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Gato E, Rodiño-Janeiro BK, Gude MJ, Fernández-Cuenca F, Pascual Á, Fernández A, Pérez A, Bou G. Diagnostic tool for surveillance, detection and monitoring of the high-risk clone K. pneumoniae ST15. J Hosp Infect 2023; 142:18-25. [PMID: 37802237 DOI: 10.1016/j.jhin.2023.09.015] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND The global spread of Klebsiella pneumoniae ST15, causing multi-continental outbreaks, contributes to the movement of resistance genes between clones increasing the antimicrobial resistance crisis. The genomic traits providing it with the ability to outcompete other bacteria and cause epidemics remain unclear. AIM To identify the specific genomic traits of K. pneumoniae ST15 to develop a diagnostic test. METHODS An outbreak caused by K. pneumoniae occurred in Hospital A Coruña, Spain. Antimicrobial susceptibility analysis and molecular typing (PGFE and MLST) were performed. One isolate of each sequence type was selected for whole-genome sequencing analysis. Comparative analysis of genomes was performed using RAST. BLASTn was used to evaluate the presence of the fhaC and kpiD genes. Two hundred and ninety-four K. pneumoniae from a Spanish nationwide collection were analysed by PCR. FINDINGS Genotyping showed that 87.5% of the isolates tested belonged to a clone with a unique PFGE pattern which corresponded to ST15. Comparative genomic analysis of the different STs enabled us to determine the specific genomic traits of K. pneumoniae ST15. Two adherence-related systems (Kpi and KpFhaB/FhaC) were specific markers of this clone. Multiplex-PCR analysis with kpiD and fhaC oligonucleotides revealed that K. pneumoniae ST15 is specifically detected with a sensitivity of 100% and a specificity of 97.76%. The PCR results showed 100% concordance with the MLST and whole-genome sequencing data. CONCLUSION K. pneumoniae ST15 possesses specific genomic traits that could favour its dissemination. They could be used as targets to detect K. pneumoniae ST15 with high sensitivity and specificity.
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Affiliation(s)
- E Gato
- Institute for Biomedical Research of A Coruña (INIBIC), A Coruña, Spain; Carlos III Health Institute (ISCIII), Madrid, Spain
| | | | - M J Gude
- University Hospital Lucus Augusti (HULA), Lugo, Spain
| | - F Fernández-Cuenca
- University Hospital Virgen Macarena, Seville, Spain; Institute of Biomedicine of Sevilla, Seville, Spain; University of Sevilla, Seville, Spain
| | - Á Pascual
- University Hospital Virgen Macarena, Seville, Spain; Institute of Biomedicine of Sevilla, Seville, Spain; University of Sevilla, Seville, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - A Fernández
- University Hospital of A Coruña (HUAC), A Coruña, Spain
| | - A Pérez
- Institute for Biomedical Research of A Coruña (INIBIC), A Coruña, Spain; Carlos III Health Institute (ISCIII), Madrid, Spain.
| | - G Bou
- University Hospital of A Coruña (HUAC), A Coruña, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Vallejo A, Moldes LM, Trigo M, Ordoñez P, Rodriguez-Otero L, Cabrera JJ, Gude MJ, Navarro D, Cañizares A, García-Campello M, Agulla A, Aguilera A. Generalized implementation of reflex testing of hepatitis C in Galicia: Results for reflection. Enferm Infecc Microbiol Clin (Engl Ed) 2022; 40:483-488. [PMID: 35729051 DOI: 10.1016/j.eimce.2022.05.010] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 06/15/2023]
Abstract
INTRODUCTION The implementation of reflex testing of active hepatitis C virus (HCV) infection, together with the incorporation of informative alerts in the reports, has shown that it significantly reduces the number of patients who were not referred for therapeutic evaluation. METHODS Since the implementation in 2018 of the DUSP in the Microbiology Services of the Galician Health Service hospitals (SERGAS), new diagnoses of active HCV infection have been retrospectively identified and characterized. RESULTS In 2018, a total of 258 patients with unknown active HCV infection (70,2% men, middle age 52 years) were identified through by reflex testing from consultations of primary and specialized care units in 54.8% and 39.8% respectively, as well as from other locations by 5.4%. Of the 258 patients, 81.0% were referred for therapeutic evaluation, with a median of 54 days from their diagnosis. In 58.3% of the cases the reflex testing was determined by viral load, the predominant genotype was 1a (30,7%) and 52,1% were treated, observing sustained viral response (SVR) in 93.7 % of these. CONCLUSION The generalized implementation of the HCV reflex testing together with informative alerts in Galicia has allowed us to obtain referral rates for treatment similar to those obtained in other studies. However, there is a wide variability between the different centers that require the incorporation of improvements, such as training or the use of rescue measures for optimization.
