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Use of Whole-Genome Sequencing to Explore Mycobacterium tuberculosis Complex Circulating in a Hotspot Department in France. Microorganisms 2022; 10:microorganisms10081586. [PMID: 36014004 PMCID: PMC9414808 DOI: 10.3390/microorganisms10081586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
The Seine-Saint-Denis is the French metropolitan department with the highest incidence of tuberculosis (TB). Our aim was to explore epidemiological and phylogenetic characteristics of TB strains in this hotspot department. We performed WGS on 227 strains of Mycobacterium tuberculosis complex isolated from patients at the Avicenne Hospital from 2016 to 2021 and randomly selected to represent the clinical diversity of French TB localization. Clinical and demographic data were recorded for each TB patient. The mean age of patients was 36 years old. They came from Africa (44%), Asia (27%), Europe (26%) and America (3%). Strains isolated from extrapulmonary samples were associated with Asian patients, whereas strains isolated from pulmonary samples were associated with European patients. We observed a high level of lineage diversity in line with the known worldwide diversity. Interestingly, lineage 3 was associated with lymph node TB. Additionally, the sensitivity of WGS for predicting resistance was 100% for rifampicin, isoniazid and ethambutol and 66.7% for pyrazinamide. The global concordance with drug-susceptibility testing using the phenotypic approach was 97%. In microbiology laboratories, WGS turns out to be an essential tool for better understanding local TB epidemiology, with direct access to circulating lineage identification and to drug susceptibilities to first- and second-line anti-TB drugs.
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Peer V, Schwartz N, Green MS. Gender differences in tuberculosis incidence rates-A pooled analysis of data from seven high-income countries by age group and time period. Front Public Health 2022; 10:997025. [PMID: 36703824 PMCID: PMC9873377 DOI: 10.3389/fpubh.2022.997025] [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: 07/18/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Gender differences in the incidence rates for tuberculosis are occasionally reported. However, the magnitude and consistency of the differences by age group, among different populations, and over extended periods of time are not clear. Materials and methods We obtained national data from seven countries from open-access internet sites or personal communications with official representatives. We computed the male-to-female incidence rate ratios (IRRs) by country and year for every age group and pooled these ratios using meta-analytic methods. Meta-regression analysis was performed to estimate the contribution of age, country, and calendar years to the variation in the IRRs. Results In the age groups of < 1, 1-4, 5-9, and 10-14, the pooled male-to-female IRRs (with 95% CI) were as follows: 1.21 (1.05, 1.40), 0.99 (0.95, 1.04), 1.01 (0.96, 1.06), and 0.83 (0.77, 0.89), respectively. In the age groups 15-44, 45-64, and 65+ years, incidence rates were significantly higher in men, with IRRs of 1.25 (1.16, 1.35), 1.79 (1.56, 2.06), and 1.81 (1.66, 1.96), respectively. Meta-regression analysis revealed that age significantly contributed to the variation in the IRRs. Conclusions There were gender differences in the incidence rates for tuberculosis, with higher rates in boys aged less than one, no significant differences in boys of ages 1-9, and higher rates in boys/men older than 15. The only excess in female gender was in the age group 10-14 years. The age-related gender differences in tuberculosis incidence rates observed over several countries indicate the importance of including sex as a biological variable when assessing the risk factors for tuberculosis.
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Affiliation(s)
- Victoria Peer
- School of Public Health, University of Haifa, Haifa, Israel
| | - Naama Schwartz
- School of Public Health, University of Haifa, Haifa, Israel
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Maitre T, Cottenet J, Godet C, Roussot A, Abdoul Carime N, Ok V, Parrot A, Bonniaud P, Quantin C, Cadranel J. Chronic pulmonary aspergillosis: prevalence, favouring pulmonary diseases and prognosis. Eur Respir J 2021; 58:13993003.03345-2020. [PMID: 33479108 DOI: 10.1183/13993003.03345-2020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/03/2021] [Indexed: 12/13/2022]
Abstract
Chronic pulmonary aspergillosis (CPA) is an emerging disease in patients with common chronic pulmonary diseases (CPDs). While its prevalence is linked to tuberculosis (TB) in endemic countries, epidemiological and prognostic data are lacking in low TB incidence countries. The aim of this study was to describe these features in CPA patients hospitalised in France between 2009 and 2018.We estimated the prevalence and mortality of hospitalised CPA patients using the French nationwide administrative hospital database. We also assessed the association with CPD, thoracic interventions and malnutrition.From 2009 to 2018, 17 290 patients were hospitalised in France for CPA, with an increasing prevalence during this period. Most patients were male (63.5%) with a median age of 65 years at CPA diagnosis, living in farming regions and large cities. The proportion of underlying chronic obstructive pulmonary disease (COPD) and emphysema during the previous 5 years was 44% and 22%, respectively, whereas it was only 3% for both TB and non-TB mycobacterial (NTM) infections. The mortality rates during the first hospitalisation, at 1 year and at 5 years were 17%, 32% and 45%, respectively. In multivariate analysis, mortality rates were increased in patients aged >65 years, male patients and patients with malnutrition, diabetes or lung cancer history. The risk of mortality in patients with COPD or emphysema was higher than in those with previous mycobacterial lung infection.In France, CPA is an emerging infection commonly associated with non-mycobacterial CPD. This shift in the distribution profile of underlying CPD will likely worsen CPA mortality.
