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Mycobacteria are ubiquitous microorganisms and may be found in many different environments, either associated or not to diseases. Culture-independent molecular techniques brought new perspectives for research regarding soil microorganisms, which is relevant to microbiologists and industry. Therefore, new research is necessary to broaden our knowledge about ecology and physiology of mycobacteria in extreme environments. The aim of this study was to verify the presence of mycobacteria in Antarctica soil samples and to standardize molecular and culture-dependent techniques to their isolation. Soil DNA was extracted and submitted to denaturing gradient gel electrophoresis (DGGE), rrs mycobacterial gene amplification and partial sequencing. Thereby, 10 colonies morphologically similar to mycobacteria were isolated from 10 different samples, resulting in 15 DNA sequences where Mycobacterium neglectum and Mycobacterium kumamotonense were identified, suggesting that Mycobacterium terrae complex representatives are ubiquitous in the region. This study proposes a simple method for mycobacteria cultivation from soil samples and shows that ornithogenic soils can be the source of organic matter and low pH, modulating the mycobacterial Antarctica diversity. Further research aiming to explore mycobacterial diversity in soil are needed to increase knowledge and better explore their evolution, their relation with animal and human species and their potential biotechnological use.

Due to tuberculosis (TB) patients’ pulmonary damages, some authors believe that a SARS-CoV-2 coinfection may result in unfavorable outcomes. A cross-sectional anti-SARS-CoV-2 antibodies seroprevalence study was conducted at a TB treatment tertiary referral unit in Rio de Janeiro, Brazil, to estimate the proportion (in %) of TB patients exposed to the new coronavirus and their main outcomes. Of 83 patients undergoing TB treatment, 26.5% have already been infected by the new coronavirus. Most patients were asymptomatic (69%) or had mild COVID-19 cases (31%). Only one patient required hospitalization. Among the symptoms and signs presented, the most frequently reported were: fever, headache, and myalgia. People with less education and less purchasing power seemed to had been more exposed to SARS-CoV-2.

Alcaligenes faecalis is a Gram-negative rod that is ubiquitous in the environment and is an opportunistic human pathogen. Here, we report the whole-genome sequencing analysis of A. faecalis HZ01, which presents mycobacterial growth inhibitory activity and was isolated from a contaminated culture of Mycobacterium chubuense ATCC 27278.

The Mycobacterium abscessus complex comprises multidrug-resistant, opportunistic, and rapidly growing pathogens responsible for severe infections. Here, we report the genome composition of four Mycobacterium abscessus subsp. massiliense isolates from three sources: two from the lung of a cystic fibrosis patient, one from a mammary cyst, and one from a gutter system.

Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade Federal do Rio de Janeiro. P?s-Gradua??o Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?ria. Rio de Janeiro, RJ, Brazil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France. London School of Hygiene & Tropical Medicine. Faculty of Infectious and Tropical Diseases. London, UK. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Institut Pasteur de Madagascar. Unit? des Mycobact?ries. Antananarivo, Madagascar. Institut Pasteur de Madagascar. Unit? des Mycobact?ries. Antananarivo, Madagascar. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. National Institute for Public Health and the Environment. Bilthoven, the Netherlands / Radboud University Nijmegen Medical Centre. Department of Medical Microbiology. Nijmegen, the Netherlands. Swiss Tropical & Public Health Institute. Basel, Switzerland / University of Basel. Basel, Switzerland. Swiss Tropical & Public Health Institute. Basel, Switzerland / University of Basel. Basel, Switzerland. Universidade de S?o Paulo. Faculdade de Medicina de Ribeir?o Preto. Ribeir?o Preto, SP, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?ria. Rio de Janeiro, RJ, Brazil. Universidade Federal do Rio de Janeiro. P?s-Gradua??o Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universit? Paris-Sud. Universit? Paris Saclay. Institut de Biologie Int?grative de la Cellule. I2BC. UMR9198. CEA. CNRS. Gif-sur-Yvette cedex, France / Universidade de S?o Paulo. Faculdade de Medicina de Ribeir?o Preto. Ribeir?o Preto, SP, Brazil. Lineage 1 (L1) is one of seven Mycobacterium tuberculosis complex (MTBC) lineages. The objective of this study was to improve the complex taxonomy of L1 using phylogenetic SNPs, and to look for the origin of the main L1 sublineage prevalent in Para, Brazil. We developed a high-throughput SNPs-typing assay based on 12-L1-specific SNPs. This assay allowed us to experimentally retrieve SNP patterns on nine of these twelve SNPs in 277 isolates previously tentatively assigned to L1 spoligotyping-based sub lineages. Three collections were used: Par?-Brazil (71); RIVM, the Netherlands (102), Madagascar (104). One-hundred more results were generated in Silico using the PolyTB database. Based on the final SNPs combination, the samples were classified into 11 clusters (C1-C11). Most isolates within a SNP-based cluster shared a mutual spoligotyping-defined lineage. However, L1/EAI1-SOM (SIT48, sp. 40) and L1/EAI6-BGD1 (SIT591, sp. 23) showed a poor correlation with SNP data and are not monophyletic. L1/EAI8-MDG and L1/EAI3-IND belonged to C5; this result suggests that they share a common ancestor. L1.1.3/SIT129, a spoligotype pattern found in SNPs-cluster C6, was found to be shared between Par?/Brazil and Malawi. SIT129 was independently found to be highly prevalent in Mozambique, which suggests a migration history from East-Africa to Brazil during the 16th?18th slave trade period to Northern Brazil.

The present study proposes a discussion about the use of breakpoints when plant derivatives are used for investigating potential agents against Mycobacterium tuberculosis strains. A systematic review on these aspects was performed and supported that an arbitrary breakpoint may be considered inadequate in this kind of study. In addition, we propose that the adoption of this limiter should be done from the toxicity value found using the same plant derivative.

Infections related to non-tuberculous mycobacteria (NTM) have recently increased worldwide. The transmission of these microorganisms from the environment has been suggested as the main source for human infections. To elucidate the epidemiological aspects and distribution of these pathogens, many studies have evaluated several decontamination methods and protocols to properly isolate NTM from environmental samples, mainly from water. However, no satisfactory strategy has been found for isolation of most of the NTM species harboring different phenotypic characteristics. Here, we evaluated the susceptibility of 23 NTM strains presenting variable growth rate and pigmentation patterns to eight different methods: oxalic acid (2.5% and 5%), cetylpyridinium chloride (CPC) (0.0025% and 0.005%), sodium hydroxide (NaOH) (2% and 4%), and sodium dodecyl sulfate (SDS) plus NaOH (SDS 1.5%-NaOH 0.5% and SDS 3%-NaOH 1%). It was found that the viability of NTM exposed to different decontamination methods varies according to their phenotypic characteristics and two methods (SDS 1.5% plus NaOH 0.5% and CPC 0.0025%) were necessary for effective isolation of all of the species tested. These findings supply important insights for future studies on the environmental occurrence of mycobacteria and improving the sensibility of traditional strategies.

