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15 páginas, 5 figuras, 1 tabla, Outbreak strains of Mycobacterium tuberculosis are promising candidates as targets in the search for intrinsic determinants of transmissibility, as they are responsible for many cases with sustained transmission; however, the use of low-resolution typing methods and restricted geographical investigations represent flaws in assessing the success of long-lived outbreak strains. We can now address the nature of outbreak strains by combining large genomic data sets and phylodynamic approaches. We retrospectively sequenced the whole genome of representative samples assigned to an outbreak circulating in the Canary Islands (the GC strain) since 1993, which accounts for ~20% of local tuberculosis cases. We selected a panel of specific single nucleotide polymorphism (SNP) markers for an in-silico search for additional outbreak-related sequences within publicly available tuberculosis genomic data. Using this information, we inferred the origin, spread, and epidemiological parameters of the GC strain. Our approach allowed us to accurately trace the historical and more recent dispersion of the GC strain. We provide evidence of a highly successful nature within the Canarian archipelago but limited expansion abroad. Estimation of epidemiological parameters from genomic data disagree with a distinctive biology of the GC strain. With the increasing availability of genomic data allowing for the accurate inference of strain spread and critical epidemiological parameters, we can now revisit the link between Mycobacterium tuberculosis genotypes and transmission, as is routinely carried out for SARS-CoV-2 variants of concern. We demonstrate that social determinants rather than intrinsically higher bacterial transmissibility better explain the success of the GC strain. Importantly, our approach can be used to trace and characterize strains of interest worldwide. IMPORTANCE Infectious disease outbreaks represent a significant problem for public health. Tracing outbreak expansion and understanding the main factors behind emergence and persistence remain critical to effective disease control. Our study allows researchers and public health authorities to use Whole-Genome Sequencing-based methods to trace outbreaks, and shows how available epidemiological information helps to evaluate the factors underpinning outbreak persistence. Taking advantage of all the freely available information placed in public repositories, researchers can accurately establish the expansion of an outbreak beyond original boundaries, and determine the potential risk of a strain to inform health authorities which, in turn, can define target strategies to mitigate expansion and persistence. Finally, we show the need to evaluate strain transmissibility in different geographic contexts to unequivocally associate spread to local or pathogenic factors, an important lesson taken from genomic surveillance of SARS-CoV-2., This project has been funded by the European Research Council (101001038-TBRECONNECT), the Ministerio de Economía, Industria y Competitividad (PID2019-104477RB-I00), and the European Commission–NextGenerationEU (Regulation EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global) to I.C. This project has been funded by the Instituto de Salud Carlos III (FIS18/0336) and the Gobierno de Aragón/Fondo Social Europeo “Construyendo Europa desde Aragón” to SS

14 paginas, 5 figuras, 2 tablas., Genomic studies of the Mycobacterium tuberculosis complex (MTBC) might shed light on the dynamics of its transmission, especially in high-burden settings, where recent outbreaks are embedded in the complex natural history of the disease. To this end, we conducted a 1 year prospective surveillance-based study in Mozambique. We applied whole-genome sequencing (WGS) to 295 positive cultures. We fully characterized MTBC isolates by phylogenetics and dating evaluation, and carried out a molecular epidemiology analysis to investigate further associations with pre-defined transmission risk factors. The majority of strains (49.5%, 136/275) belonged to lineage (L) 4; 57.8 % of them (159/275) were in genomic transmission clusters (cut-off 5 SNPs), and a strikingly high proportion (45.5%) shared an identical genotype (0 SNP pairwise distance). We found two 'likely endemic' clades, comprising 67 strains, belonging to L1.2, which dated back to the late 19th century and were associated with recent spread among people living with human immunodeficiency virus (PLHIV). We describe for the first time the population structure of MTBC in our region, a high tuberculosis (TB)/HIV burden area. Clustering analysis revealed an unforeseen pattern of spread and high rates of progression to active TB, suggesting weaknesses in TB control activities. The long-term presence of local strains in Mozambique, which were responsible for large transmission among HIV/TB-coinfected patients, calls into question the role of HIV in TB transmission., This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programmes 101001038 (TB-RECONNECT), PID2019-104477RB-I00 from Ministerio de Economía y Competitividad (Spanish Government) (to I.C.). We acknowledge support from the Spanish Ministry of Science, Innovation and Universities through the ‘Centro de Excelencia Severo Ochoa 2019–2023’.Programme (CEX2018-000806-S), and support from the Generalitat de Catalunya through the CERCA Programme. B.S receives a pre-doctoral fellowship from the Secretariat of Universities and Research, Ministry of Enterprise and Knowledge of the Government of Catalonia and co-funded by European Social Fund (AGAUR).

9 páginas, 4 figuras, 1 tabla., Background: Molecular diagnostics are considered the most promising route to achieving rapid, universal drug susceptibility testing for Mycobacterium tuberculosiscomplex (MTBC). We aimed to generate a WHO endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: A candidate gene approach was used to identify mutations as associated with resistance, or consistent with susceptibility, for 13 WHO endorsed anti-tuberculosis drugs. 38,215 MTBC isolates with paired whole-genome sequencing and phenotypic drug susceptibility testing data were amassed from 45 countries. For each mutation, a contingency table of binary phenotypes and presence or absence of the mutation computed positive predictive value, and Fisher's exact tests generated odds ratios and Benjamini-Hochberg corrected p-values. Mutations were graded as Associated with Resistance if present in at least 5 isolates, if the odds ratio was >1 with a statistically significant corrected p-value, and if the lower bound of the 95% confidence interval on the positive predictive value for phenotypic resistance was >25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: 15,667 associations were computed for 13,211 unique mutations linked to one or more drugs. 1,149/15,667 (7·3%) mutations were classified as associated with phenotypic resistance and 107/15,667 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was >80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were classified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: This first WHO endorsed catalogue of molecular targets for MTBC drug susceptibility testing provides a global standard for resistance interpretation. Its existence should encourage the implementation of molecular diagnostics by National Tuberculosis Programmes. Funding: UNITAID, Wellcome, MRC, BMGF., Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

There is scant information as to how SARS-CoV-2 antibody and T-cell immune responses elicited by mRNA COVID-19 vaccines evolve in the general population, and in particular in elderly nursing home residents, who are at increased risk of developing severe clinical forms of COVID-19. We read with interest the work by Tré-Hardy and colleagues who reported a significant antibody decrease at around 6 months after full vaccination in healthcare workers, that was more marked in SARS-CoV-2 naïve vaccinees [1]. The authors suggested that in a supply-limited environment, booster dose schemes may be spared for SARS-CoV-2-experienced individuals. The data presented herein extend this observation to elderly nursing home residents. The current prospective cohort study included 680 (478 female; median age, 87 years; range 65–100) of a cohort of 881 nursing home residents initially recruited from a representative sample of Valencian Community nursing homes (n = 13) for assessment of SARS-CoV-2 immune responses at a median of 3 months (3 M) following full-dose Comirnaty® COVID-19 vaccination [2] who were re-examined at a median of 219 days (range, 139–246) after vaccination (7 M). Out of the 680 participants, 238 had been infected by SARS-CoV-2 prior to receiving the first vaccine dose, as recorded in the electronic Valencia Health System Integrated Databases. Two residents contracted the infection (Delta variant, as documented by whole-genome sequencing) between sampling times (3 M and 7 M). The remaining 440 participants were presumably naïve for SARS-CoV-2 at the time of sampling (7 M).

Genomic studies of Mycobacterium tuberculosis complex (MTBC) might shed light on the dynamics of its transmission, especially in high-burden settings, where recent outbreaks are embedded in the complex natural history of the disease. We applied Whole-genome sequencing (WGS) to characterize the local population of MTBC, unravel potential transmission links and evaluate associations with host and pathogen factors. Methods A one-year prospective study was conducted in Mozambique, a high HIV/TB burden country. WGS was applied to 295 positive cultures. We combined phylogenetic, geographical and clustering analysis, and investigated associations between risk factors of transmission. Findings A significant high proportion of strains were in recent transmission (45.5%). We fully characterized MTBC isolates by using phylogenetic approaches and dating evaluation. We found two likely endemic clades, comprised of 67 strains, belonging to L1.2, dating from the late XIX century and associated with recent spread among PLHIV. Interpretation Our results unveil the population structure of MTBC in our setting. The clustering analysis revealed an unexpected pattern of spread and high rates of progression, suggesting the failure of control measures. The long-term presence of local strains in Mozambique, which were responsible for large transmission among HIV/TB coinfected patients, hint at possible coevolution with sympatric host populations and challenge the role of HIV in TB transmission., Ministry of Enterprise and Knowledge (Government of Catalonia & European Social Fund, AGAUR fellowship); European Research Council (ERC) European Union’s Horizon 2020.

Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic infectious diseases such as malaria. Our aim is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. We conducted serological tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal samples were taken for RT-qPCR of SARS-COV-2 and for whole viral genome sequencing. Our results show a 3.2% and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity; and 22% of malaria incidence, over the sampling period, with marked differences linked to age. Importantly, we found 2 cases of confirmed co-infection and 8 cases of suspected co-infection mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, assigned to lineages: A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A and 20B. This is the first population-based study about SARS-CoV-2 and malaria in Burkina Faso during the first wave of the pandemic, providing a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Sub-Saharan African country. Besides, it highlights the low frequency of co-infection with malaria in African communities., This research work received funding from by the European Commission NextGenerationEU (Regulation EU 2020/2094) and grant 202020E159 through CSIC Global Health Platform (PTI Salud Global).

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-R

9 Páginas, 3 figuras, 1 tabla. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fvets.2021.805004/full#supplementary-materia, Farmed minks have been reported to be highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and may represent a risk to humans. In this study, we describe the first outbreak of SARS-CoV-2 occurred on a mink farm in Spain, between June and July 2020, involving 92,700 animals. The outbreak started shortly after some farm workers became seropositive for SARS-CoV-2. Minks showed no clinical signs compatible with SARS-CoV-2 infection throughout the outbreak. Samples from 98 minks were collected for histopathological, serological, and molecular studies. Twenty out of 98 (20.4%) minks were positive by RT-qPCR and 82 out 92 (89%) seroconverted. This finding may reflect a rapid spread of the virus at the farm with most of the animals overcoming the infection. Additionally, SARS-CoV-2 was detected by RT-qPCR in 30% of brain samples from positive minks. Sequencing analysis showed that the mink sequences were not closely related with the other mink SARS-CoV-2 sequences available, and that this mink outbreak has its probable origin in one of the genetic variants that were prevalent in Spain during the first COVID-19 epidemic wave. Histological studies revealed bronchointerstitial pneumonia in some animals. Immunostaining of viral nucleocapsid was also observed in nasal turbinate tissue. Farmed minks could therefore constitute an important SARS-CoV-2 reservoir, contributing to virus spread among minks and humans. Consequently, continuous surveillance of mink farms is needed., This study was funded by Banco Santander S.A. and University of Zaragoza, through the project titled Estudio de la importancia de los animales de compañía como reservorios del SARS-CoV-2 y en la epidemiología de la enfermedad COVID-19. In addition, genome sequencing was funded by Fondo COVID COV20/00140.

We investigated whether peripheral blood levels of SARS-CoV-2 Spike (S) receptor binding domain antibodies (anti-RBD), neutralizing antibodies (NtAb) targeting Omicron S, and S-reactive-interferon (IFN)-γ-producing CD4+ and CD8+ T cells measured after a homologous booster dose (3D) with the Comirnaty® vaccine was associated with the likelihood of subsequent breakthrough infections due to the Omicron variant. An observational study including 146 nursing home residents (median age, 80 years; range, 66-99; 109 female) evaluated for an immunological response after 3D (at a median of 16 days). Anti-RBD total antibodies were measured by chemiluminescent immunoassay. NtAb were quantified by an Omicron S pseudotyped virus neutralization assay. SARS-CoV-2-S specific-IFNγ-producing CD4+ and CD8+ T cells were enumerated by whole-blood flow cytometry for intracellular cytokine staining. In total, 33/146 participants contracted breakthrough Omicron infection (symptomatic in 30/33) within 4 months after 3D. Anti-RBD antibody levels were comparable in infected and uninfected participants (21 123 vs. 24 723 BAU/ml; p = 0.34). Likewise, NtAb titers (reciprocal IC50 titer, 157 vs. 95; p = 0.32) and frequency of virus-reactive CD4+ (p = 0.82) and CD8+ (p = 0.91) T cells were similar across participants in both groups. anti-RBD antibody levels and NtAb titers estimated at around the time of infection were also comparable (3445 vs. 4345 BAU/ml; p = 0.59 and 188.5 vs. 88.9; p = 0.70, respectively). Having detectable NtAb against Omicron or SARS-CoV-2-S-reactive-IFNγ-producing CD4+ or CD8+ T cells after 3D was not correlated with increased protection from breakthrough infection (OR, 1.50; p = 0.54; OR, 0.0; p = 0.99 and OR 3.70; p = 0.23, respectively). None of the immune parameters evaluated herein, including NtAb titers against the Omicron variant, may reliably predict at the individual level the risk of contracting COVID-19 due to the Omicron variant in nursing home residents., Ignacio Torres (Río Hortega Contract; CM20/00090), Estela Giménez (Juan Rodés Contract, JR18/00053), and Eliseo Albert (Juan Rodés Contract; JR20/00011) hold contracts funded by the Carlos III Health Institute (cofinanced by the European Regional Development Fund, ERDF/FEDER). Ron Geller holds a Ramon y Cajal fellowship from the Spanish Ministerio de Economía y Competitividad (RYC‐2015‐17517). This study work was supported by Instituto de Salud Carlos III, Madrid, Spain (FIS, PI21/00563) to David Navarro, and by the European Commission NextGenerationEU fund (EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global) to Ron Geller.

14 páginas, 2 figuras, 5 tablas. Supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes13040609/s1, Genes related to DNA damage repair in Mycobacterium tuberculosis are critical for survival and genomic diversification. The aim of this study is to compare the presence of SNPs in genes related to DNA damage repair in sensitive and drug-resistant M. tuberculosis genomes isolated from patients with and without type 2 diabetes mellitus (T2DM). We collected 399 M. tuberculosis L4 genomes from several public repositories; 224 genomes belonging to hosts without T2DM, of which 123 (54.9%) had drug sensitive tuberculosis (TB) and 101 (45.1%) had drug resistance (DR)-TB; and 175 genomes from individuals with T2DM, of which 100 (57.1%) had drug sensitive TB and 75 (42.9%) had DR-TB. The presence of SNPs in the coding regions of 65 genes related to DNA damage repair was analyzed and compared with the resistance profile and the presence/absence of T2DM in the host. The results show the phylogenetic relationships of some SNPS and L4 sub-lineages, as well as differences in the distribution of SNPs present in DNA damage repair-related genes related to the resistance profile of the infecting strain and the presence of T2DM in the host. Given these differences, it was possible to generate two discriminant functions to distinguish between drug sensitive and drug resistant genomes, as well as patients with or without T2DM., This project financed with resources from CONACYT-Basic Sciences Fund: Influence of type 2 diabetes mellitus in the development of mutations associated with multidrug resistance in Tuberculosis, A1-S-22956. The doctoral students were granted scholarships by CONACYT, call “Becas Nacional (Tradicional) 2019-02” with registration number (“CVU”) 411155 and 710466.

11 páginas, 2 figuras, 1 tabla, Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance., I. Comas was supported by PID2019-104477RB-I00 from the Spanish Science Ministry and by ERC (CoG 101001038)

10 páginas, 2 figuras, 3 tablas, Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases., This work was supported by the Instituto de Salud Carlos III (Ref COV20/00140: SeqCOVID—Consorcio para la epidemiología genómica de SARS-CoV-2 en España) and by Consejo Superior de Investigaciones Científicas (CSIC) (PTI Salud Global). L.P.L. is the recipient of a Miguel Servet Research contract (CPII20/00001) from the Instituto de Salud Carlos III.

3 páginas, 1 figura, 1 tabla., This work was supported by Instituto de Salud Carlos III (Ref COV20/00140: SeqCOVID—Consorcio para la epidemiología genómica de SARSCoV-2 en España) and by Consejo Superior de Investigaciones Científicas (CSIC; PTI Salud Global). L.P.L. has a Miguel Servet Contract (CPII20/00001).