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Affiliation(s)
- Aldara Vallejo
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Luz María Moldes
- Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña, La Coruña, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Matilde Trigo
- Servicio de Microbiología, Complexo Hospitalario de Pontevedra, Pontevedra, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Patricia Ordoñez
- Servicio de Microbiología, Complexo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol (La Coruña), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Luis Rodriguez-Otero
- Servicio de Microbiología, Complexo Hospitalario Universitario de Ourense, Ourense, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Jorge Julio Cabrera
- Servicio de Microbiología, Hospital Universitario Álvaro Cunqueiro, Vigo (Pontevedra), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - María José Gude
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Daniel Navarro
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Angelina Cañizares
- Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña, La Coruña, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Marta García-Campello
- Servicio de Microbiología, Complexo Hospitalario de Pontevedra, Pontevedra, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Andrés Agulla
- Servicio de Microbiología, Complexo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol (La Coruña), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain
| | - Antonio Aguilera
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), Spain; Departamento de Microbioloxia e Parasitoloxía, Universidade de Santiago de Compostela, Santiago de Compostela (La Coruña), Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), Spain.
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Cañada-García JE, Delgado E, Gil H, Benito S, Sánchez M, Ocampo A, Cabrera JJ, Miralles C, García-Bodas E, Mariño A, Ordóñez P, Gude MJ, Ezpeleta C, Thomson MM. Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain. Front Microbiol 2022; 13:863084. [PMID: 35694315 PMCID: PMC9185580 DOI: 10.3389/fmicb.2022.863084] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Those derived from recombination between subtype B and subsubtype F1, with 18 reported, most of them of South American origin, are among the most diverse. In this study, we identified a HIV-1 BF1 recombinant cluster that is expanding in Spain, transmitted mainly via heterosexual contact, which, analyzed in near full-length genomes in four viruses, exhibited a coincident BF1 mosaic structure, with 12 breakpoints, that fully coincided with that of two viruses (10BR_MG003 and 10BR_MG005) from Brazil, previously classified as CRF72_BF1. The three remaining Brazilian viruses (10BR_MG002, 10BR_MG004, and 10BR_MG008) previously identified as CRF72_BF1 exhibited mosaic structures highly similar, but not identical, to that of the Spanish viruses and to 10BR_MG003 and 10BR_MG005, with discrepant subtypes in two short genome segments, located in pol and gp120env. Based on these results, we propose that the five viruses from Brazil previously identified as CRF72_BF1 actually belong to two closely related CRFs, one comprising 10BR_MG002, 10BR_MG004, and 10BR_MG008, which keep their CRF72_BF1 designation, and the other, designated CRF122_BF1, comprising 10BR_MG003, 10BR_MG005, and the viruses of the identified Spanish cluster. Three other BF1 recombinant genomes, two from Brazil and one from Italy, previously identified as unique recombinant forms, were classified as CRF72_BF1. CRF122_BF1, but not CRF72_BF1, was associated with protease L89M substitution, which was reported to contribute to antiretroviral drug resistance. Phylodynamic analyses estimate the emergence of CRF122_BF1 in Brazil around 1987. Given their close phylogenetic relationship and similar structures, the grouping of CRF72_BF1 and CRF122_BF1 in a CRF family is proposed.
