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Sousa S, Macedo R, Alves CM, Carvalho C, Gonçalves G, Duarte R. Coffee shops, a hub for TB clusters? Pulmonology 2024; 30:71-74. [PMID: 37236905 DOI: 10.1016/j.pulmoe.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Affiliation(s)
- S Sousa
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal.
| | - R Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - C M Alves
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal; Northern Regional Health Administration, Portugal
| | - C Carvalho
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal
| | - G Gonçalves
- Public Health Unit, ACeS Ave-Famalicão, ARS Norte, Health Ministry, Portugal
| | - R Duarte
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal; Serviço de Pneumologia, Centro Hospitalar de Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
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Sousa S, Alves CM, Macedo R, Carvalho C, Gonçalves G, Duarte R. An investigation of TB infection and reinfection among stone quarry workers. Pulmonology 2023; 29:570-572. [PMID: 37263863 DOI: 10.1016/j.pulmoe.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- S Sousa
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal.
| | - C M Alves
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal; Northern Regional Health Administration, Portugal
| | - R Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - C Carvalho
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal
| | - G Gonçalves
- Public Health Unit, ACeS Ave-Famalicão, ARS Norte, Health Ministry, Portugal
| | - R Duarte
- Multidisciplinary Unit for Biomedical Research (UMIB), Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, ICBAS-UP, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Porto, Portugal; Serviço de Pneumologia, Centro Hospitalar de Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
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Komine T, Ihara H, Inohana M, Kwok JC, Shimizu A, Terasawa T, Miyazaki A, Srivorakul S, Iwao H, Harada S, Yoshida M, Hoshino Y, Kurata O, Fukano H, Wada S. Non-tuberculous mycobacterial disease associated with Mycobacterium montefiorense in salamanders. Front Vet Sci 2023; 10:1248288. [PMID: 37954664 PMCID: PMC10637390 DOI: 10.3389/fvets.2023.1248288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/22/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Mycobacterium montefiorense is one of the causes of non-tuberculous mycobacterial infections in moray eels and salamanders. Although M. montefiorense infection could be a threat to salamanders, little information is available regarding this pathogen and associated infection. This study aimed to provide fundamental information regarding M. montefiorense and its infection in salamanders. Methods Nine M. montefiorense strains isolated from three species of salamanders, namely, Japanese black salamander (Hynobius nigrescens), Hakuba salamander (H. hidamontanus), and Tohoku hynobiid salamander (H. lichenatus), between 2010 and 2018, were characterized based on phenotypic and genetic examination. We also pathologically observed salamanders infected with the M. montefiorense strains, including Hakuba salamanders and Tohoku hynobiid salamanders. Results The microbiological and chemical characteristics of the M. montefiorense salamander and an eel strain (reference strain) matched. Susceptibility testing for antimicrobials suggested that clarithromycin may be effective. Regarding disinfectants, phtharal, peracetic acid, glutaral, sodium hypochlorite, and benzalkonium chloride may be effective. Phylogenetic analyses revealed that the strains isolated from salamanders in 2014 and 2018 were genetically closely related, which could indicate an outbreak. The main gross findings in infected salamanders include skin ulcerative lesions or nodules in the enlarged liver. Microscopically, multifocal to coalescent granulomatous lesions composed of massive macrophages containing numerous acid-fast bacilli were prominently observed in the liver. Conclusion This study contributes to our understanding of the genetic diversity and phenotypic characteristics of M. montefiorense, as well as the pathology of the infection.
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Affiliation(s)
- Takeshi Komine
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Hyogo Ihara
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Mari Inohana
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Jennifer Caroline Kwok
- Retinal Disease Studies Facility, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Akane Shimizu
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Tsumugi Terasawa
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Ayaka Miyazaki
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Saralee Srivorakul
- Center of Veterinary Diagnosis and Technology Transfer, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Osamu Kurata
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Shinpei Wada
- Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
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Macedo R, Isidro J, Ferreira R, Pinto M, Borges V, Duarte S, Vieira L, Gomes JP. Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. Int J Mol Sci 2023; 24:ijms24032912. [PMID: 36769230 PMCID: PMC9918089 DOI: 10.3390/ijms24032912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
- Correspondence:
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Smith JP, Cohen T, Dowdy D, Shrestha S, Gandhi NR, Hill AN. Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. Am J Epidemiol 2023; 192:133-145. [PMID: 36227246 PMCID: PMC10144641 DOI: 10.1093/aje/kwac181] [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: 03/15/2022] [Revised: 07/23/2022] [Accepted: 10/10/2022] [Indexed: 01/11/2023] Open
Abstract
The degree to which individual heterogeneity in the production of secondary cases ("superspreading") affects tuberculosis (TB) transmission has not been systematically studied. We searched for population-based or surveillance studies in which whole genome sequencing was used to estimate TB transmission and in which the size distributions of putative TB transmission clusters were enumerated. We fitted cluster-size-distribution data to a negative binomial branching process model to jointly infer the transmission parameters $R$ (the reproduction number) and the dispersion parameter, $k$, which quantifies the propensity of superspreading in a population (generally, lower values of $k$ ($<1.0$) suggest increased heterogeneity). Of 4,796 citations identified in our initial search, 9 studies from 8 global settings met the inclusion criteria (n = 5 studies of all TB; n = 4 studies of drug-resistant TB). Estimated $R$ values (range, 0.10-0.73) were below 1.0, consistent with declining epidemics in the included settings; estimated $k$ values were well below 1.0 (range, 0.02-0.48), indicating the presence of substantial individual-level heterogeneity in transmission across all settings. We estimated that a minority of cases (range, 2%-31%) drive the majority (80%) of ongoing TB transmission at the population level. Identifying sources of heterogeneity and accounting for them in TB control may have a considerable impact on mitigating TB transmission.