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Affiliation(s)
| | - Jonathan Cottenet
- Biostatistics and Bioinformatics Department (DIM), Dijon University Hospital, Dijon, France.,University of Bourgogne Franche-Comté, Dijon, France
| | - Cendrine Godet
- Dept of Pneumology, Assistance Publique Hôpitaux de Paris, Bichat Hospital, Paris, France
| | - Adrien Roussot
- Biostatistics and Bioinformatics Department (DIM), Dijon University Hospital, Dijon, France.,University of Bourgogne Franche-Comté, Dijon, France
| | - Nafiz Abdoul Carime
- Biostatistics and Bioinformatics Department (DIM), Dijon University Hospital, Dijon, France.,University of Bourgogne Franche-Comté, Dijon, France
| | - Vichita Ok
- Dept of Parasitology and Mycology, Assistance Publique Hôpitaux de Paris, Avicenne Hospital, Sorbonne Paris Nord, Bobigny, France
| | - Antoine Parrot
- Sorbonne Université, Paris, France.,Dept of Pneumology and Reference Centre for Rare Lung Diseases, Assistance Publique Hôpitaux de Paris, Tenon Hospital, Paris, France
| | - Philippe Bonniaud
- University of Bourgogne Franche-Comté, Dijon, France.,Dept of Pneumology and Intensive Care Unit, Dijon University Hospital, Dijon, France
| | - Catherine Quantin
- Biostatistics and Bioinformatics Department (DIM), Dijon University Hospital, Dijon, France.,University of Bourgogne Franche-Comté, Dijon, France.,Inserm, CIC 1432, Dijon, France.,Clinical Epidemiology/Clinical Trials Unit, Clinical Investigation Center, Dijon University Hospital, Dijon, France.,Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), INSERM, UVSQ, Institut Pasteur, Université Paris-Saclay, Paris, France.,Contributed equally to this work
| | - Jacques Cadranel
- Sorbonne Université, Paris, France .,Dept of Pneumology and Reference Centre for Rare Lung Diseases, Assistance Publique Hôpitaux de Paris, Tenon Hospital, Paris, France.,Contributed equally to this work
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Maitre T, Ok V, Morel F, Bonnet I, Sougakoff W, Robert J, Trosini V, Caumes E, Aubry A, Veziris N. Sampling strategy for bacteriological diagnosis of intrathoracic tuberculosis. Respir Med Res 2021; 79:100825. [PMID: 33971432 DOI: 10.1016/j.resmer.2021.100825] [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: 11/02/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is the most frequent site of TB and the one leading its spread worldwide. Multiple specimens are commonly collected for TB diagnosis including those requiring invasive procedures. This study aimed to review the sampling strategy for the microbiological diagnosis of pulmonary TB. METHODS A retrospective analysis of collected samples from September 1st 2014 to May 1st 2016 in the Bacteriology laboratory of Pitié-Salpêtrière Hospital (Paris, France) was performed. All the samples collected in patients aged over 18 years for the bacteriological diagnosis of pulmonary TB were included. RESULTS A total of 6267 samples were collected in 2187 patients. One hundred and twenty-six patients (6%) had a culture confirmed pulmonary TB. Among them, multiple sputum collections were sufficient for TB diagnosis in 63.5%, gastric lavages permitted to avoid bronchoscopy in only 7.1%, and bronchoscopy was necessary in 29.4%. The culture positivity of sputa (8.6%) was higher than that of bronchial aspirations (3.1%), bronchiolo-alveolar lavages (BAL) (2.3%) or gastric lavages (4.8%) (P<0.001). From its 70.0% theoretical PPV value, the 46.1% selection in bronchial aspirations allocated to molecular test increased PPV up to 88.9%. CONCLUSIONS Based on our data, we suggest to collect sputum consistently. If smear negative a bronchoscopy should be performed and molecular diagnosis be performed on a subset of bronchial aspirations based on expertise of the bronchoscopist.
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Affiliation(s)
- T Maitre
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France.
| | - V Ok
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - F Morel
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - I Bonnet
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - W Sougakoff
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - J Robert
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - V Trosini
- Service de pneumologie, médecine intensive et réanimation, département R3S, groupe hospitalier, Sorbonne université, Site Pitié-Salpêtrière, AP-HP, Paris, France
| | - E Caumes
- Service de maladies infectieuses et tropicales, groupe hospitalier, Sorbonne université, Site Pitié Salpêtrière, AP-HP, Paris, France
| | - A Aubry
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France
| | - N Veziris
- Laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries et de la résistance des mycobactéries aux antituberculeux, groupe hospitalier, Sorbonne Université, Site Pitié-Salpêtrière, AP-HP, Paris, France; Inserm U1135, Sorbonne université, centre d'immunologie et des maladies infectieuses (CIMI-Paris), Paris, France; Département de bactériologie, groupe hospitalier, Sorbonne université, site Saint-Antoine, AP-HP, Paris, France
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