1
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Treffon J, Prior K, Dreesman J, Egelkamp R, Flieger A, Middendorf-Bauchart B, Projahn M, Richter A, Schuh E, Harmsen D, Mellmann A. Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data. J Clin Microbiol 2023; 61:e0187322. [PMID: 36840589 PMCID: PMC10035311 DOI: 10.1128/jcm.01873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/24/2023] Open
Abstract
PCR-based screening assays targeting strain-specific genetic markers allow the timely detection and specific differentiation of bacterial strains. Especially in situations where an infection cluster occurs, fast assay development is crucial for supporting targeted control measures. However, the turnaround times (TATs) for assay setup may be high due to insufficient knowledge about screening assay methods, workflows, and software tools. Here, two blind-coded and quality-controlled ring trials were performed in which five German laboratories established PCR-based screening assays from genomic data that specifically target selected bacterial clusters within two bacterial monospecies sample panels. While the first ring trial was conducted without a time limit to train the participants and assess assay feasibility, in the second ring trial, a challenging time limit of 2 weeks was set to force fast assay development as soon as genomic data were available. During both ring trials, we detected high interlaboratory variability regarding the screening assay methods and targets, the TATs for assay setup, and the number of screening assays. The participants designed between one and four assays per cluster that targeted cluster-specific unique genetic sequences, genes, or single nucleotide variants using conventional PCRs, high-resolution melting assays, or TaqMan PCRs. Assays were established within the 2-week time limit, with TATs ranging from 4 to 13 days. TaqMan probe delivery times strongly influenced TATs. In summary, we demonstrate that a specific exercise improved the preparedness to develop functional cluster-specific PCR-based screening assays from bacterial genomic data. Furthermore, the parallel development of several assays enhances assay availability.
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Affiliation(s)
- Janina Treffon
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
| | - Karola Prior
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Johannes Dreesman
- Department of Microbiology, Infection Protection, Hospital Hygiene, and Infection Epidemiology, Public Health Agency of Lower Saxony, Hannover, Germany
| | - Richard Egelkamp
- Department of Microbiology, Infection Protection, Hospital Hygiene, and Infection Epidemiology, Public Health Agency of Lower Saxony, Hannover, Germany
| | - Antje Flieger
- Department of Enteropathogenic Bacteria and Legionella, National Reference Center for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Barbara Middendorf-Bauchart
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
| | - Michaela Projahn
- Department of Biological Safety, National Reference Laboratory for Escherichia coli Including VTEC, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anne Richter
- Department of Enteropathogenic Bacteria and Legionella, National Reference Center for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Elisabeth Schuh
- Department of Biological Safety, National Reference Laboratory for Escherichia coli Including VTEC, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Dag Harmsen
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- National Consulting Laboratory for Hemolytic Uremic Syndrome, University Hospital Münster, Münster, Germany
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2
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Buenestado-Serrano S, Herranz M, Palomino-Cabrera R, Rodríguez-Grande C, Peñas-Utrilla D, Molero-Salinas A, Veintimilla C, Catalán P, Alonso R, Muñoz P, Pérez-Lago L, García de Viedma D. Rapid Identification of Relevant Microbial Strains by Identifying Multiple Marker Single Nucleotide Polymorphisms via Amplicon Sequencing: Epidemic Monkeypox Virus as a Proof of Concept. Microbiol Spectr 2023; 11:e0419622. [PMID: 36602352 PMCID: PMC9927504 DOI: 10.1128/spectrum.04196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Despite the proven value of applying genomic data for epidemiological purposes, commonly used high-throughput sequencing formats are not adapted to the response times required to intervene and finally control outbreaks. In this study, we propose a fast alternative to whole-genome sequencing (WGS) to track relevant microbiological strains: nanopore sequencing of multiple amplicons including strain marker single nucleotide polymorphisms (SNPs). As a proof a concept, we evaluated the performance of our approach to offer a rapid response to the most recent public health global alarm, the monkeypox virus (MPXV) global outbreak. Through a multisequence alignment, a list of 42 SNPs were extracted as signature makers for this outbreak. Twenty primer pairs were designed to amplify in a multiplex PCR the regions including 22 of these SNPs. Amplicon pools were sequenced in a MinION device, and SNPs were called in real time by an in-house bioinformatic pipeline. A total of 120 specimens (95 MPXV-PCR positive, Ct values from 14 to 39) were selected. In 67.37% of the positive subset, all 22 SNPs were called. After excluding low viral load specimens, in 92% of samples ≥11 outbreak SNPs were called. No false positives were observed in any of the 25 negative specimens. The total turnaround time required for this strategy was 5 hours, and the cost per sample was 14 euros. Nanopore sequencing of multiple amplicons harboring signature SNPs escapes the targeting limitations of strain-specific PCRs and offers a powerful alternative to systematic WGS, paving the way to real-time genomic epidemiology and making immediate intervention possible to finally optimize transmission control. IMPORTANCE Nanopore sequencing of multiple amplicons harboring signature single nucleotide polymorphisms (SNPs) escapes the targeting limitations of strain-specific PCRs and offers a powerful alternative to systematic whole-genome analysis, paving the way to real-time genomic epidemiology and making immediate intervention possible to finally optimize transmission control.