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Affiliation(s)
- Jonathan P Smith
- Correspondence to Dr. Jonathan Smith, Yale School of Public Health, Yale University, 60 College Street, New Haven, CT 06510 (e-mail: )
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Uncovering Beta-Lactam Susceptibility Patterns in Clinical Isolates of Mycobacterium tuberculosis through Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0067422. [PMID: 35695524 PMCID: PMC9431576 DOI: 10.1128/spectrum.00674-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing threat of drug resistance and a stagnated pipeline of novel therapeutics endanger the eradication of tuberculosis. Beta-lactams constitute promising additions to the current therapeutic arsenal and two carbapenems are included in group C of medicines recommended by the WHO for use in longer multidrug-resistant tuberculosis regimens. However, the determinants underlining diverse Mycobacterium tuberculosis phenotypes to beta-lactams remain largely undefined. To decipher these, we present a proof-of-concept study based on a large-scale beta-lactam susceptibility screening for 172 M. tuberculosis clinical isolates from Portugal, including 72 antimycobacterial drug-resistant strains. MICs were determined for multiple beta-lactams and strains were subjected to whole-genome sequencing to identify core-genome single-nucleotide variant-based profiles. Global and cell wall-targeted approaches were then followed to detect putative drivers of beta-lactam response. We found that drug-resistant strains were more susceptible to beta-lactams, but significant differences were not observed between distinct drug-resistance profiles. Sublineage 4.3.4.2 strains were significantly more susceptible to beta-lactams, while the contrary was observed for Beijing and 4.1.2.1 sublineages. While mutations in beta-lactamase or cell wall biosynthesis genes were uncommon, a rise in beta-lactam MICs was detected in parallel with the accumulation of mutations in peptidoglycan cross-linking or cell division genes. Finally, we exposed that putative beta-lactam resistance markers occurred in genes for which relevant roles in cell wall processes have been ascribed, such as rpfC or pknA. Genetic studies to validate the relevance of the identified mutations for beta-lactam susceptibility and further improvement of the phenotype-genotype associations are needed in the future. IMPORTANCE Associations between differential M. tuberculosis beta-lactam phenotypes and preexisting antimycobacterial drug resistance, strain sublineage, or specific mutational patterns were established. Importantly, we reveal that highly drug-resistant isolates of sublineage 4.3.4.2 have an increased susceptibility to beta-lactams compared with other strains. Thus, directing beta-lactams to treat infections by specific M. tuberculosis strains and refraining its use from others emerges as a potentially important strategy to avoid resistance development. Individual mutations in blaC or genes encoding canonical beta-lactam targets, such as peptidoglycan transpeptidases, are infrequent and do not greatly impact the MICs of potent carbapenem plus clavulanic acid combinations. An improved understanding of the global effect of cumulative mutations in relevant gene sets for peptidoglycan and cell division processes on beta-lactam susceptibility is also provided.
