Population-based sequencing of Mycobacterium tuberculosis reveals how current population dynamics are shaped by past epidemics

23 páginas, 4 figuras, 1 tabla.Transmission is a driver of tuberculosis (TB) epidemics in high-burden regions, with assumed negligible impact in low-burden areas. However, we still lack a full characterization of transmission dynamics in settings with similar and different burdens. Genomic epidemiology can greatly help to quantify transmission, but the lack of whole genome sequencing population-based studies has hampered its application. Here, we generate a population-based dataset from Valencia region and compare it with available datasets from different TB-burden settings to reveal transmission dynamics heterogeneity and its public health implications. We sequenced the whole genome of 785 Mycobacterium tuberculosis strains and linked genomes to patient epidemiological data. We use a pairwise distance clustering approach and phylodynamic methods to characterize transmission events over the last 150 years, in different TB-burden regions. Our results underscore significant differences in transmission between low-burden TB settings, i.e., clustering in Valencia region is higher (47.4%) than in Oxfordshire (27%), and similar to a high-burden area as Malawi (49.8%). By modeling times of the transmission links, we observed that settings with high transmission rate are associated with decades of uninterrupted transmission, irrespective of burden. Together, our results reveal that burden and transmission are not necessarily linked due to the role of past epidemics in the ongoing TB incidence, and highlight the need for in-depth characterization of transmission dynamics and specifically tailored TB control strategies.European Research Council 638553-TB-ACCELERATE; European Research Council 101001038-TBRECONNECT; Ministerio de Ciencia e Innovación SAF2016-77346-RPeer reviewe

Evolución de la Tuberculosis en Castellón (2008-2012). Caracterización genotípica mediante 15 MIRU-VNTR