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Affiliation(s)
- Sergio Buenestado-Serrano
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Escuela de Doctorado, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Rosalía Palomino-Cabrera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Daniel Peñas-Utrilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Andrea Molero-Salinas
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Cristina Veintimilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Roberto Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III (CIBERES), Madrid, Spain
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3
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Treffon J, Heppner B, Eismann J, Bothe J, Omengo B, Mellmann A. Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations. Microbiol Spectr 2022; 10:e0303622. [PMID: 36250868 PMCID: PMC9769705 DOI: 10.1128/spectrum.03036-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 01/09/2023] Open
Abstract
Infection clusters of multidrug-resistant bacteria increase mortality and entail expensive infection control measures. Whereas whole-genome sequencing (WGS) is the current gold standard to confirm infection clusters, PCR-based assays targeting cluster-specific signatures, such as single nucleotide polymorphisms (SNPs) derived from WGS data, are more suitable to initially screen for cluster isolates within large sample sizes. Here, we evaluated four software tools (SeqSphere+, RUCS, Gegenees, and Find Differential Primers) regarding their efficiency to find SNPs within WGS data sets that were specific for two bacterial monospecies infection clusters but were absent from a WGS reference data set comprising several hundred diverse genotypes of the same bacterial species. Cluster-specific SNPs were subsequently used to establish a probe-based real-time PCR screening assay for in vitro differentiation between cluster and noncluster isolates. SeqSphere+ and RUCS found 2 and 24 SNPs for clusters 1 and 14 and 24 SNPs for cluster 2, respectively. However, some signatures detected by RUCS were not cluster specific. Interestingly, all SNPs identified by SeqSphere+ were also detected by RUCS. In contrast, analyses with the remaining tools either resulted in no SNPs (with Find Differential Primers) or failed (Gegenees). Design of six cluster-specific real-time PCR assays enabled reliable cluster screening in vitro. Our evaluation revealed that SeqSphere+ and RUCS identified cluster-specific SNPs that could be used for large-scale screening in surveillance samples via real-time PCR, thereby complementing WGS efforts. This faster and simplified approach for the surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians. IMPORTANCE Infection clusters of multidrug-resistant bacteria threaten medical facilities worldwide and cause immense health care costs. In recent years, whole-genome sequencing (WGS) has been increasingly applied to detect and to further control bacterial clusters. However, as WGS is still expensive and time-consuming, its exclusive application for screening and confirmation of bacterial infection clusters contributes to high costs and enhanced turnaround times, which many hospitals cannot afford. Therefore, there is need for alternative methods that can enable further surveillance of bacterial clusters that are initially detected by WGS in a faster and more cost-efficient way. Here, we established a system based on real-time PCR that enables rapid large-scale sample screening for bacterial cluster isolates within 7 days after the initial detection of an infection cluster, thereby complementing WGS efforts. This faster and simplified surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians.