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Affiliation(s)
- Javier E. Cañada-García
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Elena Delgado
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Horacio Gil
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Sonia Benito
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Mónica Sánchez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Antonio Ocampo
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Jorge Julio Cabrera
- Department of Microbiology, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Celia Miralles
- Department of Internal Medicine, Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Elena García-Bodas
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Ana Mariño
- Infectious Diseases Unit, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Patricia Ordóñez
- Department of Microbiology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - María José Gude
- Department of Microbiology, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Carmen Ezpeleta
- Department of Clinical Microbiology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Michael M. Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- *Correspondence: Michael M. Thomson,
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Ayuso B, Lalueza A, Arrieta E, Romay EM, Marchán-López Á, García-País MJ, Folgueira D, Gude MJ, Cueto C, Serrano A, Lumbreras C. Derivation and external validation of a simple prediction rule for the development of respiratory failure in hospitalized patients with influenza. Respir Res 2022; 23:323. [PMID: 36419130 PMCID: PMC9684757 DOI: 10.1186/s12931-022-02245-w] [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] [Received: 01/10/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Influenza viruses cause seasonal epidemics worldwide with a significant morbimortality burden. Clinical spectrum of Influenza is wide, being respiratory failure (RF) one of its most severe complications. This study aims to elaborate a clinical prediction rule of RF in hospitalized Influenza patients. METHODS A prospective cohort study was conducted during two consecutive Influenza seasons (December 2016-March 2017 and December 2017-April 2018) including hospitalized adults with confirmed A or B Influenza infection. A prediction rule was derived using logistic regression and recursive partitioning, followed by internal cross-validation. External validation was performed on a retrospective cohort in a different hospital between December 2018 and May 2019. RESULTS Overall, 707 patients were included in the derivation cohort and 285 in the validation cohort. RF rate was 6.8% and 11.6%, respectively. Chronic obstructive pulmonary disease, immunosuppression, radiological abnormalities, respiratory rate, lymphopenia, lactate dehydrogenase and C-reactive protein at admission were associated with RF. A four category-grouped seven point-score was derived including radiological abnormalities, lymphopenia, respiratory rate and lactate dehydrogenase. Final model area under the curve was 0.796 (0.714-0.877) in the derivation cohort and 0.773 (0.687-0.859) in the validation cohort (p < 0.001 in both cases). The predicted model showed an adequate fit with the observed results (Fisher's test p > 0.43). CONCLUSION we present a simple, discriminating, well-calibrated rule for an early prediction of the development of RF in hospitalized Influenza patients, with proper performance in an external validation cohort. This tool can be helpful in patient's stratification during seasonal Influenza epidemics.
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Affiliation(s)
- Blanca Ayuso
- grid.411171.30000 0004 0425 3881Department of Internal Medicine, University Hospital, 12 de Octubre, Av Córdoba Km 5,400, 28041 Madrid, Spain
| | - Antonio Lalueza
- grid.411171.30000 0004 0425 3881Department of Internal Medicine, University Hospital, 12 de Octubre, Av Córdoba Km 5,400, 28041 Madrid, Spain