La tuberculosis (TB) es considerada una de las primeras enfermedades infecciosas humanas de las que se tiene constancia y aún hoy, en pleno siglo XXI, es una de las más importantes causantes de morbilidad y mortalidad en todo el mundo. Según describe la Organización Mundial de la Salud (OMS) en su 19º informe, 9 millones de personas enfermaron de TB a nivel mundial en el año 2013, aunque en éste se refiere que ha habido una disminución de casos en los últimos años. También el Centro Europeo para la Prevención y Control de Enfermedades (ECDC) y el Centro Nacional de Epidemiología (CNE) informan que en Europa y en España, en el año 2012, el número de casos de TB disminuyó respecto al año anterior. La presente Tesis Doctoral tiene como objetivos conocer la evolución de la TB en la provincia de Castellón a lo largo del periodo comprendido entre enero de 2008 a diciembre de 2012, describir las características clínico-epidemiológicas y microbiológicas de los casos diagnosticados con cultivo positivo, detallar la frecuencia de resistencias de Mycobacterium tuberculosis frente a fármacos tuberculostáticos de primera línea, y analizar los patrones de transmisión de TB en Castellón durante los años 2010, 2011 y 2012 mediante tipificación molecular, utilizando la técnica 15 MIRU-VNTR. Para conseguir los 3 primeros objetivos consultamos varias fuentes de información como son el Sistema de Información del Laboratorio (SIL), el Sistema del Análisis de la Vigilancia Epidemiológica (AVE) y los informes de TB editados por la Generalitat Valenciana. Para llevar a cabo el cuarto objetivo, analizamos las cepas congeladas y recuperadas de los tres años indicados mediante la técnica de epidemiología molecular 15 MIRU-VNTR. En la provincia de Castellón se declararon 387 casos de TB, de los que 320 (82,7%) tuvieron el cultivo positivo; en 2008 se diagnosticaron microbiológicamente 74 casos, 83 en el 2009, 66 en el 2010, 56 en el 2011 y 41 en el 2012. En cuanto a las características de los pacientes, la razón hombre/mujer fue de 1,9 y la edad media fue de 32,5 años, concentrándose el 60,6% en el grupo de adultos jóvenes (15-44 años). El 43,7% de los pacientes eran extranjeros, el 93,8% fueron casos no tratados previamente, el 29,4% presentaba al menos un factor de riesgo para desarrollar enfermedad tuberculosa y, por último, el 67,2% de los pacientes fueron hospitalizados. Respecto a las formas clínicas, un 87,2% fueron TB pulmonar, predominando la ganglionar entre las formas extrapulmonares. A partir del estudio convencional de contactos se sospechó 7 posibles brotes de 2 miembros. El estudio de sensibilidad se realizó a las 320 cepas aisladas, resultando resistentes el 13,5%, siendo la resistencia a isoniazida del 8,1%. En población de origen español el porcentaje de resistencias fue del 10,6% mientras que en extranjeros fue del 15,7%. Se realizó la tipificación molecular a 151 cepas de las 163 aisladas en los tres años. Los loci más polimórficos fueron el VNTR 4052, el VNTR 2163b y el VNTR 3690, y los que presentaron un poder de discriminación elevado, calculado a partir del índice de diversidad de Hunter-Gaston, fueron los MIRU 26, 40 y 10, y los VNTR 577, 2401, 3690, 2163b, 1955 y 4052. Evidenciamos que 122 cepas presentaron un patrón único y que 29 cepas se agruparon en 12 clusters, siendo el porcentaje de agrupación del 19,2% y la tasa de transmisión reciente de un 11,3%. En el presente estudio se concluye que la tasa de TB, y paralelamente el número de casos con cultivo positivo, en la provincia de Castellón ha disminuido a lo largo de los años analizados; que el fenómeno de la inmigración tiene una influencia importante en la TB de nuestra provincia; que el número de hospitalizaciones, aún siendo menor que en estudios previos, sigue siendo elevado y que la resistencia global de un 13,5% es también más elevada a la descrita en trabajos anteriores en Castellón. De estas resistencias, la de isoniazida superior al 5% obliga a tratar la TB en los dos primeros meses con asociación de 4 fármacos, como recomienda la OMS; el porcentaje elevado de resistencia a isoniazida en el año 2010 fue debido a un brote que fue confirmado con tipificación molecular. Aplicando la técnica 15 MIRU-VNTR, con un índice de discriminación elevado de 0,998, se ha detectado una baja tasa de transmisión durante los 3 años analizados

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

Artículo con 20 páginas, 5 figuras, 1 tabla. All the sequence data are deposited in the European Nucleotide Archive under the Bioproject number PRJEB29604 (https://www.ebi.ac.uk/ena/data/view/PRJEB29604) and the accession numbers ERR2099780 (https://www.ebi.ac.uk/ena/data/search?query=ERR2099780) and ERR2099784 (https://www.ebi.ac.uk/ena/data/search?query=ERR2099784).BACKGROUND: Whole genome sequencing provides better delineation of transmission clusters in Mycobacterium tuberculosis than traditional methods. However, its ability to reveal individual transmission links within clusters is limited. Here, we used a 2-step approach based on Bayesian transmission reconstruction to (1) identify likely index and missing cases, (2) determine risk factors associated with transmitters, and (3) estimate when transmission happened. METHODS AND FINDINGS: We developed our transmission reconstruction method using genomic and epidemiological data from a population-based study from Valencia Region, Spain. Tuberculosis (TB) incidence during the study period was 8.4 cases per 100,000 people. While the study is ongoing, the sampling frame for this work includes notified TB cases between 1 January 2014 and 31 December 2016. We identified a total of 21 transmission clusters that fulfilled the criteria for analysis. These contained a total of 117 individuals diagnosed with active TB (109 with epidemiological data). Demographic characteristics of the study population were as follows: 80/109 (73%) individuals were Spanish-born, 76/109 (70%) individuals were men, and the mean age was 42.51 years (SD 18.46). We found that 66/109 (61%) TB patients were sputum positive at diagnosis, and 10/109 (9%) were HIV positive. We used the data to reveal individual transmission links, and to identify index cases, missing cases, likely transmitters, and associated transmission risk factors. Our Bayesian inference approach suggests that at least 60% of index cases are likely misidentified by local public health. Our data also suggest that factors associated with likely transmitters are different to those of simply being in a transmission cluster, highlighting the importance of differentiating between these 2 phenomena. Our data suggest that type 2 diabetes mellitus is a risk factor associated with being a transmitter (odds ratio 0.19 [95% CI 0.02-1.10], p < 0.003). Finally, we used the most likely timing for transmission events to study when TB transmission occurred; we identified that 5/14 (35.7%) cases likely transmitted TB well before symptom onset, and these were largely sputum negative at diagnosis. Limited within-cluster diversity does not allow us to extrapolate our findings to the whole TB population in Valencia Region. CONCLUSIONS: In this study, we found that index cases are often misidentified, with downstream consequences for epidemiological investigations because likely transmitters can be missed. Our findings regarding inferred transmission timing suggest that TB transmission can occur before patient symptom onset, suggesting also that TB transmits during sub-clinical disease. This result has direct implications for diagnosing TB and reducing transmission. Overall, we show that a transition to individual-based genomic epidemiology will likely close some of the knowledge gaps in TB transmission and may redirect efforts towards cost-effective contact investigations for improved TB control.IC was supported by European Research Council (638553-TB-ACCELERATE), the Ministerio de Economía y Competitividad (SAF2016-77346-R). CC and YX were supported by the Engineering and Physical Sciences Research Council of the UK (EPSRC EP/K026003/1 (CC) and EPSRC EP/N014529/1 (CC and YX).Peer reviewe