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Affiliation(s)
- Janina Treffon
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | - Bianca Heppner
- University Hospital Münster, Institute of Hygiene, Münster, Germany
| | | | - Julia Bothe
- inno-train Diagnostik GmbH, Kronberg, Germany
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4
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Martínez-Lirola M, Jajou R, Mathys V, Martin A, Cabibbe AM, Valera A, Sola-Campoy PJ, Abascal E, Rodríguez-Maus S, Garrido-Cárdenas JA, Bonillo M, Chiner-Oms Á, López B, Vallejo-Godoy S, Comas I, Muñoz P, Cirillo DM, van Soolingen D, Pérez-Lago L, García de Viedma D. Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe. J Travel Med 2021; 28:6211020. [PMID: 33822988 DOI: 10.1093/jtm/taab054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Growing international migration has increased the complexity of tuberculosis transmission patterns. Italy's decision to close its borders in 2018 made of Spain the new European porte entrée for migration from the Horn of Africa (HA). In one of the first rescues of migrants from this region at the end of 2018, tuberculosis was diagnosed in eight subjects, mainly unaccompanied minors. METHODS Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU-VNTR) and subsequent whole genome sequencing (WGS) analysis. Data were compared with those from collections from other European countries receiving migrants from the HA and a strain-specific PCR was applied for a fast searching of common strains. Infections in a cellular model were performed to assess strain virulence. RESULTS MIRU-VNTR analysis allowed identifying an epidemiological cluster involving three of the eight cases from Somalia (0 single-nucleotide polymorphisms between isolates, HA cluster). Following detailed interviews revealed that two of these cases had shared the same migratory route in most of the trip and had spent a long time at a detention camp in Libya. To confirm potential en route transmission for the three cases, we searched the same strain in collections from other European countries receiving migrants from the HA. MIRU-VNTR, WGS and a strain-specific PCR for the HA strain were applied. The same strain was identified in 12 cases from Eritrea diagnosed soon after their arrival in 2018 to the Netherlands, Belgium and Italy. Intracellular replication rate of the strain did not reveal abnormal virulence. CONCLUSIONS Our study suggests a potential en route transmission of a pan-susceptible strain, which caused at least 15 tuberculosis cases in Somalian and Eritrean migrants diagnosed in four different European countries.
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Affiliation(s)
| | - Rana Jajou
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Anandi Martin
- Université catholique de Louvain (UCLouvain) & Syngulon, 4102, Seraing, Belgium
| | - Andrea Maurizio Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ana Valera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Estefanía Abascal
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra Rodríguez-Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Magdalena Bonillo
- Unidad de Prevención, Promoción y Vigilancia de la Salud del Área Sanitaria Norte de Almería. Consejería de Salud. Junta de Andalucia, Almería, Spain
| | - Álvaro Chiner-Oms
- Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | - Begoña López
- UPPV Distrito Sanitario Granada metropolitano, Granada, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain.,CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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5
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Jbara S, Herranz M, Sola-Campoy PJ, Rodríguez-Grande C, Chiner-Oms Á, Comas I, Muñoz P, García de Viedma D, Pérez-Lago L. Overlapping prison/community tuberculosis outbreaks in Costa Rica revealed by alternative analysis of suboptimal material. Transbound Emerg Dis 2021; 69:1065-1072. [PMID: 33687788 DOI: 10.1111/tbed.14063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/15/2021] [Accepted: 03/05/2021] [Indexed: 11/29/2022]
Abstract
Costa Rica has a low incidence of tuberculosis. Thus, identifying transmission hotspots is key to implement interventions. A tuberculosis outbreak was suspected in a prison in Costa Rica. Given the suboptimal quality of the samples received in our laboratory in Madrid, we applied alternative schemes for their analysis. In the first scheme, we bypassed the standard approach of applying systematic mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and used a strain-specific polymerase chain reaction (PCR) that allowed identifying a cluster involving six cases (C1). The second scheme followed the canonical MIRU-VNTR path coupled with a whole-genomic amplification step, by which a second unsuspected overlapping cluster (C2), was detected in the same prison. These findings justified the implementation of a surveillance programme adapted to local resources based on a tailored multiplex allele-specific oligonucleotide (ASO)-PCR targeting C1 and C2. Presence of the C2 strain at a different prison was determined. ASO-PCR was applied extensively and alerted to the active circulation of one of the strains within and beyond prisons. Our study shows that alternative methodological strategies may provide useful data in settings with lack of resources for performing systematic standard molecular epidemiology programmes and/or with suboptimal material for analysis.