Maria Carolina Sisco,1,2 Marlei Gomes da Silva,1 Luciana Distasio de Carvalho,3 Carlos Eduardo Dias Campos,3 Paulo Cesar De Souza Caldas,3 Beatriz Lopez,4 Claudia Argüelles,5 Ana Carolina Carvalho,6 Jacobus de Waard,7,8 Philip Suffys,2 Rafael Silva Duarte1 1Laboratório de Micobactérias, Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; 2Laboratório de Biologia Molecular Aplicada às Micobactérias, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil; 3Laboratório de Referência Nacional Para Tuberculose e Micobacterioses, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Rio de Janeiro, Brazil; 4Instituto Nacional de Enfermedades Infecciosas, Buenos Aires, Argentina; 5Instituto Nacional de Producción de Biológicos – ANLIS Carlos G Malbrán, Buenos Aires, Argentina; 6Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Rio de Janeiro, Brazil; 7Departamento de Tuberculosis, Instituto Autónomo de Biomedicina Dr. Jacinto Convit, Caracas, Venezuela; 8One Health Research Group, Facultad de Ciencias de La Salud, Universidad de Las Américas, Quito, EcuadorCorrespondence: Philip Suffys Email psuffys@gmail.comPurpose: Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the only vaccine licensed against tuberculosis. Despite the protection offered by the vaccine, in some circumstances children and immunocompromised individuals can develop associated infections, known as BCGitis. Drug susceptibility patterns of BCG clinical strains have rarely been described. We aimed to describe the susceptibility pattern of BCG clinical strains isolated in two different countries.Methods: We performed culture-based drug susceptibility testing of thirty one BCG strains isolated from patients in Brazil (n=5, 16%) and Argentina (n=26, 84%) using the broth micro-dilution method (phenotypic method). Final antibiotic concentrations for susceptibility testing ranged from 0.5 to 16 mg/L for amikacin, 0.3125 to 10 mg/L for ethambutol, 0.05 to 1.6 mg/L for isoniazid and 0.25 to 8 mg/L for rifampicin, streptomycin and ofloxacin. Additionally, we compared the results with genetic data obtained by whole genome sequencing.Results: By using the phenotypic method we detected one strain resistant to ethambutol, three strains resistant to rifampicin and one resistant to isoniazid. Additionally, two strains that were phenotypically resistant to both isoniazid and rifampicin carried mutations in the katG and rpoB genes simultaneously.Conclusion: There is evidence of the emergence of BCG-resistant strains isolated from vaccine-related complications. We recommend drug susceptibility testing of the BCG strain causing the infection in order to prevent treatment failure.Keywords: BCG, mycobacteria, resistance, vaccine

24 páginas, 3 figuras, 1 tabla. The sequence data generated by this study has been deposited on SRA (https://www.ncbi.nlm.nih.gov/sra) under the accession number PRJNA670836. Extended data is available here: https://github.com/fmenardo/MTBC_L1_L3. DOI: https://doi.org/10.5281/zenodo.4609804 (Menardo, 2021)., Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans., This work was supported by the Swiss National Science Foundation (grants 310030_188888, CRSII5_177163, IZRJZ3_164171 and IZLSZ3_170834) and the European Research Council (309540 EVODRTB and 883582-ECOEVODRTB).

Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Programa de P?s-Gradua??o em Pesquisa Cl?nica e Doen?as Infecciosas. Rio de Janeiro, RJ, Brasil / Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laborat?rio de Bacteriologia e Bioensaios em Micobact?rias. Rio de Janeiro, RJ, Brasil / Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil. Universidade Federal do Rio Grande do Sul. Programa de P?s-Gradua??o em Biologia Celular e Molecular. Porto Alegre, RS, Brasil / Secretaria Estadual de Sa?de do Rio Grande do Sul. Centro Estadual de Vigil?ncia em Sa?de. Centro de Desenvolvimento Cient?fico e Tecnol?gico. Porto Alegre, RS, Brasil. Funda??o Oswaldo Cruz. Escola Nacional de Sa?de P?blica Sergio Arouca. Centro de Refer?ncia Professor H?lio Fraga. Laborat?rio de Refer?ncia Nacional para Tuberculose e outras Micobacterioses. Rio de Janeiro, RJ, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Geoprocessamento. Ananindeua, PA, Brasil. International Institute of Information Technology. Department of Data Science. Bangalore, India. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Secretaria Estadual de Sa?de do Rio Grande do Sul. Centro Estadual de Vigil?ncia em Sa?de. Centro de Desenvolvimento Cient?fico e Tecnol?gico. Porto Alegre, RS, Brasil. Universidade de S?o Paulo. Faculdade de Medicina. Departamento de Cl?nica M?dica. Ribeir?o Preto, SP, Brasil. Universidade de S?o Paulo. Faculdade de Medicina. Departamento de Cl?nica M?dica. Ribeir?o Preto, SP, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil / Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Paulo de G?es. Laborat?rio de Micobact?rias. Rio de Janeiro, RJ, Brasil. Universidade Federal de S?o Paulo. Departamento de Microbiologia, Imunologia e Parasitologia. S?o Paulo, SP, Brasil. Instituto Adolfo Lutz. Centro de Bacteriologia. N?cleo de Tuberculose e Micobacterioses. S?o Paulo, SP, Brasil. Universit e Paris-Saclay. Ecologie Systematique Evolution. Centre National de la Recherche Scientifique. AgroParisTech, Orsay, France. Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laborat?rio de Bacteriologia e Bioensaios em Micobact?rias. Rio de Janeiro, RJ, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil. Coordena??o Geral de Vigil?ncia das Doen?as de Transmiss?o Respirat?ria de Condi??es Cr?nicas. Bras?lia, DF, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Gen?tica Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Paulo de G?es. Laborat?rio de Micobact?rias. Rio de Janeiro, RJ, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRUVNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in S?o Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes

