antibiotics was predicted. ESBL production was associated with the blaCTX-M-15 gene carried on an IncFII(K) plasmid. Native freshwater fishes could be a vehicle for transmission of critical-priority pathogens.
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Affiliation(s)
- Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Australia; One Health Brazilian Resistance Project (OneBR), Brazil.
| | - Daniel F M Monte
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Food and Experimental Nutrition, Food Research Center, Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de 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
| | - Ingrith Neves
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Larissa Rodrigues
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Food Research Center, Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
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19
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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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20
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Nakamura-Silva R, Macedo LMD, Cerdeira L, Oliveira-Silva M, Silva-Sousa YTC, Pitondo-Silva A. First report of hypermucoviscous Klebsiella variicola subsp. variicola causing primary endodontic infection. Clin Microbiol Infect 2020; 27:303-304. [PMID: 32771643 DOI: 10.1016/j.cmi.2020.07.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/10/2020] [Accepted: 07/30/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Rafael Nakamura-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Louise Cerdeira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Mariana Oliveira-Silva
- Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - André Pitondo-Silva
- Postgraduate Program in Dentistry, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil; Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil.
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21
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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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22
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Mohsin M, Azam M, Ur Rahman S, Esposito F, Sellera FP, Monte DF, Cerdeira L, Lincopan N. Genomic background of a colistin-resistant and highly virulent MCR-1-positive Escherichia coli ST6395 from a broiler chicken in Pakistan. Pathog Dis 2020; 77:5647353. [PMID: 31782775 DOI: 10.1093/femspd/ftz064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 08/08/2019] [Accepted: 11/28/2019] [Indexed: 11/12/2022] Open
Abstract
The convergence of high virulence and multidrug resistance (MDR) in Gram-negative pathogens circulating at the human-animal interface is a critical public health issue. We hereby report the genomic characteristics and virulent behavior of a colistin-resistant Escherichia coli, serotype ONT:H26, belonging to ST6395, isolated from a healthy broiler in Pakistan. This strain harbored multiple antimicrobial resistance genes, including mcr-1.1 and blaCARB-2, besides cma (colicin M) and astA [heat-stable enterotoxin 1 (EAST1) toxin] virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that MCR-1-positive E. coli ST6395 killed 96.4% of the larvae at 18 hour post-infection. Interplay between resistance and virulence in clinically important pathogens could be a potential threat, representing a serious challenge to global public health.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Mariya Azam
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Sajjad Ur Rahman
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, CEP 05508-000, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, CEP 05508-270, Brazil
| | - Daniel F Monte
- Department of Food and Experimental Nutrition, Food Research Center, Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes 580, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Louise Cerdeira
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, CEP 05508-000, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, CEP 05508-000, Brazil
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23
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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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24
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Quezada-Aguiluz M, Lincopan N, Cerdeira L, Fuga B, Silva F, Barrera B, Cifuentes M, Bello-Toledo H, Opazo-Capurro A, González-Rocha G. Draft genome sequence of a multidrug-resistant KPC-2 and SRT-2 co-producing Serratia marcescens strain isolated from a hospitalised patient in Chile. J Glob Antimicrob Resist 2020; 21:1-2. [PMID: 32061814 DOI: 10.1016/j.jgar.2020.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/14/2019] [Revised: 01/21/2020] [Accepted: 02/06/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Serratia marcescens is a neglected opportunistic pathogen of public-health concern, especially due to its antimicrobial resistance features. Here we report the draft genome sequence of the first KPC-2 and SRT-2 co-producing S. marcescens strain (UCO-366) recovered from a catheter tip culture of a hospitalised patient in Santiago, Chile, in 2014. METHODS Whole genomic DNA of strain UCO-366 was extracted and was sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Unicycler v.0.4.0 and the genome was annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.8. Genomic features were analysed using bioinformatic tools available at the Center for Genomic Epidemiology, the Comprehensive Antibiotic Resistance Database (CARD) and Pathosystems Resource Integration Center (PATRIC). RESULTS The genome size of strain UCO-366 was 5 267 357bp, with a G+C content of 59.7% and comprising 5299 coding sequences (CDS), 42 tRNAs and 115 pseudogenes. The genome of UCO-366 also included an IncL/M plasmid. The resistome comprised various antimicrobial resistance genes (ARGs) conferring resistance to carbapenems, cephalosporins, aminoglycosides, sulfonamides, chloramphenicol, rifampicin and fluoroquinolones. Importantly, S. marcescens UCO-366 harboured blaKPC-2 and blaSRT-2, representing the first description of these β-lactamase genes in this species in Chile. CONCLUSION Here we report the genome of the first KPC-positive multidrug-resistant S. marcescens strain identified in Chile, which co-harboured several ARGs. The genome sequence of S. marcescens UCO-366 provides an insight into the antimicrobial resistance characteristics of this species in this country and offers important data for further genomic studies on this critical priority pathogen.