| | - Estibaliz Arrieta
- grid.411171.30000 0004 0425 3881Department of Internal Medicine, University Hospital, 12 de Octubre, Av Córdoba Km 5,400, 28041 Madrid, Spain
| | - Eva María Romay
- grid.414792.d0000 0004 0579 2350Infectious Diseases Unit, University Hospital Lucus Augusti, Lugo, Spain
| | - Álvaro Marchán-López
- grid.411171.30000 0004 0425 3881Department of Internal Medicine, University Hospital, 12 de Octubre, Av Córdoba Km 5,400, 28041 Madrid, Spain
| | - María José García-País
- grid.414792.d0000 0004 0579 2350Infectious Diseases Unit, University Hospital Lucus Augusti, Lugo, Spain
| | - Dolores Folgueira
- grid.144756.50000 0001 1945 5329Department of Microbiology, University Hospital 12 de Octubre, Madrid, Spain
| | - María José Gude
- grid.414792.d0000 0004 0579 2350Department of Microbiology, University Hospital Lucus Augusti, Lugo, Spain
| | - Cecilia Cueto
- grid.144756.50000 0001 1945 5329Department of Biochemistry, University Hospital 12 de Octubre, Madrid, Spain
| | - Antonio Serrano
- grid.144756.50000 0001 1945 5329Department of Immunology, University Hospital 12 de Octubre, Madrid, Spain
| | - Carlos Lumbreras
- grid.411171.30000 0004 0425 3881Department of Internal Medicine, University Hospital, 12 de Octubre, Av Córdoba Km 5,400, 28041 Madrid, Spain ,grid.144756.50000 0001 1945 5329Infectious Diseases Unit, University Hospital 12 de Octubre, Madrid, Spain
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Pérez A, Gato E, Pérez-Llarena J, Fernández-Cuenca F, Gude MJ, Oviaño M, Pachón ME, Garnacho J, González V, Pascual Á, Cisneros JM, Bou G. High incidence of MDR and XDR Pseudomonas aeruginosa isolates obtained from patients with ventilator-associated pneumonia in Greece, Italy and Spain as part of the MagicBullet clinical trial. J Antimicrob Chemother 2021; 74:1244-1252. [PMID: 30753505 DOI: 10.1093/jac/dkz030] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/24/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES To characterize the antimicrobial susceptibility, molecular epidemiology and carbapenem resistance mechanisms in Pseudomonas aeruginosa isolates recovered from respiratory tract samples from patients with ventilator-associated pneumonia enrolled in the MagicBullet clinical trial. METHODS Isolates were collected from 53 patients from 12 hospitals in Spain, Italy and Greece. Susceptibility was determined using broth microdilution and Etest. MALDI-TOF MS was used to detect carbapenemase activity and carbapenemases were identified by PCR and sequencing. Molecular epidemiology was investigated using PFGE and MLST. RESULTS Of the 53 isolates, 2 (3.8%) were considered pandrug resistant (PDR), 19 (35.8%) were XDR and 16 (30.2%) were MDR. Most (88.9%) of the isolates from Greece were MDR, XDR or PDR, whereas fewer of the isolates from Spain (33.3%) and Italy (43.5%) showed antibiotic resistance. Three Greek isolates were resistant to colistin. Overall, the rates of resistance of P. aeruginosa isolates to imipenem, ciprofloxacin, ceftolozane/tazobactam and ceftazidime/avibactam were 64.1%, 54.7%, 22.6% and 24.5%, respectively. All isolates resistant to ceftolozane/tazobactam and ceftazidime/avibactam (Greece, n = 10; and Italy, n = 2) carried blaVIM-2. Spanish isolates were susceptible to the new drug combinations. Forty-eight restriction patterns and 27 STs were documented. Sixty percent of isolates belonged to six STs, including the high-risk clones ST-111, ST-175 and ST-235. CONCLUSIONS MDR/XDR isolates were highly prevalent, particularly in Greece. The most effective antibiotic against P. aeruginosa was colistin, followed by ceftolozane/tazobactam and ceftazidime/avibactam. blaVIM-2 is associated with resistance to ceftolozane/tazobactam and ceftazidime/avibactam, and related to highly resistant phenotypes. ST-111 was the most frequent and disseminated clone and the clonal diversity was lower in XDR and PDR strains.