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Deneke C, Uelze L, Brendebach H, Tausch SH, Malorny B. Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST. Front Microbiol 2021; 12:649517. [PMID: 34220740 PMCID: PMC8244591 DOI: 10.3389/fmicb.2021.649517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
Whole-genome sequencing (WGS)-based outbreak investigation has proven to be a valuable method for the surveillance of bacterial pathogens. Its utility has been successfully demonstrated using both gene-by-gene (cgMLST or wgMLST) and single-nucleotide polymorphism (SNP)-based approaches. Among the obstacles of implementing a WGS-based routine surveillance is the need for an exchange of large volumes of sequencing data, as well as a widespread reluctance to share sequence and metadata in public repositories, together with a lacking standardization of suitable bioinformatic tools and workflows. To address these issues, we present chewieSnake, an intuitive and simple-to-use cgMLST workflow. ChewieSnake builds on the allele calling software chewBBACA and extends it by the concept of allele hashing. The resulting hashed allele profiles can be readily compared between laboratories without the need of a central allele nomenclature. The workflow fully automates the computation of the allele distance matrix, cluster membership, and phylogeny and summarizes all important findings in an interactive HTML report. Furthermore, chewieSnake can join allele profiles generated at different laboratories and identify shared clusters, including a stable and intercommunicable cluster nomenclature, thus facilitating a joint outbreak investigation. We demonstrate the feasibility of the proposed approach with a thorough method comparison using publically available sequencing data for Salmonella enterica. However, chewieSnake is readily applicable to all bacterial taxa, provided that a suitable cgMLST scheme is available. The workflow is freely available as an open-source tool and can be easily installed via conda or docker.
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Affiliation(s)
- Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Laura Uelze
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Holger Brendebach
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H Tausch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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Pinto M, Borges V, Isidro J, Rodrigues JC, Vieira L, Borrego MJ, Gomes JP. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microb Genom 2021; 7:000481. [PMID: 33245688 PMCID: PMC8208699 DOI: 10.1099/mgen.0.000481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.
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Affiliation(s)
- Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Carlos Rodrigues
- Laboratory of Microbiology, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculty of Medical Sciences, New University of Lisbon, Lisbon, Portugal
| | - Maria José Borrego
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
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10
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Oliveira O, Gaio R, Carvalho C, Correia-Neves M, Duarte R, Rito T. A nationwide study of multidrug-resistant tuberculosis in Portugal 2014-2017 using epidemiological and molecular clustering analyses. BMC Infect Dis 2019; 19:567. [PMID: 31262256 PMCID: PMC6604307 DOI: 10.1186/s12879-019-4189-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/13/2019] [Indexed: 12/03/2022] Open
Abstract
Background Increasing multidrug-resistant tuberculosis (MDR-TB) incidence is a major threat against TB eradication worldwide. We aim to conduct a detailed MDR-TB study in Portugal, an European country with endemic TB, combining genetic analysis and epidemiological data, in order to assess the efficiency of public health containment of MRD-TB in the country. Methods We used published MIRU-VNTR data, that we reanalysed using a phylogenetic analysis to better describe MDR-TB cases transmission occurring in Portugal from 2014 to 2017, further enriched with epidemiological data of these cases. Results We show an MDR-TB transmission scenario, where MDR strains likely arose and are transmitted within local chains. 63% of strains were clustered, suggesting high primary transmission (estimated as 50% using MIRU-VNTR data and 15% considering epidemiological links). These values are higher than those observed across Europe and even for sensitive strains in Portugal using similar methodologies. MDR-TB cases are associated with individuals born in Portugal and evolutionary analysis suggests a local evolution of strains. Consistently the sublineage LAM, the most common in sensitive strains in Europe, is the more frequent in Portugal in contrast with the remaining European MDR-TB picture where immigrant-associated Beijing strains are more common. Conclusions Despite efforts to track and contain MDR-TB strains in Portugal, their transmission patterns are still as uncontrolled as that of sensitive strains, stressing the need to reinforce surveillance and containment strategies. Electronic supplementary material The online version of this article (10.1186/s12879-019-4189-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olena Oliveira
- Population Health Research Domain, Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B, PT Government Associate Laboratory, 4710-057 Braga, 4805-017, Guimarães, Portugal.,EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-600, Porto, Portugal
| | - Rita Gaio
- Department of Mathematics, Faculty of Sciences, Porto, Portugal.,Centre of Mathematics, University of Porto, Porto, Portugal
| | - Carlos Carvalho
- Department of Public Health, Northern Regional Health Administration, 4000-078, Porto, Portugal.,Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-013, Porto, Portugal
| | - Margarida Correia-Neves
- Population Health Research Domain, Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B, PT Government Associate Laboratory, 4710-057 Braga, 4805-017, Guimarães, Portugal
| | - Raquel Duarte
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-600, Porto, Portugal.,Departamento de Ciências da Saúde Pública e Forenses e Educação Médica, Faculdade de Medicina, Universidade do Porto, 4200-319, Porto, Portugal.,Pulmonology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho EPE, 4400-129, Vila Nova de Gaia, Portugal
| | - Teresa Rito
- Population Health Research Domain, Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal. .,ICVS/3B, PT Government Associate Laboratory, 4710-057 Braga, 4805-017, Guimarães, Portugal.
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