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Affiliation(s)
- Sarah Jbara
- Centro Nacional de Referencia de Micobacteriología, Inciensa, Tres Ríos, Costa Rica
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Álvaro Chiner-Oms
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO), Universitat de València, Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain.,Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Acosta F, Fernández-Cruz A, Maus SR, Sola-Campoy PJ, Marín M, Cercenado E, Sierra O, Muñoz P, García de Viedma D, Pérez-Lago L. In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms. Am J Epidemiol 2020; 189:841-849. [PMID: 32128575 DOI: 10.1093/aje/kwaa025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 02/21/2020] [Indexed: 12/23/2022] Open
Abstract
In 2013-2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011-2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.
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7
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Abascal E, Pérez-Lago L, Martínez-Lirola M, Chiner-Oms Á, Herranz M, Chaoui I, Comas I, El Messaoudi MD, Cárdenas JAG, Santantón S, Bouza E, García-de-Viedma D. Whole genome sequencing-based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696526 PMCID: PMC6351995 DOI: 10.2807/1560-7917.es.2019.24.4.1800005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background The analysis of transmission of tuberculosis (TB) is challenging in areas with a large migrant population. Standard genotyping may fail to differentiate transmission within the host country from new importations, which is key from an epidemiological perspective. Aim To propose a new strategy to simplify and optimise cross-border surveillance of tuberculosis and to distinguish between recent transmission in the host country and new importations Methods We selected 10 clusters, defined by 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR), from a population in Spain rich in migrants from eastern Europe, north Africa and west Africa and reanalysed 66 isolates by whole-genome sequencing (WGS). A multiplex-allele-specific PCR was designed to target strain-specific marker single nucleotide polymorphisms (SNPs), identified from WGS data, to optimise the surveillance of the most complex cluster. Results In five of 10 clusters not all isolates showed the short genetic distances expected for recent transmission and revealed a higher number of SNPs, thus suggesting independent importations of prevalent strains in the country of origin. In the most complex cluster, rich in Moroccan cases, a multiplex allele-specific oligonucleotide-PCR (ASO-PCR) targeting the marker SNPs for the transmission subcluster enabled us to prospectively identify new secondary cases. The ASO-PCR-based strategy was transferred and applied in Morocco, demonstrating that the strain was prevalent in the country. Conclusion We provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration.
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Affiliation(s)
- Estefanía Abascal
- These authors have contributed equally.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Laura Pérez-Lago
- These authors have contributed equally.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Álvaro Chiner-Oms
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | - Marta Herranz
- CIBER Enfermedades respiratorias (CIBERES), Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Imane Chaoui
- Unité de Biologie et Recherches Médicales, Division des Sciences du Vivant, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN), Rabat, Morocco
| | - Iñaki Comas
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain.,Instituto de Biomedicina de Valencia (IBV) Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | | | | | - Sheila Santantón
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilio Bouza
- Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain.,CIBER Enfermedades respiratorias (CIBERES), Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Darío García-de-Viedma
- CIBER Enfermedades respiratorias (CIBERES), Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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8
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Monteserin J, Pérez-Lago L, Yokobori N, Paul R, Rodríguez Maus S, Simboli N, Eldholm V, López B, García de Viedma D, Ritacco V. Trends of Two Epidemic Multidrug-Resistant Strains of Mycobacterium tuberculosis in Argentina Disclosed by Tailored Molecular Strategy. Am J Trop Med Hyg 2020; 101:1308-1311. [PMID: 31628738 DOI: 10.4269/ajtmh.19-0397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Two Mycobacterium tuberculosis strains-M (sublineage 4.1) and Ra (sublineage 4.3)-have long prevailed in Argentina among patients with multidrug-resistant tuberculosis (MDR-TB). Recently, budget constraints have hampered the surveillance of MDR-TB transmission. Based on whole-genome sequence analysis, we used M- and Ra-specific single nucleotide polymorphisms to tailor two multiplex allele-specific polymerase chain reactions (PCRs), which we applied to 252 stored isolates (95% of all newly diagnosed MDR-TB cases countrywide, 2015-2017). Compared with the latest data available (2007-2009), the M strain has receded (80/324 to 20/252, P < 0.0001), particularly among cross-border migrants (12/58 to 0/53, P = 0.0003) and HIV-infected people (30/97 to 7/74, P = 0.0007), but it still accounts for 4/12 new cases of extensively drug-resistant TB. Differently, the Ra strain remained stable in frequency (39/324 to 33/252) and contributed marginally to the extensive drug-resistance load (1/12). Our novel strategy disclosed recent trends of the two major MDR-TB strains, providing meaningful data to allocate control interventions more efficiently.