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Affiliation(s)
- Astrid Pérez
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Eva Gato
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - José Pérez-Llarena
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Felipe Fernández-Cuenca
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla, Seville, Spain
| | - María José Gude
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Marina Oviaño
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María Eugenia Pachón
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - José Garnacho
- Department of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocio, CSIC, University of Seville, Seville, Spain
| | - Verónica González
- Department of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocio, CSIC, University of Seville, Seville, Spain
| | - Álvaro Pascual
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - José Miguel Cisneros
- Department of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocio, CSIC, University of Seville, Seville, Spain
| | - Germán Bou
- Microbiology Department, Biomedical Research Institute A Coruña (INIBIC), University Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
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Vallejo A, Moldes LM, Trigo M, Ordoñez P, Rodriguez-Otero L, Cabrera JJ, Gude MJ, Navarro D, Cañizares A, García-Campello M, Agulla A, Aguilera A. Generalized implementation of reflex testing of hepatitis C in Galicia: Results for reflection. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00025-2. [PMID: 33632540 DOI: 10.1016/j.eimc.2020.12.019] [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: 11/15/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 01/18/2023]
Abstract
INTRODUCTION The implementation of reflex testing of active hepatitis C virus (HCV) infection, together with the incorporation of informative alerts in the reports, has shown that it significantly reduces the number of patients who were not referred for therapeutic evaluation. METHODS Since the implementation in 2018 of the DUSP in the microbiology services of the Galician Health Service hospitals (SERGAS), new diagnoses of active HCV infection have been retrospectively identified and characterized. RESULTS In 2018, a total of 258 patients with unknown active HCV infection (70,2% men, middle age 52 years) were identified through by reflex testing from consultations of primary and specialized care units in 54.8% and 39.8% respectively, as well as from other locations by 5.4%. Of the 258 patients, 81.0% were referred for therapeutic evaluation, with a median of 54 days from their diagnosis. In 58.3% of the cases the reflex testing was determined by viral load, the predominant genotype was 1a (30,7%) and 52,1% were treated, observing sustained viral response in 93.7% of these. CONCLUSION The generalized implementation of the HCV reflex testing together with informative alerts in Galicia has allowed us to obtain referral rates for treatment similar to those obtained in other studies. However, there is a wide variability between the different centers that require the incorporation of improvements, such as training or the use of rescue measures for optimization.
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Affiliation(s)
- Aldara Vallejo
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Luz María Moldes
- Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña, La Coruña, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Matilde Trigo
- Servicio de Microbiología, Complexo Hospitalario de Pontevedra, Pontevedra, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Patricia Ordoñez
- Servicio de Microbiología, Complexo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol (La Coruña), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Luis Rodriguez-Otero
- Servicio de Microbiología, Complexo Hospitalario Universitario de Ourense, Orense, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Jorge Julio Cabrera
- Servicio de Microbiología, Hospital Universitario Álvaro Cunqueiro, Vigo (Pontevedra), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - María José Gude
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Daniel Navarro
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Angelina Cañizares
- Servicio de Microbiología, Complexo Hospitalario Universitario de A Coruña, La Coruña, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Marta García-Campello
- Servicio de Microbiología, Complexo Hospitalario de Pontevedra, Pontevedra, España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Andrés Agulla
- Servicio de Microbiología, Complexo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol (La Coruña), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España
| | - Antonio Aguilera
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela (La Coruña), España; Departamento de Microbioloxia e Parasitoloxía, Universidade de Santiago de Compostela, Santiago de Compostela (La Coruña), España; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela (La Coruña), España.
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de Salazar A, Aguilera A, Trastoy R, Fuentes A, Alados JC, Causse M, Galán JC, Moreno A, Trigo M, Pérez-Ruiz M, Roldán C, Pena MJ, Bernal S, Serrano-Conde E, Barbeito G, Torres E, Riazzo C, Cortes-Cuevas JL, Chueca N, Coira A, Sanchez-Calvo JM, Marfil E, Becerra F, Gude MJ, Pallarés Á, Pérez Del Molino ML, García F. Sample pooling for SARS-CoV-2 RT-PCR screening. Clin Microbiol Infect 2020; 26:1687.e1-1687.e5. [PMID: 32919074 PMCID: PMC7481316 DOI: 10.1016/j.cmi.2020.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/05/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/21/2022]
Abstract
Objective To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of coronavirus disease 2019 (COVID-19) by using different commercial platforms for nucleic acid extraction and amplification. Methods A total of 3519 nasopharyngeal samples received at nine Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of ten samples and 11 pools of nine samples) according to the existing methodology in place at each centre. Results We found that 253 pools (2519 samples) were negative and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples), we found discordant results when compared to their correspondent individual samples, as follows: in 22 of 29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity and positive and negative predictive values for pooling were 97.10% (95% confidence interval (CI), 94.11–98.82), 100%, 100% and 99.79% (95% CI, 99.56–99.90) respectively; accuracy was 99.80% (95% CI, 99.59–99.92), and the kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted in a median loss of 2.87 (95% CI, 2.46–3.28) cycle threshold (Ct) for E gene, 3.36 (95% CI, 2.89–3.85) Ct for the RdRP gene and 2.99 (95% CI, 2.56–3.43) Ct for the N gene. Conclusions We found a high efficiency of pooling strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA testing across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity and positive and negative predictive values.