Background Bacterial biofilm on surfaces of mammary implants is a predisposing factor for several outcomes. Because Gram-positive bacteria are potential agents of biomaterial-associated infections (BAIs), their abilities to form biofilm on breast implants should be elucidated. Objectives The aim of this study was to evaluate biofilm formation on different mammary prosthesis surfaces by major Gram-positive bacterial pathogens involved in BAIs. Methods We initially evaluated biofilm formation on polystyrene plates with and without fibrinogen or collagen for 1 reference strain and 1 clinical isolate of Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus pyogenes. We also tested the ability of clinical isolates to form biofilm on 4 different implant surfaces: polyurethane foam and smooth, microtextured, and standard textured silicone. Biofilm structure and cell viability were observed by scanning electron microscopy and confocal laser scanning microscopy. Results All strains showed strong biofilm formation on polystyrene. After fibrinogen or collagen treatment, biofilm formation varied. With fibrinogen, reference strains of S. aureus and S. pyogenes increased biofilm formation (P Conclusions All species produced biofilm on all prosthesis surfaces and under different conditions. Micrographies indicated thicker bacterial biofilm formation on microtextured and/or standard textured silicone by all species, except E. faecalis.

Lineage 1 (L1) and 3 (L3) are two lineages of theMycobacterium tuberculosiscomplex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We show that South Asia played a central role in the dispersion of these two lineages to neighboring regions. Moreover, we found that L1 exhibits signatures of local adaptation at theesxHlocus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.