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Affiliation(s)
- Johana Monteserin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Laura Pérez-Lago
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Noemí Yokobori
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Sandra Rodríguez Maus
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | | | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Viviana Ritacco
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
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9
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Abascal E, Herranz M, Acosta F, Agapito J, Cabibbe AM, Monteserin J, Ruiz Serrano MJ, Gijón P, Fernández-González F, Lozano N, Chiner-Oms Á, Cáceres T, Pintado PG, Acín E, Valencia E, Muñoz P, Comas I, Cirillo DM, Ritacco V, Gotuzzo E, García de Viedma D. Screening of inmates transferred to Spain reveals a Peruvian prison as a reservoir of persistent Mycobacterium tuberculosis MDR strains and mixed infections. Sci Rep 2020; 10:2704. [PMID: 32066749 PMCID: PMC7026066 DOI: 10.1038/s41598-020-59373-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/22/2020] [Indexed: 11/09/2022] Open
Abstract
It is relevant to evaluate MDR-tuberculosis in prisons and its impact on the global epidemiology of this disease. However, systematic molecular epidemiology programs in prisons are lacking. A health-screening program performed on arrival for inmates transferred from Peruvian prisons to Spain led to the diagnosis of five MDR-TB cases from one of the biggest prisons in Latin America. They grouped into two MIRU-VNTR-clusters (Callao-1 and Callao-2), suggesting a reservoir of two prevalent MDR strains. A high-rate of overexposure was deduced because one of the five cases was coinfected by a pansusceptible strain. Callao-1 strain was also identified in 2018 in a community case in Spain who had been in the same Peruvian prison in 2002-5. A strain-specific-PCR tailored from WGS data was implemented in Peru, allowing the confirmation that these strains were currently responsible for the majority of the MDR cases in that prison, including a new mixed infection.
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Affiliation(s)
- Estefanía Abascal
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Marta Herranz
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, (CIBERES), Spain
| | - Fermín Acosta
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Juan Agapito
- TB Research Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andrea M Cabibbe
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - María Jesús Ruiz Serrano
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, (CIBERES), Spain
| | - Paloma Gijón
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Francisco Fernández-González
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Nuria Lozano
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Álvaro Chiner-Oms
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | - Tatiana Cáceres
- TB Research Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pilar Gómez Pintado
- General Subdirection of Penitentiary Health - Penitentiary Institutions - Ministry of Interior of Spain, Madrid, Spain
| | - Enrique Acín
- General Subdirection of Penitentiary Health - Penitentiary Institutions - Ministry of Interior of Spain, Madrid, Spain
| | | | - Patricia Muñoz
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, (CIBERES), Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV) Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain.,CIBER en Epidemiología y Salud, Pública, Spain
| | - Daniela M Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Eduardo Gotuzzo
- TB Research Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain. .,CIBER Enfermedades Respiratorias, (CIBERES), Spain.