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Affiliation(s)
- Adolfo de Salazar
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Antonio Aguilera
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Rocio Trastoy
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Ana Fuentes
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Juan Carlos Alados
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Manuel Causse
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan Carlos Galán
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Antonio Moreno
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Matilde Trigo
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Mercedes Pérez-Ruiz
- Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain; Clinical Microbiology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Carolina Roldán
- Clinical Microbiology Unit, Hospital Universitario de Jae, Jaen, Spain
| | - Maria José Pena
- Clinical Microbiology Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de GC, Gran Canaria, Spain
| | - Samuel Bernal
- Unit of Infectious Disease and Clinical Microbiology, Hospital Universitario de Valme, Seville, Spain
| | - Esther Serrano-Conde
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Gema Barbeito
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Eva Torres
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Cristina Riazzo
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | | | - Natalia Chueca
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Amparo Coira
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | | | - Eduardo Marfil
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Federico Becerra
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María José Gude
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Ángeles Pallarés
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - María Luisa Pérez Del Molino
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Federico García
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain.
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8
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Oviaño M, Rodríguez-Sánchez B, Gómara M, Alcalá L, Zvezdanova E, Ruíz A, Velasco D, Gude MJ, Bouza E, Bou G. Direct identification of clinical pathogens from liquid culture media by MALDI-TOF MS analysis. Clin Microbiol Infect 2017; 24:624-629. [PMID: 28962998 DOI: 10.1016/j.cmi.2017.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 07/28/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVES We propose using MALDI-TOF MS as a tool for identifying microorganisms directly from liquid cultures after enrichment of the clinical sample in the media, to obtain a rapid microbiological diagnosis and an adequate administration of the antibiotic therapy in a clinical setting. METHODS To evaluate this approach, a series of quality control isolates were grown in thioglycollate (TG) broth and brain heart infusion (BHI) broth and extracted under four different protocols before finally being identified by MALDI-TOF MS. After establishing the best extraction protocol, we validated the method in a total of 300 liquid cultures (150 in TG broth and 150 in BHI broth) of different types of clinical samples obtained from two tertiary Spanish hospitals. RESULTS The initial evaluation showed that the extraction protocol including a 5 minute sonication step yielded 100% valid identifications, with an average score value of 2.305. In the clinical validation of the procedure, 98% of the microorganisms identified from the TG broth were correctly identified relative to 97% of those identified from the BHI broth. In 24% of the samples analysed, growth by direct sowing was only successful in the liquid medium, and no growth was observed in the direct solid agar cultures. CONCLUSIONS Use of MALDI-TOF MS plus the sonication-based extraction method enabled direct and accurate identification of microorganisms in liquid culture media in 15 minutes, in contrast to the 24 hours of subculture required for conventional identification, allowing the administration of a targeted antimicrobial therapy.
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Affiliation(s)
- M Oviaño
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - B Rodríguez-Sánchez
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - M Gómara
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - L Alcalá
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - E Zvezdanova
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - A Ruíz
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - D Velasco
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - M J Gude
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - E Bouza
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - G Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain.