Molecular epidemiology of SARS-CoV-2 aims to monitor the appearance of new variants with the potential to change the virulence or transmissibility of the virus. During the first year of SARS-CoV-2 evolution, numerous variants with possible public health impact have emerged. We have detected two mutations in the Spike protein at amino acid positions 1163 and 1167 that have appeared independently multiple times in different genetic backgrounds, indicating they may increase viral fitness. Interestingly, the majority of these sequences appear in transmission clusters, with the genotype encoding mutations at both positions increasing in frequency more than single-site mutants. This genetic outcome that we denote as Lineage B.1.177.637, belongs to clade 20E and includes 12 additional single nucleotide polymorphisms but no deletions with respect to the reference genome (first sequence in Wuhan). B.1.177.637 appeared after the first wave of the epidemic in Spain, and subsequently spread to eight additional countries, increasing in frequency among sequences in public databases. Positions 1163 and 1167 of the Spike protein are situated in the HR2 domain, which is implicated in the fusion of the host and viral membranes. To better understand the effect of these mutations on the virus, we examined whether B.1.177.637 altered infectivity, thermal stability, or antibody sensitivity. Unexpectedly, we observed reduced infectivity of this variant relative to the ancestral 20E variant in vitro while the levels of viral RNA in nasopharyngeal swabs did not vary significantly. In addition, we found the mutations do not impact thermal stability or antibody susceptibility in vaccinated individuals but display a moderate reduction in sensitivity to neutralization by convalescent sera from early stages of the pandemic. Altogether, this lineage could be considered a Variant of Interest (VOI), we denote VOI1163.7. Finally, we detected a sub-cluster of sequences within VOI1163.7 that have acquired two additional changes previously associated with antibody escape and it could be identified as VOI1163.7.V2. Overall, we have detected the spread of a new Spike variant that may be advantageous to the virus and whose continuous transmission poses risks by the acquisition of additional mutations that could affect pre-existing immunity., This work was funded by the Instituto de Salud Carlos III project COV20/00140 and COV20/00437, Spanish National Research Council project CSIC-COV19-021 and CSIC-COVID19-082, and the Generalitat Valenciana (SEJI/2019/011 and Covid_19-SCI). Action co-financed by the European Union through the Operational Program of the European Regional Development Fund (ERDF) of the Valencian Community 2014-2020. M.C. and R.G. are supported by Ramon y Cajal program from Ministerio de Ciencia.

The use of SARS-CoV-2 metagenomics in wastewater can allow the detection of variants circulating at community level. After comparing with clinical databases, we identified three novel variants in the spike gene, and six new variants in the spike detected for the first time in Spain. We finally support the hypothesis that this approach allows the identification of unknown SARS-CoV-2 variants or detected at only low frequencies in clinical genomes., This study was supported by projects VIRIDIANA (AGL2017-82909/ AEI/FEDER, UE) funded by Spanish Ministry of Science, Innovation and Universities; CSIC (202070E101), and Generalitat Valenciana (Covid_19-SCI). EC-F is recipient of a predoctoral contract from the MICINN, Call 2018.

9 páginas, 1 figurra, 3 tablas. Te online version contains supplementary material available at https://doi.org/10.1038/s41598-020-80919-5., Whole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years., AC-JR and CFM-M were CONACYT fellows of the Health Sciences Master of the Health Sciences Institute of Universidad Veracruzana. RZ-C and IC were funded by i-COOP-20017-COOPB2032.

Póster presentado a la Applied Bioinformatics and Public Health Microbiology 2021 Virtual Conference, celebrada del 5 al 7 de mayo de 2021., The COVID-19 pandemic has shaken the world since the beginning of 2020. Spain is among the European countries with the highest incidence of the disease during the first pandemic wave. We established a multidisciplinary consortium to monitor and study the evolution of the epidemic, with the aim of contributing to decision making and stopping rapid spreading across the country. We present the results for 2170 sequences from the first wave of the SARS-Cov-2 epidemic in Spain, representing 12% of diagnosed cases until 14th March. This effort allows us to document at least 500 initialintroductions, between early February-March from multiple international sources. Importantly, we document the early raise of two dominant genetic variants in Spain (Spanish Epidemic Clades), named SEC7 and SEC8, likely amplified by superspreading events. In sharp contrast to other non Asian countries those two variants were closely related to the initial variants of SARS-CoV-2 described in Asia and represented 40% of the genome sequences analyzed. The two dominant SECs were widely spread across the country compared to other genetic variants with SEC8 reaching a 60% prevalence just before the lockdown. Employing Bayesian phylodynamic analysis, we inferred a reduction in the effective reproductive number of these two SECs from around 2.5 to below 0.5 after the implementation of strict public-health interventions in mid-March. The effects of lockdown on the genetic variants of the virus are reflected in the general replacement of pre-existing SECs by a new variant at the beginning of the summer season. Our results reveal a significant difference in the genetic makeup of the epidemic in Spain and support the effectiveness of lockdown measures in controlling virus spread even for the most successful genetic variants., This work was funded by the Instituto de Salud Carlos III project COV20/00140, Spanish National Research Council project CSIC-COV19-021, Ministerio de Ciencia PID2019-104477RB-I00 and ERC StG 638553 to IC, and BFU2017-89594R to FGC. MC is supported by Ramón y Cajal program from Ministerio de Ciencia and grants RTI2018-094399-A-I00 and SEJI/2019/011.

16 p´ginas, 12 figuras, 1 tabla. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Supplementary data files can be found at 10.6084/m9.figshare.14562321., The occurrence of multiple strains of a bacterial pathogen such as M. tuberculosis or C. difficile within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However, methods for detecting it, and especially determining the proportion and identities of the underlying strains, from WGS (whole-genome sequencing) data, have been limited. In this paper we introduce SplitStrains, a novel method for addressing these challenges. Grounded in a rigorous statistical model, SplitStrains not only demonstrates superior performance in proportion estimation to other existing methods on both simulated as well as real M. tuberculosis data, but also successfully determines the identity of the underlying strains. We conclude that SplitStrains is a powerful addition to the existing toolkit of analytical methods for data coming from bacterial pathogens and holds the promise of enabling previously inaccessible conclusions to be drawn in the realm of public health microbiology, This work has been funded in part by a CANSSI Collaborative Research Team grant, 'Statistical methods for challenging problems in public health microbiology' and a Genome Canada grant, 'Machine Learning Methods to Predict Drug Resistance in Pathogenic Bacteria'. LC acknowledges funding from a Sloan Foundation fellowship (FG-2016–6392) and the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth and Development Office (FCDO), under the MRC/FCDO Concordat agreement, and is part of the EDCTP2 programme supported by the European Union. ML acknowledges funding from a NSERC Discovery grant.

Following its emergence in late 2019, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1,2 has been tracked via phylogenetic analysis of viral genome sequences in unprecedented detail3–5. While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, within Europe travel resumed in the summer of 2020. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread across Europe. We find no evidence of increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant’s success. Despite travel restrictions, we estimate 20E (EU1) was introduced hundreds of times to European countries by summertime travelers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes., This work was supported by the Swiss National Science Foundation (SNSF) through grant numbers 31CA30 196046 (to RAN, EBH, CLA), 31CA30 196267 (to TS), European Union’s Horizon 2020 research and innovation programme - project EpiPose (No 101003688) (MLR, CLA), core funding by the University of Basel and ETH Zürich, the National Institute of General Medical Sciences (R01GM120553 to DV), the National Institute of Allergy and Infectious Diseases (DP1AI158186 and HHSN272201700059C to DV), a Pew Biomedical Scholars Award (DV), an Investigators in the Pathogenesis of Infectious Disease Awards from the Burroughs Wellcome Fund (DV and JDB), a Fast Grants (DV), and NIAID grants R01AI141707 (JDB) and F30AI149928 (KHDC). SeqCOVID-SPAIN is funded by the Instituto de Salud Carlos III project COV20/00140, Spanish National Research Council and ERC StG 638553 to IC and BFU2017-89594R from MICIN to FGC. JDB is an Investigator of the Howard Hughes Medical Institute.

11 páginas, 5 figuras, 1 tabla, Polyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples., The authors were supported by projects SAF2016-77346-R and PID2019-104477RB-I00 awarded to IC and the grant BES-2017-079656 awarded to MM by the Spanish Ministry of Economy and Competitiveness and Ministry of Science, the ERC project 638553-TBACCELERATE awarded to IC, Spanish Government-FEDER Funds through CV contract CPII18/00031 and grant PI16/01511, and Generalitat Valencia Grant to I.C. (code PROMETEO/2020/012). The grant providers played no part in study design, data collection, and analysis, or the preparation of the manuscript.