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10
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García de Viedma D. Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 72:4-9. [DOI: 10.1016/j.meegid.2019.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
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11
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A Mycobacterium tuberculosis Beijing strain persists at high rates and extends its geographic boundaries 20 years after importation. Sci Rep 2019; 9:4687. [PMID: 30886337 PMCID: PMC6423232 DOI: 10.1038/s41598-019-40525-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/04/2019] [Indexed: 11/15/2022] Open
Abstract
Transmission of Beijing Mycobacterium tuberculosis can be investigated based on genotypic analysis of clinical isolates. A Beijing strain began to spread on Gran Canaria Island, Spain, at the end of the last century. In 1996, only 3 years after its importation to the island, its frequency had increased to 27.1% of all the isolates. The strain was tracked during the following years, and the most recent data obtained corresponded to 2007-8, when its presence continued to be alarming (21%). In the current study, we updated data on the distribution of this strain 20 years (2013–2014) after it was first detected on the island and extended the analysis for the first time to all the mycobacteriology laboratories covering the population of the Canary Island archipelago. Rapid updating was enabled by means of 2 different strain-specific PCRs: one targeting a peculiar feature of the strain, which was identified based on an IS6110 copy mapping in the Rv2180c gene, and a newly defined strain-specific single nucleotide polymorphism, which was identified by whole-genome sequencing. The results showed that the strain has remained highly prevalent (20.90% of all isolates), has spread throughout the neighbouring islands, and has also reached high representativeness in them (11–32%).
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12
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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13
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Coll P, García de Viedma D. Molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin 2018; 36:233-240. [PMID: 29463429 DOI: 10.1016/j.eimc.2018.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 01/13/2018] [Indexed: 01/05/2023]
Abstract
The application of genotyping tools allowed us to discriminate between the Mycobacterium tuberculosis isolates obtained in the laboratory. The differentiation between single strains opened the door to molecular epidemiology studies, which had helped us to progress in our knowledge of how this pathogen is transmitted in the progressively more complex socio-epidemiological scenario. The genetic stability of this microorganism led to develop specific methodologies, which are thoroughly revised in this chapter. In addition to their application in epidemiology, we review, how they can offer a response to different diagnostic and clinical challenges. Finally, we focus on describing the novel genomic revolution we are experiencing in the analysis of tuberculosis, the methodology in which it is based and the novel possibilities it offers, including new routes of integrating both the molecular and genomic languages in innovative post-genomic proposals, better suited to our real-life context.
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Affiliation(s)
- Pere Coll
- Servicio Microbiología, Hospital de Sant Pau, Barcelona, España; Departament de Genètica i Microbiologia, UniversitatAutònoma de Barcelona, , Bellaterra, España; Institut de Recerca, Hospital de Sant Pau, Barcelona, España.
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, España; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, España; CIBER Enfermedades respiratorias, CIBERES, Madrid, España.
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14
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Genomic Epidemiology of Tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:79-93. [DOI: 10.1007/978-3-319-64371-7_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis. J Clin Microbiol 2016; 54:2969-2974. [PMID: 27682128 DOI: 10.1128/jcm.01718-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/14/2016] [Indexed: 11/20/2022] Open
Abstract
Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis.
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16
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Salas-Coronas J, Rogado-González MC, Lozano-Serrano AB, Cabezas-Fernández MT. [Tuberculosis and immigration]. Enferm Infecc Microbiol Clin 2016; 34:261-9. [PMID: 26851978 DOI: 10.1016/j.eimc.2015.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 11/19/2022]
Abstract
The incidence of tuberculosis worldwide is declining. However, in Western countries this decline is slower due to the impact of immigration. Tuberculosis in the immigrant population is related to health status in the country of origin and with overcrowding and poverty conditions in the host country. Immigrants with tuberculosis are younger, have a higher prevalence of extrapulmonary forms, greater proportion of drug resistance and higher treatment default rates than those of natives. New molecular techniques not only reduce diagnostic delay time but also allow the rapid identification of resistances and improve knowledge of transmission patterns. It is necessary to implement measures to improve treatment compliance in this population group like facilitating access to health card, the use of fixed-dose combination drugs, the participation of cultural mediators and community health workers and gratuity of drugs.
