RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro
Hospital bloodstream infection (BSI) caused by methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of morbidity and mortality and is frequently related to invasive procedures and medically complex patients. An important feature of MRSA is the clonal structure of its population. Speci...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-11-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1275918/full |
| _version_ | 1797561153404010496 |
|---|---|
| author | Matheus Assis Côrtes Esteves Alice Slotfeldt Viana Gabriela Nogueira Viçosa Ana Maria Nunes Botelho Ahmed M. Moustafa Ahmed M. Moustafa Felipe Raposo Passos Mansoldo Adriana Lucia Pires Ferreira Adriana Lucia Pires Ferreira Alane Beatriz Vermelho Bernadete Teixeira Ferreira-Carvalho Paul Joseph Planet Paul Joseph Planet Agnes Marie Sá Figueiredo Agnes Marie Sá Figueiredo |
| author_facet | Matheus Assis Côrtes Esteves Alice Slotfeldt Viana Gabriela Nogueira Viçosa Ana Maria Nunes Botelho Ahmed M. Moustafa Ahmed M. Moustafa Felipe Raposo Passos Mansoldo Adriana Lucia Pires Ferreira Adriana Lucia Pires Ferreira Alane Beatriz Vermelho Bernadete Teixeira Ferreira-Carvalho Paul Joseph Planet Paul Joseph Planet Agnes Marie Sá Figueiredo Agnes Marie Sá Figueiredo |
| author_sort | Matheus Assis Côrtes Esteves |
| collection | DOAJ |
| description | Hospital bloodstream infection (BSI) caused by methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of morbidity and mortality and is frequently related to invasive procedures and medically complex patients. An important feature of MRSA is the clonal structure of its population. Specific MRSA clones may differ in their pathogenic, epidemiological, and antimicrobial resistance profiles. Whole-genome sequencing is currently the most robust and discriminatory technique for tracking hypervirulent/well-adapted MRSA clones. However, it remains an expensive and time-consuming technique that requires specialized personnel. In this work, we describe a pangenome protocol, based on binary matrix (1,0) of open reading frames (ORFs), that can be used to quickly find diagnostic, apomorphic sequence mutations that can serve as biomarkers. We use this technique to create a diagnostic screen for MRSA isolates circulating in the Rio de Janeiro metropolitan area, the RdJ clone, which is prevalent in BSI. The method described here has 100% specificity and sensitivity, eliminating the need to use genomic sequencing for clonal identification. The protocol used is relatively simple and all the steps, formulas and commands used are described in this work, such that this strategy can also be used to identify other MRSA clones and even clones from other bacterial species. |
| first_indexed | 2024-03-10T18:10:10Z |
| format | Article |
| id | doaj.art-8712b56eb9034959a526b1420e8ce6e1 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-10T18:10:10Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-8712b56eb9034959a526b1420e8ce6e12023-11-20T08:12:03ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-11-011410.3389/fmicb.2023.12759181275918RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de JaneiroMatheus Assis Côrtes Esteves0Alice Slotfeldt Viana1Gabriela Nogueira Viçosa2Ana Maria Nunes Botelho3Ahmed M. Moustafa4Ahmed M. Moustafa5Felipe Raposo Passos Mansoldo6Adriana Lucia Pires Ferreira7Adriana Lucia Pires Ferreira8Alane Beatriz Vermelho9Bernadete Teixeira Ferreira-Carvalho10Paul Joseph Planet11Paul Joseph Planet12Agnes Marie Sá Figueiredo13Agnes Marie Sá Figueiredo14Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilDepartamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilDepartamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilBiomanguinhos, Fundação Oswaldo Cruz, Rio de Janeiro, BrazilChildren’s Hospital of Philadelphia, Philadelphia, PA, United StatesDepartment of Pediatrics, University of Pennsylvania, Philadelphia, PA, United StatesDepartamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilHospital Universitário Clementino Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilDasa Medicina Diagnóstica, Duque de Caxias, BrazilDepartamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilDepartamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilChildren’s Hospital of Philadelphia, Philadelphia, PA, United StatesDepartment of Pediatrics, University of Pennsylvania, Philadelphia, PA, United StatesDepartamento de Microbiologia Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilFaculdade de Medicina, Programa de Pós-graduação em Patologia, Universidade Federal Fluminense, Niterói, BrazilHospital bloodstream infection (BSI) caused by methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of morbidity and mortality and is frequently related to invasive procedures and medically complex patients. An important feature of MRSA is the clonal structure of its population. Specific MRSA clones may differ in their pathogenic, epidemiological, and antimicrobial resistance profiles. Whole-genome sequencing is currently the most robust and discriminatory technique for tracking hypervirulent/well-adapted MRSA clones. However, it remains an expensive and time-consuming technique that requires specialized personnel. In this work, we describe a pangenome protocol, based on binary matrix (1,0) of open reading frames (ORFs), that can be used to quickly find diagnostic, apomorphic sequence mutations that can serve as biomarkers. We use this technique to create a diagnostic screen for MRSA isolates circulating in the Rio de Janeiro metropolitan area, the RdJ clone, which is prevalent in BSI. The method described here has 100% specificity and sensitivity, eliminating the need to use genomic sequencing for clonal identification. The protocol used is relatively simple and all the steps, formulas and commands used are described in this work, such that this strategy can also be used to identify other MRSA clones and even clones from other bacterial species.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1275918/fullemerging MRSArapid test for clonality detectionbiomarker searchpangenome matrixbacterial genomics |
| spellingShingle | Matheus Assis Côrtes Esteves Alice Slotfeldt Viana Gabriela Nogueira Viçosa Ana Maria Nunes Botelho Ahmed M. Moustafa Ahmed M. Moustafa Felipe Raposo Passos Mansoldo Adriana Lucia Pires Ferreira Adriana Lucia Pires Ferreira Alane Beatriz Vermelho Bernadete Teixeira Ferreira-Carvalho Paul Joseph Planet Paul Joseph Planet Agnes Marie Sá Figueiredo Agnes Marie Sá Figueiredo RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro Frontiers in Microbiology emerging MRSA rapid test for clonality detection biomarker search pangenome matrix bacterial genomics |
| title | RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro |
| title_full | RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro |
| title_fullStr | RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro |
| title_full_unstemmed | RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro |
| title_short | RdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro |
| title_sort | rdj detection tests to identify a unique mrsa clone of st105 sccmecii lineage and its variants disseminated in the metropolitan region of rio de janeiro |
| topic | emerging MRSA rapid test for clonality detection biomarker search pangenome matrix bacterial genomics |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1275918/full |
| work_keys_str_mv | AT matheusassiscortesesteves rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT aliceslotfeldtviana rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT gabrielanogueiravicosa rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT anamarianunesbotelho rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT ahmedmmoustafa rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT ahmedmmoustafa rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT feliperaposopassosmansoldo rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT adrianaluciapiresferreira rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT adrianaluciapiresferreira rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT alanebeatrizvermelho rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT bernadeteteixeiraferreiracarvalho rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT pauljosephplanet rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT pauljosephplanet rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT agnesmariesafigueiredo rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro AT agnesmariesafigueiredo rdjdetectionteststoidentifyauniquemrsacloneofst105sccmeciilineageanditsvariantsdisseminatedinthemetropolitanregionofriodejaneiro |