Trabajo presentado al 31st European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), celebrado online del 9 al 12 de julio de 2021., This work was funded by the Instituto de Salud Carlos III project COV2o/oo140 and COV2o/ o0437,Spanish National Research Council project CSIC­ COV19·0l1 and CSIC-COVID19-082,and the Generalitat Valenciana (SEJI/2019/011 and Covid_19-SCI).Action co-financed by the European Union through the Operatianal Program of the European Regional Development Fund (ERDF) of the Valencian Community 2014-2020.MC is supported by Ramón y Cajal program from Ministerio de Ciencia,grant RTI2018-094399-A-I00.

SeqCOVID-Spain consortium: Álvaro Chiner-Oms, Irving Cancino-Muñoz, Mariana G. López, Manuela Torres-Puente, Inmaculada Gómez-Navarro, Santiago Jiménez-Serrano, Jordi Pérez-Tur, Darío García de Viedma, Laura Pérez-Lago, Marta Herranz, Jon Sicilia, Pilar Catalán-Alonso, Julia Suárez González, Patricia Muñoz, Mireia Coscolla, Paula Ruiz-Rodríguez, Fernando González-Candelas, Iñaki Comas, Lidia Ruiz-Roldán, María Alma Bracho, Neris García-González, Llúcia Martínez Priego, Inmaculada Galán-Vendrell, Paula Ruiz-Hueso, Griselda De Marco, María Loreto Ferrús-Abad, Sandra Carbó-Ramírez, Giuseppe D’Auria, Galo Adrian Goig, Juan Alberola, Jose Miguel Nogueira, Juan José Camarena, David Navarro, Eliseo Albert, Ignacio Torres, Maitane Aranzamendi Zaldumbide, Óscar Martínez Expósito, Nerea Antona Urieta, María de Toro, María Pilar Bea-Escudero, Jose Antonio Boga, Cristian Castelló-Abietar, Susana Rojo-Alba, Marta Elena Álvarez-Argüelles, Santiago Melón, Elisa Martró, Antoni E. Bordoy, Anna Not, Adrián Antuori, Anabel Fernández-Navarro, Andrés Canut-Blasco, Silvia Hernáez Crespo, Maria Luz Cordón Rodríguez, Maria Concepción Lecaroz Agara, Carmen Gómez-González, Amaia Aguirre-Quiñonero, José Israel López-Mirones, Marina Fernández-Torres, Maria Rosario Almela-Ferrer, Ana Carvajal, Juan Miguel Fregeneda-Grandes, Héctor Argüello, Gustavo Cilla Eguiluz, Milagrosa Montes Ros, Luis Piñeiro Vázquez, Ane Sorarrain, José María Marimón, José J. Costa-Alcalde, Rocío Trastoy, Gema Barbeito Castiñeiras, Amparo Coira, María Luisa Pérez del Molino, Antonio Aguilera, Begoña Palop-Borrás, Inmaculada de Toro Peinado, Maria Concepción Mediavilla Gradolph, Mercedes Pérez-Ruiz, Mirian Fernández-Alonso, Jose Luis del Pozo, Oscar González-Recio, Mónica Gutiérrez-Rivas, Jovita Fernández-Pinero, Miguel Ángel Jiménez Clavero, Begoña Fuster Escrivá, Concepción Gimeno Cardona, María Dolores Ocete Mochón, Rafael Medina-Gonzalez, José Antonio Lepe, Verónica González Galán, Ángel Rodríguez-Villodres, Nieves Gonzalo Jiménez, Jordi Reina, Carla López-Causapé, Maria Dolores Gómez-Ruiz, Eva M. Gonzalez-Barbera, José Luis López-Hontangas, Vicente Martín, Antonio J. Molina, Tania Fernandez-Villa, Ana Milagro Beamonte, Nieves Felisa Martínez-Cameo, Yolanda Gracia-Grataloup, Rosario Moreno-Muñoz, Maria Dolores Tirado Balaguer, José María Navarro-Marí, Irene Pedrosa-Corral, Sara Sanbonmatsu-Gámez, Antonio Oliver, Mónica Parra Grande, Bárbara Gómez Alonso, Francisco José Arjona Zaragozí, Maria Carmen Pérez González, Francisco Javier Chamizo López, Ana Bordes-Benítez, Núria Rabella, Ferran Navarro, Elisenda Miró, Antonio Rezusta, Alexander Tristancho, Encarnación Simarro Córdoba, Julia Lozano-Serra, Lorena Robles Fonseca, Álex Soriano, Francisco Javier Roig Sena, Hermelinda Vanaclocha Luna, Isabel Sanmartín, Daniel García-Souto, Ana Pequeño-Valtierra, Jose M. C. Tubio, Javier Temes, Jorge Rodríguez-Castro, Martín Santamarina García, Manuel Rodríguez-Iglesias, Fátima Galán-Sanchez, Salud Rodríguez-Pallares, José Manuel Azcona-Gutiérrez, Miriam Blasco-Alberdi, Alfredo Mayor, Alberto L. García-Basteiro, Gemma Moncunill, Carlota Dobaño, Pau Cisteró, Oriol Mitjà, Camila González-Beiras, Martí Vall-Mayans, Marc Corbacho-Monné, Andrea Alemany, Cristina Muñoz-Cuevas, Guadalupe Rodríguez-Rodríguez, Rafael Benito, Sonia Algarate, Jessica Bueno, Andrea Vergara-Gómez, Miguel J. Martínez, Jordi Vila, Elisa Rubio, Aida Peiró-Mestres, Jessica Navero-Castillejos, David Posada, Diana Valverde, Nuria Estévez, Iria Fernández-Silva, Loretta de Chiara, Pilar Gallego-García, Nair Varela, Ulises Gómez-Pinedo, Mónica Gozalo-Margüello, Maria Eliecer Cano García, José Manuel Méndez-Legaza, Jesus Rodríguez-Lozano, María Siller, Daniel Pablo-Marcos, Maria Montserrat Ruiz-García, Antonio Galiana, Judith Sánchez-Almendro, Maria Isabel Gascón Ros, Cristina Juana Torregrosa-Hetland, Eva María Pastor Boix, Paloma Cascales Ramos, Pedro Luis Garcinuño Enríquez, Salvador Raga Borja, Julia González Cantó, Olalla Martínez Macias, Adolfo de Salazar, Laura Viñuela González, Natalia Chueca, Federico García, Cristina Gómez-Camarasa, Amparo Farga Martí, Rocío Falcón, Victoria Domínguez-Márquez, Anna M. Planas, Israel Fernández-Cádenas, Maria Ángeles Marcos, Carmen Ezpeleta, Ana Navascués, Ana Miqueleiz Zapatero, Manuel Segovia, Antonio Moreno-Docón, Esther Viedma, Raúl Recio Martínez, Irene Muñoz-Gallego, Sara Gonzalez-Bodi, Maria Dolores Folgueira, Jesús Mingorance, Elias Dahdouh, Fernando Lázaro-Perona, María Rodríguez-Tejedor, María Pilar Romero-Gómez, Julio García-Rodríguez, Juan Carlos Galán, Mario Rodríguez-Dominguez, Laura Martínez-García, Melanie Abreu Di Berardino, Manuel Ponce-Alonso, Jose Maria González-Alba, Ivan Sanz-Muñoz, Diana Pérez San José, Maria Gil Fortuño, Juan B. Bellido-Blasco, Alberto Yagüe Muñoz, Noelia Hernández Pérez, Helena Buj Jordá, Óscar Pérez Olaso, Alejandro González Praetorius, Nora Mariela Martínez Ramírez, Aida Ramírez Marinero, Eduardo Padilla León, Alba Vilas Basil, Mireia Canal Aranda, Albert Bernet Sánchez, Alba Bellés Bellés, Eric López González, Iván Prats Sánchez, Mercè García-González, Miguel José Martínez-Lirola, Manuel Ángel Rodríguez Maresca, Maria Teresa Cabezas Fernández, María Eugenia Carrillo Gil, Maria Paz Ventero Martín, Carmen Molina Pardines, Nieves Orta Mira, María Navarro Cots, Inmaculada Vidal Catalá, Isabel García Nava, Soledad Illescas Fernández-Bermejo, José Martínez-Alarcón, Marta Torres-Narbona, Cristina Colmenarejo, Lidia García-Agudo, Jorge A. Pérez García, Martín Yago López, María Ángeles Goberna Bravo, Victoria Simón García, Gonzalo Llop Furquet, Agustín Iranzo Tatay, Sandra Moreno-Marro, Noelia Lozano Rodríguez, Amparo Broseta Tamarit, Juan José Badiola Díez, Amparo Martínez-Ramírez, Ana Dopazo, Sergio Callejas, Alberto Benguría, Begoña Aguado, Antonio Alcamí, Marta Bermejo Bermejo, Ricardo Ramos-Ruíz, Víctor Manuel Fernández Soria, Fernando Simón Soria & Mercedes Roig Cardells, The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re, This work was mainly funded by the Instituto de Salud Carlos III project COV20/00140, with additional funding by Spanish National Research Council project CSIC-COV19-021, Ministerio de Ciencia project PID2019-104477RB-100, ERC StG 638553 and ERC CoG 101001038 to I.C., and BFU2017-89594R to F.G.C. M.C. is supported by Ramón y Cajal program from Ministerio de Ciencia and grants RTI2018-094399-A-I00 and Generalitat Valenciana (Regional Government) project SEJI/2019/011. We gratefully acknowledge Hospital Universitari Vall d’Hebron, Instituto de Salud Carlos III, IrsiCaixa AIDS Research Lab and all the international researchers and institutions that submitted sequenced SARS-CoV-2 genomes to the GISAID’s EpiCov Database (Supplementary Table 1), as an important part of our analyses has been made possible by the sharing of their work. We also thank Unidad de Bioinformática y Estadística, Centro de Investigación Príncipe Felipe, for allowing us to use the Computer Cluster to perform some of the bioinformatic analysis.