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Affiliation(s)
- Joaquín Salas-Coronas
- Unidad de Medicina Tropical, Hospital de Poniente, El Ejido, Almería, España; Centro de Estudio de las Migraciones y Relaciones Interculturales (CEMyRI). Universidad de Almería, Almería, España.
| | | | | | - M Teresa Cabezas-Fernández
- Unidad de Medicina Tropical, Hospital de Poniente, El Ejido, Almería, España; Centro de Estudio de las Migraciones y Relaciones Interculturales (CEMyRI). Universidad de Almería, Almería, España
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17
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Ultrafast Assessment of the Presence of a High-Risk Mycobacterium tuberculosis Strain in a Population. J Clin Microbiol 2015; 54:779-81. [PMID: 26719445 DOI: 10.1128/jcm.02851-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023] Open
Abstract
A persistent 8-year infection by a Beijing Mycobacterium tuberculosis strain from a previous outbreak after importation from West Africa obliged us to investigate secondary cases. We developed a multiplex PCR method based on whole-genome sequencing to target strain-specific single nucleotide polymorphisms (SNPs). In 1 week, we analyzed 868 isolates stored over 6 years. Only 2 cases (immigrants from Guinea Conakry) harbored the strain, which ruled out transmission-despite opportunities-and challenged some of the advantages associated with Beijing strains.
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18
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Theron G, Jenkins HE, Cobelens F, Abubakar I, Khan AJ, Cohen T, Dowdy DW. Data for action: collection and use of local data to end tuberculosis. Lancet 2015; 386:2324-33. [PMID: 26515676 PMCID: PMC4708262 DOI: 10.1016/s0140-6736(15)00321-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accelerating progress in the fight against tuberculosis will require a drastic shift from a strategy focused on control to one focused on elimination. Successful disease elimination campaigns are characterised by locally tailored responses that are informed by appropriate data. To develop such a response to tuberculosis, we suggest a three-step process that includes improved collection and use of existing programmatic data, collection of additional data (eg, geographic information, drug resistance, and risk factors) to inform tailored responses, and targeted collection of novel data (eg, sequencing data, targeted surveys, and contact investigations) to improve understanding of tuberculosis transmission dynamics. Development of a locally targeted response for tuberculosis will require substantial investment to reconfigure existing systems, coupled with additional empirical data to evaluate the effectiveness of specific approaches. Without adoption of an elimination strategy that uses local data to target hotspots of transmission, ambitious targets to end tuberculosis will almost certainly remain unmet.
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Affiliation(s)
- Grant Theron
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and South African Medical Research Council Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Lung Infection and Immunity Unit, Department of Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Helen E Jenkins
- Department of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Cobelens
- KNCV Tuberculosis Foundation, The Hague, Netherlands; Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, Netherlands
| | | | - Aamir J Khan
- Interactive Research & Development, Karachi, Pakistan
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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19
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Takiff HE, Feo O. Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. THE LANCET. INFECTIOUS DISEASES 2015; 15:1077-1090. [PMID: 26277037 DOI: 10.1016/s1473-3099(15)00071-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/27/2015] [Accepted: 05/20/2015] [Indexed: 01/25/2023]
Abstract
Whole-genome sequencing (WGS) is now common as a result of new technologies that can rapidly sequence a complete bacterial genome for US$500 or less. Many studies have addressed questions about tuberculosis with WGS, and knowing the sequence of the entire genome, rather than only a few fragments, has greatly increased the precision of molecular epidemiology and contact tracing. Additionally, topics such as the mutation rate, drug resistance, the target of new drugs, and the phylogeny and evolution of the Mycobacterium tuberculosis complex bacteria have been elucidated by WGS. Nonetheless, WGS has not explained differences in transmissibility between strains, or why some strains are more virulent than others or more prone to development of multidrug resistance. With advances in technology, WGS of clinical specimens could become routine in high-income countries; however, its relevance will probably depend on easy to use software to efficiently process the sequences produced and accessible genomic databases that can be mined in future studies.
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Affiliation(s)
- Howard E Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela; Unité de Génétique Mycobactérienne, Insitut Pasteur, Paris, France.
| | - Oscar Feo
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
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