Pseudomonas aeruginosa antibiotic susceptibility profiles, genomic epidemiology and resistance mechanisms: a nation-wide five-year time lapse analysisResearch in context

Summary: Background: Pseudomonas aeruginosa healthcare-associated infections are one of the top antimicrobial resistance threats world-wide. In order to analyze the current trends, we performed a Spanish nation-wide high-resolution analysis of the susceptibility profiles, the genomic epidemiology and the resistome of P. aeruginosa over a five-year time lapse. Methods: A total of 3.180 nonduplicated P. aeruginosa clinical isolates from two Spanish nation-wide surveys performed in October 2017 and 2022 were analyzed. MICs of 13 antipseudomonals were determined by ISO-EUCAST. Multidrug resistance (MDR)/extensively drug resistance (XDR)/difficult to treat resistance (DTR)/pandrug resistance (PDR) profiles were defined following established criteria. All XDR/DTR isolates were subjected to whole genome sequencing (WGS). Findings: A decrease in resistance to all tested antibiotics, including older and newer antimicrobials, was observed in 2022 vs 2017. Likewise, a major reduction of XDR (15.2% vs 5.9%) and DTR (4.2 vs 2.1%) profiles was evidenced, and even more patent among ICU isolates [XDR (26.0% vs 6.0%) and DTR (8.9% vs 2.6%)] (p < 0.001). The prevalence of Extended-spectrum β-lactamase/carbapenemase production was slightly lower in 2022 (2.1%. vs 3.1%, p = 0.064). However, there was a significant increase in the proportion of carbapenemase production among carbapenem-resistant strains (29.4% vs 18.1%, p = 0.0246). While ST175 was still the most frequent clone among XDR, a slight reduction in its prevalence was noted (35.9% vs 45.5%, p = 0.106) as opposed to ST235 which increased significantly (24.3% vs 12.3%, p = 0.0062). Interpretation: While the generalized decrease in P. aeruginosa resistance, linked to a major reduction in the prevalence of XDR strains, is encouraging, the negative counterpart is the increase in the proportion of XDR strains producing carbapenemases, associated to the significant advance of the concerning world-wide disseminated hypervirulent high-risk clone ST235. Continued high-resolution surveillance, integrating phenotypic and genomic data, is necessary for understanding resistance trends and analyzing the impact of national plans on antimicrobial resistance. Funding: MSD and the Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea—NextGenerationEU