The COVID-19 pandemic has shaken the world since the beginning of 2020. Spain is among the European countries with the highest incidence of the disease during the first pandemic wave. We established a multidisciplinar consortium to monitor and study the evolution of the epidemic, with the aim of contributing to decision making and stopping rapid spreading across the country. We present the results for 2170 sequences from the first wave of the SARS-Cov-2 epidemic in Spain and representing 12% of diagnosed cases until 14th March. This effort allows us to document at least 500 initial introductions, between early February-March from multiple international sources. Importantly, we document the early raise of two dominant genetic variants in Spain (Spanish Epidemic Clades), named SEC7 and SEC8, likely amplified by superspreading events. In sharp contrast to other non-Asian countries those two variants were closely related to the initial variants of SARS-CoV-2 described in Asia and represented 40% of the genome sequences analyzed. The two dominant SECs were widely spread across the country compared to other genetic variants with SEC8 reaching a 60% prevalence just before the lockdown. Employing Bayesian phylodynamic analysis, we inferred a reduction in the effective reproductive number of these two SECs from around 2.5 to below 0.5 after the implementation of strict public-health interventions in mid March. The effects of lockdown on the genetic variants of the virus are reflected in the general replacement of preexisting SECs by a new variant at the beginning of the summer season. Our results reveal a significant difference in the genetic makeup of the epidemic in Spain and support the effectiveness of lockdown measures in controlling virus spread even for the most successful genetic variants. Finally, earlier control of SEC7 and particularly SEC8 might have reduced the incidence and impact of COVID-19 in our country., This work was funded by the Instituto de Salud Carlos III project COV20/00140, Spanish 593 National Research Council project CSIC-COV19-021 and ERC StG 638553 to IC, and BFU2017- 594 89594R to FGC. MC is supported by Ramón y Cajal program from Ministerio de Ciencia and 595 grants RTI2018-094399-A-I00 and SEJI/2019/011. 596 We gratefully acknowledge Hospital Universitari Vall d'Hebron, Instituto de Salud Carlos 597 III, IrsiCaixa AIDS Research Lab and all the international researchers and institutions that 598 submitted sequenced SARS-CoV-2 genomes to the GISAID’s EpiCov™ Database, as an 599 important part of our analyses have been made possible by the share of their work.

A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and has since spread to multiple European countries. The variant was first observed in Spain in June and has been at frequencies above 40% since July. Outside of Spain, the frequency of this variant has increased from very low values prior to 15th July to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about other European countries because few recent sequences are available. Sequences in this cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this variant was exported from Spain to other European countries multiple times and that much of the diversity of this cluster in Spain is observed across Europe. It is currently unclear whether this variant is spreading because of a transmission advantage of the virus or whether high incidence in Spain followed by dissemination through tourists is sufficient to explain the rapid rise in multiple countries., This work was supported by the SNF through grant numbers 31CA30 196046 (to RAN, EBH) and 31CA30 196267 and core funding by the University of Basel. SeqCOVID-SPAIN is funded by the Instituto de Salud Carlos III project COV20/00140, Spanish National Research Council and ERC StG 638553 to IC.

9 páginas, 4 figuras. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors. Sequencing reads have been submitted to the European Nucleotide Archive (EMBL-EBI) under study accession PRJEB34582 and PRJEB34609. The analysis scripts used in this study are available online at GitHub (https://github.com/StopTB/Single_Colony_Project)., Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naïve patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner., This work was supported by the National Natural Science Foundation of China (91631301 and 81661128043 to Q.G., 81701975 to Q.L., and 31771416 to X.L.), the National Science and Technology Major Project of China (2017ZX10201302 to Q.G. and 2018ZX10714002-001-005 to Z.Z.), the Sanming Project of Medicine in Shenzhen (SZSM201611030 to Q.G.), European Research Council 638553-TB-AcCELERATE (to I.C.), the Key Research Program of the Chinese Academy of Sciences (KFZD-SW-220-1 to X.L.), and the CAS Light of West China Program (to X.L.). Y.F. is supported in part by NIH R01HG009524. Support was also received from NIH awards P01 AI132130 and AI142793 to S.M.F.

11 páginas, 6 figuras, 2 tablas. Accesible en PubMedCentral: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295914/, A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China-the country with the third highest tuberculosis burden-we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population., This work was supported by the Natural Science Foundation of China (91631301 and 81661128043 to Q.G. and 81701975 to Q.L.). C.S.P. was supported by the National Institutes of Health (grant 1R01AI113287-01A1). S.G. was supported by the Swiss National Science Foundation (grants IZRJZ3_164171, 310030_166687, IZLSZ3_170834 and CRSII5_177163). This work was also supported by MINECO research grant SAF2016-77346-R (to I.C.), the European Research Council (638553-TB-ACCELERATE to I.C.), the National Science and Technology Major Project of China (2017ZX10201302 to Q.G., 2018ZX10103001 to Y.Z.), the Sanming Project of Medicine in Shenzhen (SZSM201611030 to Q.G.), JSGG20170413142559220 (to Q.G.), and National Basic Research programme of China (2014CB744403 to Y.Z.).

Conferencia presentada en el ESCMID Conference on Coronavirus Disease (ECCVID). Congreso Virtual, 23-25 de septiembre de 2020. La lista completa de personas e instituciones que forman parte de Seqcovid-Spain Consortium se puede ver en http://seqcovid.csic.es/collaborating-institutions/, [Background] The rapid expansion of SARS-CoV-2 has represented a significant change in how scientists face a multidimensional problem. One of the most useful tools to find solutions to this problem is through the complete genome sequencing of viral samples. Hundreds of laboratories around the world have embarked in this task, sharing almost immediately their data. In Spain, we have established a multidisciplinary consortium including research laboratories and groups (the full list can be found at http://seqcovid.csic.es/collaborating-institutions/). Our initial goal is to obtain complete genome sequences of 20,000 viral samples from patients attending Spanish hospitals and health centers., [Methods] We have used remnants of diagnostic samples for Covid-19 to obtain almost complete viral genome sequences. We have essentially followed the ARTIC v3 protocol for Illumina sequencing, with some labs using MiniION or IonTorrent technologies.Sequences passing quality controls were uploaded to www.gisaid.org. Preliminary analyses were performed with NextStrain and Microrreact tools Additional analyses have been performed using IQTREE2 and iToL., [Results] We report results obtained until July 31, 2020, but an update summary is accessible at http://seqcovid.csic.es. We have received almost 6400 samples from which 3819 have been sequenced so far. Most sequenced samples were obtained in March (1674) and April (634). The epidemic in Spain is dominated by lineages B.1.5 (n=1250 ), A.2(907), B.1 (434), B.1.1 (336), and A.5 (273), representing 83.8% of the total (Figure 1). These samples conform at least 13 Spanish-dominated lineages (monophyletic groups of at least 20 sequences compared to aprox. 32000 complete genomes from GISAID with >50% sequences from Spain), most of which were already present in Spain when strict lockdown measures were enforced on March 14 (Figure 2). The D614 variant of the spike protein was found in 24% of the sequences, although its frequency has decreased significantly since April., [Conclusions] Similarly to other European countries, the Covid-19 epidemics in Spain is driven by a limited number of locally expanding lineages, which represent a fraction of the total number of independent introductions from other locations. The high frequency of lineages A.2 and A.5 point to a very early, mosty unnoticed entry of SARS-CoV-2 in Spain.