CNPq (207,071/2014-4), CAPES (Finance Code 001), Swiss National Science Foundation (grants 310030_166687 and IZRJZ3_164171) Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. International Institute of Information Technology. Department of Data Science. Bangalore, India. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil. University of Basel. Basel, Switzerland / Swiss Tropical & Public Health Institute. Basel, Switzerland. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Centro de Inova??es Tecnol?gicas. Ananindeua, PA, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Esp?rito Santo. N?cleo de Doen?as Infecciosas. Vit?ria, ES, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Gen?tica Molecular de Microrganismos. Rio de Janeiro, RJ, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de G?es. Laborat?rio de Micobact?rias. Rio de Janeiro, RJ, Brasil. University of Basel. Basel, Switzerland / Swiss Tropical & Public Health Institute. Basel, Switzerland. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil. Universidade do Estado do Par?. Instituto de Ci?ncias Biol?gicas e da Sa?de. P?s-Gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brasil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada a Micobact?rias. Rio de Janeiro, RJ, Brasil / Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Programa de P?s-Gradua??o em Pesquisa Cl?nica e Doen?as Infecciosas. Rio de Janeiro, RJ, Brasil / Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laborat?rio de Bacteriologia e Bioensaios em Micobact?rias. Rio de Janeiro, RJ, Brasil. BACKGROUND The evaluation of procedures for drug susceptibility prediction of Mycobacterium tuberculosis based on genomic data against the conventional reference method test based on culture is realistic considering the scenario of growing number of tools proposals based on whole-genome sequences (WGS). OBJECTIVES This study aimed to evaluate drug susceptibility testing (DST) outcome based on WGS tools and the phenotypic methods performed on isolates of M. tuberculosis Lineage 1 from the state of Par?, Brazil, generally associated with low levels of drug resistance. METHODOLOGY Culture based DST was performed using the Proportion Method in L?wenstein-Jensen medium on 71 isolates that had been submitted to WGS. We analysed the seven main genome sequence-based tools for resistance and lineage prediction applied to M. tuberculosis and for comparison evaluation we have used the Kappa concordance test. FINDINGS When comparing the WGS-based tools against the DST, we observed the highest level of agreement using TBprofiler. Among the tools, TB-profiler, KvarQ and Mykrobe were those which identified the largest number of TB-MDR cases. Comparing the four most sensitive tools regarding resistance prediction, agreement was observed for 43 genomes. MAIN CONCLUSIONS Drug resistance profiling using next-generation sequencing offers rapid assessment of resistanceassociated mutations, therefore facilitating rapid access to effective treatment.

Purpose Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is the only vaccine licensed against tuberculosis. Despite the protection offered by the vaccine, in some circumstances children and immunocompromised individuals can develop associated infections, known as BCGitis. Drug susceptibility patterns of BCG clinical strains have rarely been described. We aimed to describe the susceptibility pattern of BCG clinical strains isolated in two different countries. Methods We performed culture-based drug susceptibility testing of thirty one BCG strains isolated from patients in Brazil (n=5, 16%) and Argentina (n=26, 84%) using the broth micro-dilution method (phenotypic method). Final antibiotic concentrations for susceptibility testing ranged from 0.5 to 16 mg/L for amikacin, 0.3125 to 10 mg/L for ethambutol, 0.05 to 1.6 mg/L for isoniazid and 0.25 to 8 mg/L for rifampicin, streptomycin and ofloxacin. Additionally, we compared the results with genetic data obtained by whole genome sequencing. Results By using the phenotypic method we detected one strain resistant to ethambutol, three strains resistant to rifampicin and one resistant to isoniazid. Additionally, two strains that were phenotypically resistant to both isoniazid and rifampicin carried mutations in the katG and rpoB genes simultaneously. Conclusion There is evidence of the emergence of BCG-resistant strains isolated from vaccine-related complications. We recommend drug susceptibility testing of the BCG strain causing the infection in order to prevent treatment failure.

Bacillus Calmette Guerin (BCG) vaccines comprise a family of related strains. Whole genome sequencing has allowed the better characterisation of the differences between many of the BCG vaccines. As sequencing technologies improve, updating of publicly available sequence data becomes common practice. We hereby announce the draft genome of four commonly used BCG vaccines in Brazil, Argentina and Venezuela.

INTRODUCTION: Laboratory and clinical features of childhood tuberculosis (TB) are non-specific and establishing an accurate diagnosis remains a challenge. This study evaluated a Single tube nested-PCR (STNPCR) to detect genomic DNA of Mycobacterium tuberculosis complex in blood and urine. METHODS: Biological samples were obtained from children (