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Affiliation(s)
- Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - 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
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- 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
| | - Francisco Silva
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Boris Barrera
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Marcela Cifuentes
- Comité de Prevención y Control de Infecciones Asociadas a la Atención de Salud y Epidemiología Hospitalaria, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
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25
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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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26
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Valencia-Bacca J, Silva MM, Cerdeira L, Esposito F, Cardoso B, Muñoz ME, Jiménez-Villegas T, Cardenas-Arias A, Pessoa DAN, Lincopan N. Detection and Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST340/CG258 Producing CTX-M-15 in a Companion Animal. Microb Drug Resist 2019; 26:611-615. [PMID: 31809242 DOI: 10.1089/mdr.2019.0190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Indexed: 01/16/2023] Open
Abstract
The emergence and dissemination of high-risk clones of Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) in animal infections is a critical issue. We report the detection and genomic features of a multidrug-resistant (MDR) ESBL (CTX-M-15)-producing K. pneumoniae infecting a domestic cat. Whole-genome sequencing analysis identified the international ST340 (clonal group CG258), and genes and mutations conferring resistance to β-lactams, aminoglycosides, macrolides, phenicols, fosfomycin, sulfonamides, tetracycline, trimethoprim, and fluoroquinolones. In addition, the presence of genes encoding resistance to disinfectant and heavy metals hazardous to humans was also confirmed. The MDR profile exhibited by the strain contributed to treatment failure and death of the companion animal. Therefore, active surveillance of critical priority lineages of K. pneumoniae should not only focus on human infections but also on veterinary infections.
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Affiliation(s)
- Juan Valencia-Bacca
- Department of Preventive Veterinary Medicine and Animal Health, Universidade de São Paulo, São Paulo, Brazil
| | - Meire M Silva
- Veterinary Medicine Academic Unit, University Center of João Pessoa, Paraíba, Brazil
| | - Louise Cerdeira
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Maria E Muñoz
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tatiana Jiménez-Villegas
- Department of Preventive Veterinary Medicine and Animal Health, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Danielle A N Pessoa
- School of Veterinary Medicine, Federal University of Campina Grande, Paraíba, Brazil
| | - Nilton Lincopan
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
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27
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Monte DF, Nelson V, Cerdeira L, Keelara S, Greene S, Griffin D, Rath S, Hall R, Page N, Lawson T, Springer D, Fedorka-Cray PJ, Thakur S. Corrigendum: Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human. J Med Microbiol 2019; 68:1694. [PMID: 31685092 DOI: 10.1099/jmm.0.001057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Daniel F Monte
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.,Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Valerie Nelson
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Shermalyn Greene
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Denise Griffin
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Shadia Rath
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Robbie Hall
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Nichole Page
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Thomas Lawson
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Debra Springer
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory and Microbiology Units at the North Carolina State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
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28
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Fernandes MR, Cerdeira L, Silva MM, Sellera FP, Muñoz M, Junior FG, Azevedo SS, Power P, Gutkind G, Lincopan N. Novel mcr-5.3 variant in a CTX-M-8-producing Escherichia coli ST711 isolated from an infected horse. J Antimicrob Chemother 2019; 73:3520-3522. [PMID: 30202925 DOI: 10.1093/jac/dky341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Miriam R Fernandes
- Department of Clinical Analysis School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Meire M Silva
- Academic Unit of Veterinary Medicine, 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
| | - Maria Muñoz
- Department of Clinical Analysis School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Felicio G Junior
- Academic Unit of Veterinary Medicine, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Sergio S Azevedo
- Academic Unit of Veterinary Medicine, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Pablo Power
- Cátedra de Microbiología, Departmento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel Gutkind
- Cátedra de Microbiología, Departmento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nilton Lincopan
- Department of Clinical Analysis School of Pharmacy, Universidade de 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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Sellera FP, Fernandes MR, Ruiz R, Falleiros ACM, Rodrigues FP, Cerdeira L, Lincopan N. Identification of KPC-2-producing Escherichia coli in a companion animal: a new challenge for veterinary clinicians. J Antimicrob Chemother 2019; 73:2259-2261. [PMID: 29800301 DOI: 10.1093/jac/dky173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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
| | - Regina Ruiz
- Microbiology Sector, Provet Diagnostic Center, 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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30
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Monte DF, Lincopan N, Berman H, Cerdeira L, Keelara S, Thakur S, Fedorka-Cray PJ, Landgraf M. Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016. Sci Rep 2019; 9:11058. [PMID: 31363103 PMCID: PMC6667439 DOI: 10.1038/s41598-019-45838-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 01/29/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
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Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. .,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
| | - 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
| | - Hanna Berman
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, 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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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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Monte DF, Nelson V, Cerdeira L, Keelara S, Greene S, Griffin D, Rath S, Hall R, Page N, Lawson T, Springer D, Fedorka-Cray PJ, Thakur S. Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human. J Med Microbiol 2019; 68:986-990. [PMID: 31162025 DOI: 10.1099/jmm.0.001012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A colistin-resistant Salmonella enterica 4, [5],12:i:- sequence type (ST) 34 harbouring mcr-3.1 was recovered from a patient who travelled to China 2 weeks prior to diarrhoea onset. Genomic analysis revealed the presence of the mcr-3.1 gene located in the globally disseminated IncHI2 plasmid, highlighting the intercontinental dissemination of the colistin-resistant S. enterica 4, [5],12:i:- ST34 pandemic clone.