9 páginas, 3 figuras, Background Direct whole-genome sequencing of Mycobacterium tuberculosis from clinical specimens will be a major breakthrough in tuberculosis diagnosis and control. To date, direct whole-genome sequencing has never been used in genomic epidemiology, and its accuracy in transmission inference remains unknown. We investigated the technical challenges imposed by direct whole-genome sequencing, and used it to infer transmission clusters and predict drug resistance. Methods Using an optimised workflow, we did direct whole-genome sequencing for 37 clinical specimens from 23 tuberculosis patients. Nine sputum samples from nine patients who were infected with different non-tuberculous mycobacteria and culture-negative for tuberculosis were used as controls in the qPCR assays and pre-sequencing runs. Additionally, 780 clinical isolates in the region of Comunidad Valenciana (Spain) were whole-genome sequenced between Jan 1, 2014, and Dec 31, 2016. We analysed the genomic variants to build a tuberculosis transmission network for the region, including the clinical specimens, and to predict drug susceptibility profiles. Findings After sequencing 37 clinical specimens, 28 specimens (22 [85%] of 26 smear-positive and six [55%] of 11 smear-negative) met the quality criteria for downstream analysis. All 28 clinical specimens clustered with their matching culture isolates, with a median distance of 0 single nucleotide polymorphisms. Of the 28 clinical specimens, 16 (57%) were accurately assigned to ten transmission clusters in the region, and 12 (43%) were unique cases. Transmission inferences and drug-susceptibility predictions from direct whole-genome sequencing data were concordant with sequences from corresponding cultures and phenotypic drug-susceptibility testing. Complete genomic analysis, within a week of specimen receipt, cost €217 per sample (excluding personnel costs). Interpretation Direct whole-genome sequencing could be used to accurately delineate transmission clusters of tuberculosis and conduct culture-independent surveillance. Compared with conventional approaches, direct wholegenome sequencing allows researchers to do real-time genomic epidemiology and drug resistance surveillance in settings where culture and drug susceptibility testing are not available., This work was supported by projects of the European Research Council (638553-TB-ACCELERATE), Ministerio de Economía y Competitividad, and Ministerio de Ciencia, Innovación y Universidades (Spanish Government; SAF2013-43521-R, SAF2016-77346-R, and SAF2017-92345-EXP [to IC], and BES-2014-071066 [to GAG])

9 páginas, 3 figuras. The data that support the findings of this study (Fastq files) are publicly available. Fastq files above the GISAID thresholds were deposited at GISAID (hCoV-19/Spain/MD-IBV-99007733/2020, hCoV-19/Spain/MD-IBV-99007151/2020, hCoV-19/Spain/MD-IBV-99007734/2020, and hCoV-19/Spain/MDIBV-99007170/2020). All sequences were also deposited at the ENA (European Nucleotide Archive; https:// www.ebi.ac.uk/ena/browser/home) (ERR5698024, ERR5697187, ERR6459974, ERR5698025, and ERR5697254)., The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions. Our analysis was supported by host genetics, viral whole-genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April 2020 and a much more severe second episode 4-1/2 months later, with SARS-CoV-2 seroconversion in August, that required hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A's reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August-September 2020, but absent at the time range corresponding to Case A's first episode. IMPORTANCE We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases., This work was supported by Instituto de Salud Carlos III (Ref COV20/00140: SeqCOVID - Consorcio para la epidemiología genómica de SARS-CoV-2 en España) and by Consejo Superior de Investigaciones Científicas (CSIC) (PTI Salud Global), Miguel Servet contract CP15/00075, to L.P.L.

10 páginas, 3 figuras, 3 tablas. Material suplementario en: https://advances.sciencemag.org/content/suppl/2020/02/10/6.7.eaay4453.DC1, The postreplicative mismatch repair (MMR) is an almost ubiquitous DNA repair essential for maintaining genome stability. It has been suggested that Mycobacteria have an alternative MMR in which NucS, an endonuclease with no structural homology to the canonical MMR proteins (MutS/MutL), is the key factor. Here, we analyze the spontaneous mutations accumulated in a neutral manner over thousands of generations by Mycobacterium smegmatis and its MMR-deficient derivative (ΔnucS). The base pair substitution rates per genome per generation are 0.004 and 0.165 for wild type and ΔnucS, respectively. By comparing the activity of different bacterial MMR pathways, we demonstrate that both MutS/L- and NucS-based systems display similar specificity and mutagenesis bias, revealing a functional evolutionary convergence. However, NucS is not able to repair indels in vivo. Our results provide an unparalleled view of how this mycobacterial system works in vivo to maintain genome stability and how it may affect Mycobacterium evolution., This work was supported by Plan Nacional de I + D + i 2013–2016 and the Instituto de Salud Carlos III, Subdireccion General de Redes y Centros de Investigacion Cooperativa, Ministerio de Economia, Industria y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0009)—cofinanced by the European Development Regional Fund “A Way to Achieve Europe”—by Operative Program Intelligent Growth 2014-2020 and grants FIS PI17/00159 from the Instituto de Salud Carlos III and SAF2015-72793-EXP from the Spanish Ministry of Science and Competitiveness (MINECO)-FEDER. E.C.-S. was the recipient of a PFIS predoctoral research fellowship (FI18/00036) cofinanced by the Instituto de Salud Carlos III and the European Social Fund. I.C., A.C.-O., and M.T.-P. are funded by projects of the 581 European Research Council (ERC) (638553-TB-ACCELERATE) and Ministerio de Economía y Competitividad research grant SAF2016-77346-R.