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9
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Garrido A, Seral C, Gude MJ, Casado C, González-Domínguez M, Sáenz Y, Castillo FJ. Characterization of plasmid-mediated β-lactamases in fecal colonizing patients in the hospital and community setting in Spain. Microb Drug Resist 2013; 20:301-4. [PMID: 24328895 DOI: 10.1089/mdr.2013.0109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM Active surveillance of plasmid-mediated β-lactamase-producing Enterobacteriaceae (PMBL-E) in fecal carriers in the hospital and in the community setting in a non-outbreak period of time. METHODS Patients were screened for carriage of Enterobacteriaceae resistant to expanded-spectrum cephalosporins and PMBL-E were characterized (extended-spectrum-β-lactamase [ESBL], plasmid-mediated AmpC β-lactamase [pAmpC], and carbapenemases) by PCR and sequencing. RESULTS The prevalence of ESBL and pAmpC carriers was 5.06% and 0.59%, respectively. Overall, CTX-M-like enzymes were the ESBL dominate enzymes (96.15%). The group CTX-M-9 was the most prevalent (81, 54%) [CTX-M-14 (74, 91.35%), CTX-M-9 (5, 6.17%), CTX-M-24 (1, 1.23%), and CTX-M-27 (1, 1.23%)] followed by the group CTX-M-1 (64, 42.67%) [CTX-M-15 (42, 65.63%), CTX-M-1 (13, 20.31%), CTX-M-32 (8, 12.5%), and CTX-M-3 (1, 1.56%)]. One CTX-M-10, one CTX-M-59, and three CTX-M-8 were also found. A very small representation of SHV or TEM ESBL enzymes was found (3.2% and 0.64%, respectively). pAmpC characterization revealed a predominance of CMY-2 (81.25%), followed by DHA-1 (18.75%). We did not detect the presence of carbapenemase producers. CONCLUSIONS The prevalence of ESBL-producers from fecal carriers is stable in our area, but colonization by pAmpC producers has emerged recently as we have confirmed. Periodic active surveillance is useful to identify these human reservoirs and control the evolution of PMBL carriage in a community over time.
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Affiliation(s)
- Ana Garrido
- 1 Department of Microbiology, Hospital Clínico Universitario "Lozano Blesa," Zaragoza, Spain
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10
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Seral C, Rojo-Bezares B, Garrido A, Gude MJ, Sáenz Y, Castillo FJ. Caracterización de Shigella sonnei portadora de CTX-M-15 en un paciente español sin antecedentes de viaje al extranjero. Enferm Infecc Microbiol Clin 2012; 30:469-71. [DOI: 10.1016/j.eimc.2011.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 10/26/2011] [Accepted: 11/02/2011] [Indexed: 10/14/2022]
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11
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Seral C, Gude MJ, Castillo FJ. [Emergence of plasmid mediated AmpC β-lactamasas: Origin, importance, detection and therapeutical options]. Rev Esp Quimioter 2012; 25:89-99. [PMID: 22707098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
AmpC β-lactamases can hydrolyze penicillins, oxyimino-, 7-α-methoxycephalosporins and monobactams. Susceptibility to cefepime or cefpirome is little affected and is unchanged for carbapenems. Originally such genes are thought to have been mobilized to mobile genetic elements from the chromosomal ampC genes from members of Enterobacteriaceae facilitating their spread and now they can appear in bacterial lacking or poorly expressing a chromosomal ampC gene. The prevalence of infection by plasmid mediated AmpC (pAmpC) varies depending on the type of enzyme and geographical location and blaCMY-2 is the most frequently detected worldwide. Typically, pAmpC producing isolates are associated with resistance to multiple antibiotics making the selection of an effective antibiotic difficult. Phenotypic and molecular methods to detect pAmpC are described and the role of different antibiotics in the treatment of these infections is examined. Surveillance studies about the evolution of this emerging resistant mechanism are important in clinical isolates. Evaluate the in vitro susceptibility of these isolates and the clinical efficacy of other therapeutic options is required.
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Affiliation(s)
- Cristina Seral
- Servicio de Microbiología, Hospital Clínico Universitario Lozano Blesa, Avda San Juan Bosco 15, 50009 Zaragoza, Spain
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