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Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Valerie Nelson
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Shermalyn Greene
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory Unit at State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Denise Griffin
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory Unit at State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Shadia Rath
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory Unit at State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Robbie Hall
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory Unit at State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | - Nichole Page
- Department of Health and Human Services, Molecular Diagnostic and Epidemiology Laboratory Unit at State Laboratory of Public Health, Division of Public Health, Raleigh, NC, USA
| | | | | | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
| | - Siddhartha Thakur
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
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34
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Sacramento AG, Fernandes MR, Sellera FP, Dolabella SS, Zanella RC, Cerdeira L, Lincopan N. VanA-type vancomycin-resistant Enterococcus faecium ST1336 isolated from mussels in an anthropogenically impacted ecosystem. Mar Pollut Bull 2019; 142:533-536. [PMID: 31232334 DOI: 10.1016/j.marpolbul.2019.04.014] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
We report the occurrence and genomic features of multidrug-resistant vancomycin-resistant Enterococcus faecium vanA belonging to a novel sequence type (designated ST1336), carrying a Tn1546-like element, in marine brown mussels (Perna perna) from anthropogenically affected coastal waters of the Atlantic coast of Brazil, highlighting a potential source of dissemination for related ecosystems, with additional consequences for seafood safety and quality.
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Affiliation(s)
- Andrey G Sacramento
- Department of Morphology, Federal University of Sergipe, São Cristóvão, 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
| | - Silvio S Dolabella
- Department of Morphology, Federal University of Sergipe, São Cristóvão, 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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35
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Opazo-Capurro A, San Martín I, Quezada-Aguiluz M, Morales-León F, Domínguez-Yévenes M, Lima CA, Esposito F, Cerdeira L, Bello-Toledo H, Lincopan N, González-Rocha G. Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals. Infect Genet Evol 2019; 73:93-97. [PMID: 31029791 DOI: 10.1016/j.meegid.2019.04.022] [Citation(s) in RCA: 15] [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] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/16/2019] [Accepted: 04/21/2019] [Indexed: 12/31/2022]
Abstract
We analyze the evolutionary dynamics of ninety carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected between 1990 and 2015 in Chile. CRAB were identified at first in an isolate collected in 2005, which harbored the ISAba1-blaOXA-69 arrangement. Later, OXA-58- and OXA-23-producing A. baumannii strains emerged in 2007 and 2009, respectively. This phenomenon was associated with variations in the epidemiology of OXA-type carbapenemases, linked to nosocomial lineages belonging to ST109, ST162, ST15 (CC15) and ST318 (CC15).
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Affiliation(s)
- Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - Iván San Martín
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Felipe Morales-León
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Celia A Lima
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Fernanda Esposito
- 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
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - 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
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile.