Tesis doctoral 256 págs, imágenes y tablas, [EN] Tuberculosis (TB) is an infectious disease caused by the airborne transmitted bacterial pathogens belonging to the Mycobacterium tuberculosis complex (MTBC). Tuberculosis is a curable and preventable disease although it is one of the top ten causes of death worldwide according to the World Health Organization (WHO). The last report of the WHO estimated that 10 millions of people got infected with TB in 2018. Of these, 1.45 million cases died because of TB disease. TB can be transmitted in aerosolized droplets by coughing from a person with active disease. Thus, the most common infection site is the respiratory system but any organ can be infected. Transmission is the main cause of the number of TB cases in high-burden countries, but also low-burden regions. Interrupting transmission is essential in order to reduce the TB incidence and to advance towards eradication. It is estimated that about one-quarter of the worldwide population has latent TB (LTBI), which is characterized by no suffering TB symptoms and presumably non transmissible disease. Treatment of TB aims to cure all the patients that had active or LTBI to stop the transmission of the disease or at least minimize it. Nowadays, WGS is becoming an essential tool in the TB field, not only in basic research areas but also in diagnostics and public health. Currently, we have the ability to whole-genome sequence from dozens to thousand MTBC strains at the same time. In fact, MTCB has become the most whole-genome sequenced pathogen bacteria. the main WGS applications in TB focused on disease control by: 1) improving drug susceptibility prediction; 2) rapid detection of transmission clusters; 3) strain genotype surveillance across country borders and 4) diagnosis of MTBC strains and lineage identification. In this thesis, we used WGS to genomically characterize a large proportion of MTBC clinical isolates from Valencia Region. First, we performed an epidemiological study, estimated the genomic transmission rate and identified risk factors associated. Second, we also evaluated the use of WGS to predict drug resistance in the studied population and to identify novel resistance determinants and assist on personalizing the treatment of a challenging TB patient. Finally, we studied the global genomic diversity of the bacteria to propose a new, efficient and rapid methodology for strain genotyping. Our results were compared with those of the local health system. To our knowledge, this is the first regional and likely national project of this kind. We demonstrated that WGS is an accurate and reliable tool for detecting TB transmission events and predicting drug resistance. It could become a transformative methodology for the public health surveillance system., [ES] La tuberculosis (TB) es una enfermedad infecciosa causada y transmitida por miembros patógenos que pertenecen al complejo de Mycobacterium tuberculosis (MTBC). En el 2018, la Organización Mundial de la Salud (OMS) estimó que 10 millones de personas se infectaron de TB, de los cuales, 1,45 millones de casos murieron a causa de esta. Con estos números, la TB es una de las diez principales causas de muerte en todo el mundo. La TB se transmite por el aire a través de gotas en aerosol generadas al toser por una persona contagiada, por lo que, el sitio de infección más común es el sistema respiratorio. La transmisión es la causa principal de TB en países de alta y baja incidencia. Por este motivo, la interrupción de la transmisión es esencial para reducir la incidencia de TB y avanzar hacia su erradicación. Se estima que una cuarta parte de la población mundial está infectada por tuberculosis latente, que se caracteriza por no padecer y/o manifestar síntomas de TB, y presumiblemente no transmitir la enfermedad. El tratamiento de la tuberculosis tiene como principal objetivo curar a todos los pacientes que presenten la enfermedad activa o latente, además, de detener la transmisión o al menos minimizarla. La secuenciación de genomas completos (WGS, por sus siglas en inglés) se está convirtiendo en una herramienta esencial en el campo de la TB, no solo en las áreas de investigación básica sino también en el diagnóstico de la enfermedad con aplicaciones directas a la salud pública. Actualmente, se tiene la capacidad de secuenciar el genoma completo de cientos de cepas de MTBC al mismo tiempo. Las principales aplicaciones de WGS en tuberculosis son: 1) mejorar la predicción de la sensibilidad de los fármacos antituberculosos; 2) detección rápida de grupos de transmisión; 3) vigilancia genómica-epidemiológica de los diferentes genotipos que circulan en una zona específica; y 4) la identificación y clasificación de cepas en linajes pertenecientes al MTBC. En esta tesis, utilizamos WGS para caracterizar genómicamente aislados clínicos de MTBC de la región de Valencia. Mediante un estudio genómico-epidemiológico, estimamos la tasa de transmisión e identificamos factores de riesgo asociados a dicha transmisión. También evaluamos el uso de WGS para predecir resistencia a fármacos antituberculosos en la población estudiada, así como para identificar nuevas mutaciones asociadas a resistencia, con el fin de guiar y personalizar el tratamiento de un paciente con tuberculosis crónica. Finalmente, estudiamos la diversidad genómica global de MTBC para proponer un método alterno, eficiente y rápido para el genotipado de aislados. En conclusión, demostramos que la técnica de WGS es una herramienta precisa y confiable para detectar eventos de transmisión y predecir la resistencia a fármacos contra la TB, que podría utilizarse como metodología esencial en el sistema de vigilancia epidemiológica de salud pública a nivel regional y nacional.

11 págs., 6 figuras. All data generated or analyzed during this study are included in this published article (and its SupplementaryInformation fles) at https://doi.org/10.1038/s41598-020-75853-5., Glucocorticoid (GC) actions are mediated through two closely related ligand-dependent transcription factors, the GC receptor (GR) and the mineralocorticoid receptor (MR). Given the wide and effective use of GCs to combat skin inflammatory diseases, it is important to understand the relative contribution of these receptors to the transcriptional response to topical GCs. We evaluated the gene expression profiles in the skin of mice with epidermal-specific loss of GR (GREKO), MR (MREKO), or both (double KO; DKO) in response to dexamethasone (Dex). The overall transcriptional response was abolished in GREKO and DKO skin suggesting dependence of the underlying dermis on the presence of epidermal GR. Indeed, the observed dermal GC resistance correlated with a constitutive decrease in GR activity and up-regulation of p38 activity in this skin compartment. Upon Dex treatment, more than 90% of differentially expressed genes (DEGs) in CO overlapped with MREKO. However, the number of DEGs was fourfold increased and the magnitude of response was higher in MREKO vs CO, affecting both gene induction and repression. Taken together our data reveal that, in the cutaneous transcriptional response to GCs mediated through endogenous receptors, epidermal GR is mandatory while epidermal MR acts as a chief modulator of gene expression., Tis work was supported by grant SAF2017-88046-R (MICINN, Spanish Government). J. Bigas is recipient of FPI fellowship of MINECO. We thank NURCAMEIN (SAF2017-90604-REDT) for support for dissemination.We also thank Julia Boix for assisting with the animal experiments.

8 páginas, 4 figuras, 1 tabla. Información suplementaria accesible en: https://doi.org/10.1038/s41598-020-59373-w, 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., This work was supported by ERANet-LAC [ELAC2015/T08–0664, E035-ERANet-LAC/J110-2016/FONDECYT, PER-2012-ELAC2015/T08-0664] and Instituto de Salud Carlos III [AC16/00057, FIS15/01554, FIS13/01207] and cofunded by European Regional Development Funds from the European Commission: “A way of making Europe”. FA holds a grant from IFARHUSENACYT [270-2016-293].

5 páginas, 2 figuras. AVAILABILITY AND IMPLEMENTATION: The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online: http://dx.doi.org/10.1093/bioinformatics/btz729, MOTIVATION: Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. RESULTS: In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research., This work was supported by projects of the European Research Council (ERC) (638553-TB-ACCELERATE), Ministerio de Economía y Competitividad and Ministerio de Ciencia, Innovación y Universidades (Spanish Government), SAF2013-43521-R, SAF2016-77346-R and SAF2017–92345–EXP (to I.C.), BES-2014-071066 (to G.A.G.), FPU 13/00913 (to A.C.O.).

11 págs, 4 figuras y fórmulas matemáticas. Material suplementario en: http://dx.doi.org/10.1093/molbev/msaa069, The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap's simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species., D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant no. 101237/Z/13/B) and is a Big Data Institute Robertson Fellow. The CRyPTIC Consortium was supported by grants from the Bill and Melinda Gates Foundation (OPP1133541) and a Wellcome Trust/Newton Fund-MRC Collaborative Award (200205/Z/15/Z). F.A.D. was supported by the Imperial Biomedical Research Centre

18 páginas, 11 figuras, 3 tablas. Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fimmu.2019.02464/full#supplementary-material, The administration of a high fat content diet is an accelerating factor for metabolic syndrome, impaired glucose tolerance, and early type 2 diabetes. The present study aims to assess the impact of a high fat diet on tuberculosis progression and microbiota composition in an experimental animal model using a C3HeB/FeJ mouse strain submitted to single or multiple consecutive aerosol infections. These models allowed us to study the protection induced by Bacillus Calmette-Guérin vaccination as well as by the natural immunity induced by chemotherapy after a low dose Mycobacterium tuberculosis infection. Our results show that a high fat diet is able to trigger a pro-inflammatory response, which results in a faster progression toward active tuberculosis and an impaired protective effect of BCG vaccination, which is not the case for natural immunity. This may be related to dysbiosis and a reduction in the Firmicutes/Bacteroidetes ratio in the gut microbiota caused by a decrease in the abundance of the Porphyromonadaceae family and, in particular, the Barnesiella genus. It should also be noted that a high fat diet is also related to an increase in the genera Alistipes, Parasuterella, Mucispirillum, and Akkermansia, which have previously been related to dysbiotic processes. As diabetes mellitus type 2 is a risk factor for developing tuberculosis, these findings may prove useful in the search for new prophylactic strategies for this population subset., This work was supported by the European Commission Horizon 2020 research and innovation program under grant agreement TBVAC2020 No. 643381, European Research Council research grant 638553-TB-ACCELERATE and Ministerio de Economía y Competitividad (Spanish government) research grant SAF2017-92345- EXP (to IC). CV has a project Servet II contract funded by the Instituto de Salud Carlos III (ISCIII, CPII 18/00031). LA received an Improvement and Mobility Program grant from the Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES). GG contract was funded by Ministerio de Economia y Competitividad (Spanish Government) (BES-2014-071066). PC contract was funded by the Instituto de Salud Carlos III (IFI14/00015). The Experimental Tuberculosis Unit is accredited by the Catalan Agency for Management of University and Research Grants with code 2017 SGR500 and the IGTP is a member of the CERCA network of institutes. The funders played no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