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36
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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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37
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Francisco GR, Bueno MFC, Cerdeira L, Lincopan N, Ienne S, Souza TA, de Oliveira Garcia D. Draft genome sequences of KPC-2- and CTX-M-15-producing Klebsiella pneumoniae ST437 isolated from a clinical sample and urban rivers in Sao Paulo, Brazil. J Glob Antimicrob Resist 2019; 16:74-75. [DOI: 10.1016/j.jgar.2018.12.003] [Citation(s) in RCA: 5] [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: 08/21/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 11/29/2022] Open
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38
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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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39
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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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40
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Oliveira FA, Zaccariotto TR, Piveta C, Hofling CC, Resende MR, Levy CE, Esposito F, Fernandes MR, Cerdeira L, Lincopan N. MCR-1-positive colistin-resistant Escherichia coli in immunocompromised hospitalised patients. Int J Antimicrob Agents 2018; 52:438-440. [PMID: 29944955 DOI: 10.1016/j.ijantimicag.2018.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/02/2018] [Accepted: 06/16/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Flavio A Oliveira
- Hospital de Clínicas, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Cristiane Piveta
- Hospital de Clínicas, Universidade Estadual de Campinas, Campinas, Brazil
| | | | | | - Carlos E Levy
- Hospital de Clínicas, Universidade Estadual de Campinas, Campinas, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, Universidade de São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
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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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Silva MM, Fernandes MR, Sellera FP, Cerdeira L, Medeiros LKG, Garino F, Azevedo SS, Lincopan N. Multidrug-resistant CTX-M-15-producing Klebsiella pneumoniae ST231 associated with infection and persistent colonization of dog. Diagn Microbiol Infect Dis 2018; 92:259-261. [PMID: 30025966 DOI: 10.1016/j.diagmicrobio.2018.06.012] [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: 03/19/2018] [Revised: 06/09/2018] [Accepted: 06/15/2018] [Indexed: 01/29/2023]
Abstract
Extended spectrum β-lactamase (ESBL)-producing bacterial infections in veterinary medicine are a clinical and epidemiological challenge. We report a case of CTX-M-15-producing Klebsiella pneumoniae infection followed by persistent colonization, in a dog presenting with bilateral purulent nasal discharge and dyspnea. In this regard, 5 broad-spectrum cephalosporin-resistant K. pneumoniae isolates were recovered from infection and surveillance cultures, collected during 1 year and eight months study. Genomic analysis of a representative clone of K. pneumoniae (KpPB76) revealed the presence of the human-associated lineage ST231, whereas resistome data confirmed the presence of genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones, fosfomycin, phenicols, sulfonamides, tetracyclines and trimethoprim. In the absence of therapeutic options, meropenem therapy was used, contributing to the control of infection during persistent carriage of K. pneumoniae CTX-M-15/ST231. Persistent colonization of companion animals with ESBL-producing bacteria could be result from a variety of situations, including multi introduction from the owner or household family members to pets, or from environmental exposure; whereas colonized animals may serve as an important source for the spread of ESBL-producing strains in the human-animal interface.
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Affiliation(s)
- Meire M Silva
- Academic Veterinary Medicine Unit, Universidade Federal de Campina Grande, Patos, Paraíba, Brazil
| | - Miriam R Fernandes
- 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
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Lylian K G Medeiros
- Academic Veterinary Medicine Unit, Universidade Federal de Campina Grande, Patos, Paraíba, 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 Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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43
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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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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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Nascimento T, Cantamessa R, Melo L, Fernandes MR, Fraga E, Dropa M, Sato MIZ, Cerdeira L, Lincopan N. International high-risk clones of Klebsiella pneumoniae KPC-2/CC258 and Escherichia coli CTX-M-15/CC10 in urban lake waters. Sci Total Environ 2017; 598:910-915. [PMID: 28458208 DOI: 10.1016/j.scitotenv.2017.03.207] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 01/16/2017] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
The emergence of high-risk clones of multidrug-resistant (MDR) bacteria in aquatic environments has generated an important public health problem, creating an urgent need to strengthen surveillance. This study reports the occurrence of clinically significant MDR Enterobacteriaceae and non-fermentative bacteria carrying carbapenemases (KPC-2), extended-spectrum β-lactamases (CTX-M) and plasmid-mediated quinolone resistance (PMQR) genes in urban lakes and reservoirs, in Southeastern Brazil. In this regard, the detection of hospital-associated lineages of KPC-2-producing Klebsiella pneumoniae belonging to the international clonal complex CC258 (ST11) and CTX-M-15-producing Escherichia coli belonging to the international CC10 (ST617), in an urban lake, is reported for the first time. Whole genome sequencing (WGS) analysis of KPC-2-producing K. pneumoniae ST11 revealed that blaKPC-2 gene was carried by an IncN plasmid on a Tn4401b element. This study support that aquatic environments with public access can act as reservoirs of clinically important MDR bacteria, constituting a potential risk to human and animal health. On the other hand, the detection of high-risk clones highlights the extra-hospital spread of clinically significant bacteria into urban aquatic environments.
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Affiliation(s)
- Tatiane Nascimento
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Rodrigo Cantamessa
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Luana Melo
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Edmir Fraga
- School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Milena Dropa
- School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Maria I Z Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - 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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Lopes R, Cerdeira L, Tavares GS, Ruiz JC, Blom J, Horácio ECA, Mantovani HC, Queiroz MVD. Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens. World J Microbiol Biotechnol 2017; 33:185. [DOI: 10.1007/s11274-017-2347-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/19/2017] [Indexed: 02/02/2023]
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47
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Martins ER, Casella T, Bueno MFC, Francisco GR, Tolentino FM, de Freitas ACT, Cerdeira L, Costa MN, Cevada C, Lincopan N, Garcia DDO, Nogueira MCL. Draft genome sequence of an aminoglycoside-resistant RmtD2-producing Enterobacter cloacae subsp. cloacae ST395 in Brazil. J Glob Antimicrob Resist 2017; 10:308-309. [DOI: 10.1016/j.jgar.2017.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/17/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022] Open
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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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49
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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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50
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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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