12 páginas, 6 figuras, 4 tablas, The Mycobacterium tuberculosis complex (MTBC) comprises the species that causes tuberculosis (TB) which affects 10 million people every year. A robust classification of species, lineages, and sub-lineages is important to explore associations with drug resistance, epidemiological patterns or clinical outcomes. We present a rapid and easy-to-follow methodology to classify clinical TB samples into the main MTBC clades. Approaches are based on the identification of lineage and sub-lineage diagnostic SNP using a real-time PCR high resolution melting assay and classic Sanger sequencing from low-concentrated, low quality DNA. Thus, suitable for implementation in middle and low-income countries. Once we validated our molecular procedures, we characterized a total of 491 biological samples from human and cattle hosts, representing countries with different TB burden. Overall, we managed to genotype ~95% of all samples despite coming from unpurified and low-concentrated DNA. Our approach also allowed us to detect zoonotic cases in eight human samples from Nigeria. To conclude, the molecular techniques we have developed, are accurate, discriminative and reproducible. Furthermore, it costs less than other classic typing methods, resulting in an affordable alternative method in TB laboratories., This work was supported by European Research Council (grant, 638553-TB-ACCELERATE) and the Ministerio de Economía y Competitividad grants (SAF2013-43521-R and SAF2016-77346-R) both to I.C.

5 páginas, 2 figuras, Understanding Multidrug-resistant tuberculosis cases not detected by rapid phenotypic and genotypic routine clinical tests is essential to improve diagnostics and advance towards personalized TB treatments. Here, we combine WGS with single-colony phenotyping testing to diagnose a MDR strain infecting a patient over nine years. Our investigation revealed the failure of rapid testing assays and genome-based prediction tools to identify the MDR strain. The false negative outcome was caused by uncommon RIF and INH resistance mutations. Despite WGS data helped to personalize treatment, the patient developed XDR-TB, highlighting the importance of coupling new diagnostic methods with appropriate treatment regimens., This work was supported by the European Research Council (638553-TB-ACCELERATE to I. C.) and the Ministerio de Economía y Competitividad (SAF2016-77346-R to I. C.).

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).

14 páginas, 7 figuras, BackgroundThe 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.AimTo 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 importationsMethodsWe 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.ResultsIn 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.ConclusionWe provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration., This project was funded by ISCIII: ERANET-LAC (TRANS-TB-TRANS REF AC16/00057; ELAC2015/T08-0664), FIS (13/01207; 15/01554) and cofunded by ERDF Funds from the European Commission: “A way of making Europe”. Miguel Servet grant (CP15/00075) for LPL. Ministerio de Economía y Competitividad (grant SAF2016-77346-R), ERC (638553-TB-ACCELERATE) to IC. FPU13/00913 (Ministerio de Educación y Ciencia) to ACO.

de la comunicación oral presentada al Scientific Meeting on Mycobacteria. MycoPORTO 2019 Porto (Portugal), 19-20 de septiembre de 2019, Whole-genome sequencing of M. tuberculosis (MTB) directly from clinical specimens (dWGS) will suppose a major breakthrough in tuberculosis diagnosis and control. To date, different strategies have been followed to sequence MTB from sputum samples and accurately predict drug-resistance. However, dWGS of MTB has never been used in genomic epidemiology. Here, we test and optimize both the laboratory and computational protocols to implement a dWGS pipeline able to produce a detailed genomic analysis from sputum samples in a week. We used dWGS on clinical specimens of 27 TB patients to evaluate its performance for drugresistance prediction and genomic epidemiology. We were able to predict full drug resistance profiles and epidemiological links for the 28 out of the 37 specimens analyzed. In these samples, the agreement between dWGS and WGS from matching cultures was of 100% for both drug-resistance prediction and epidemiological clusters. In our work, we evaluate the state-of-the-art of dWGS for MTB and provide a cost-effective diagnostic algorithm for tuberculosis based on dWGS. We demonstrate that dWGS is a powerful tool to conduct highprecision genomic epidemiology in real time.

2 páginas.

Tesis doctoral, 152 págs, ANTECEDENTES: La tuberculosis (TB) es una enfermedad asociada a importante morbi-mortalidad en todo el mundo. En la Comunidad Valenciana (CV), al igual que en el resto de España, la tasa de TB según datos oficiales ha disminuido entre el año 2011 y 2015, así como el porcentaje de enfermos inmigrantes y coinfectados con el virus de la inmunodeficiencia humana (VIH), descenso que no se ha visto reflejado, sin embargo, en los datos oficiales del Departamento de Salud (DS) La Fe. La inmigración desde países de alta endemia de TB hace necesario revisar la epidemiología de los pacientes atendidos en el Hospital Universitario y Politécnico (HUP) La Fe y el patrón de resistencias de las cepas aisladas, para comprobar la utilidad de las nuevas técnicas moleculares incorporadas, así como la de la secuenciación completa del genoma (SCG) de Mycobacterium tuberculosis, método que está siendo evaluado como herramienta para el diagnóstico precoz de la enfermedad y de predicción de resistencias. OBJETIVO: Conocer las características epidemiológicas y clínicas de los enfermos con TB confirmada por microbiología en el HUP La Fe de Valencia entre enero de 2011 y diciembre de 2015, así como la repercusión de la SCG de los aislados de MTBC en la gestión de los pacientes. METODOLOGÍA: Estudio descriptivo retrospectivo de las características de los pacientes con TB confirmada por microbiología en el HUP La Fe entre 2011 y 2015 y análisis comparativo con los resultados de linaje y resistencias obtenidos tras SCG de las cepas aisladas en 2014 y 2015. RESULTADOS PRINCIPALES: De los 194 casos confirmados en el HUP La Fe, sólo el 39,8% pertenecían al DS La Fe, por lo que las tasas calculadas no se corresponden con los datos oficiales. La tasa media fue de 9,7 casos/100.000 hab, con mortalidad asociada del 5%. La edad media de los enfermos fue 39,6 años, con un 5,7% de casos en edad infantil, un 10% de coinfectados con el VIH y un 51,3% de inmigrantes, no presentando este grupo diferencias importantes respecto al resto. La mayoría de los casos se concentraron en Torrefiel-Rascaña, en Secciones Censales de alta vulnerabilidad. La presentación clínica predominante fue la pulmonar (62,9%), y la existencia de coinfección con VIH se asoció a forma extrapulmonar. El tiempo de crecimiento medio en medio líquido fue 14,87 días frente a 21,4 en medio sólido. Hubo un 16% de resistencia fenotípica a los fármacos de primera línea, con resistencia a isoniacida (INH) del 9,2% y a rifampicina (RIF) del 3,6%. El linaje predominante fue el L4, con linajes distintos al L4 en pacientes extranjeros. La concordancia kappa de la resistencia detectada por SCG con la fenotípica fue para INH 0,95 (IC: 0,83-0,999) y para RIF 0,999, siendo las mutaciones más frecuentes las localizadas en -15 fabG1-inhA y codón 315 del gen katG para el primer fármaco y codón 450 del gen rpoB para el segundo. CONCLUSIONES: A pesar de que la tasa de TB es menor, el número de inmigrantes afectados es mayor al estimado en el resto de la CV y de España. La presencia de enfermedades de base no es determinante para el desarrollo de enfermedad tuberculosa, pero sí para el desarrollo de formas extrapulmonares, en concreto en el caso de coinfección con VIH. Las técnicas de biología molecular ayudan al diagnóstico, siendo más útiles en las formas pulmonares y en la detección precoz de resistencia a RIF. La SCG es una herramienta más precisa que las moleculares, en concreto para la detección precoz de resistencia a INH en nuestra área, y para el estudio epidemiológico de contactos.

2 Páginas

17 páginas, 1 figura, 7 tablas, BACKGROUND: Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico. METHODS: WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized. FINDINGS: Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively. Lastly, four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition. CONCLUSIONS: The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug- and multidrug-resistant tuberculosis., CFM-M was a CONACYT fellow of the Maestría en Ciencias de la Salud of the Instituto de Ciencias de la Salud Universidad Veracruzana. RZ-C and IC were partially funded by I-COOP-2017- COOPB2032. RMS was funded by CONACyT-Problemas nacionales grant no. 2015-01-147. XS was funded by GACD-FONCICYT Conacyt No.264693.

Tesis doctoral, 151 páginas., 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 [...]