Universidade Federal de Goi?s. Hospital das Cl?nicas. Goi?nia, GO, Brazil. Funda??o Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Programa de P?s-gradua??o em Pesquisa Cl?nica e Doen?as Infecciosas. Rio de Janeiro, RJ, Brazil / Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada em Micobacterias. Rio de Janeiro, RJ, Brazil. Universidade Federal de Goi?s. Hospital das Cl?nicas. Goi?nia, GO, Brazil. Universidade Federal de Goi?s. Hospital das Cl?nicas. Goi?nia, GO, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada em Micobacterias. Rio de Janeiro, RJ, Brazil / Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Instituto de Biomedicina Dr. Jacinto Convit. Instituto de Biomedicina. San Jose, Caracas, Venezuela / Universidad de Las Am?ricas. Facultad de Ciencias de La Salud. One Health Research Group. Quito, Ecuador. Funda??o Oswaldo Cruz. Centro de Refer?ncia Professor H?lio Fraga. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Centro de Refer?ncia Professor H?lio Fraga. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Centro de Refer?ncia Professor H?lio Fraga. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Centro de Refer?ncia Professor H?lio Fraga. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Centro de Refer?ncia Professor H?lio Fraga. Rio de Janeiro, RJ, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. International Institute of InformationTechnology - Bangalore. Department of Data Science. Bangalore, India. Corporaci?n para Investigaciones Biol?gicas. Medell?n, Colombia. Corporaci?n para Investigaciones Biol?gicas. Medell?n, Colombia. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de G?es. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada em Micobacterias. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada em Micobacterias. Rio de Janeiro, RJ, Brazil. Institute of Tropical Medicine. Mycobacteriology Unit. Antwerp, Belgium. Institute of Tropical Medicine. Mycobacteriology Unit. Antwerp, Belgium. Universidade Federal de Goi?s. Instituto de Patologia Tropical e Sa?de P?blica. Goi?nia, GO, Brazil. Funda??o Oswaldo Cruz. Instituto Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada em Micobacterias. Rio de Janeiro, RJ, Brazil. Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), including Mycobacterium tuberculosis var. tuberculosis (MTB) and Mycobacterium tuberculosis var. africanum (MAF). While MTB is isolated worldwide, MAF is almost completely restricted to the African continent, and despite the historical proximity between Brazil and Africa during the slave trade, no case of TB being caused by MAF has been reported in Brazil to date. We hereby describe the first case of TB caused by MAF in Brazil comparing its genome against the published ones. A female patient who had never visited Africa presented with clinical symptoms typical of pulmonary TB. Based on 16S rRNA gene sequencing, the cultured isolate was identified as belonging to MTBC and partial sequence of the hsp65 gene was identical to that of MAF. This was confirmed by genotyping based on detection of Single Nucleotide Polymorphism (SNP), Region of Difference (RD) and spoligotyping. The isolate presented the Shared International Typing (SIT) 181. In the whole-genome comparison against MAF genomes available on published EMBL-EBI European Nucleotide Archive (ENA), the Brazilian genome (MAFBRA00707) was identified as belonging to Lineage 6 and clustered with isolates from The Gambia. This is the first report of the isolation of MAF from a patient from Brazil, without evidence of having any contact with an African index case

The work done at Institut Pasteur de la Guadeloupe was supported by a FEDER grant, financed by the European Union and Guadeloupe Region (Programme Op?rationnel FEDER-Guadeloupe-Conseil R?gional 2014?2020, Grant number 2015-FED-192). The ECC and IPF received support from Capes and FAPESPA respectively. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia. Rio de Janeiro, RJ, Brazil. Institut Pasteur de Guadeloupe. Unit? de la Tuberculose et des Mycobact?ries. WHO Supranational TB Reference Laboratory. Abymes, Guadeloupe, France. Institut Pasteur de Guadeloupe. Unit? de la Tuberculose et des Mycobact?ries. WHO Supranational TB Reference Laboratory. Abymes, Guadeloupe, France. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade do Estado do Par?. Programa de P?s-gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brazil. Funda??o Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada as Micobact?rias. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada as Micobact?rias. Rio de Janeiro, RJ, Brazil. Funda??o Oswaldo Cruz. Laborat?rio de Biologia Molecular Aplicada as Micobact?rias. Rio de Janeiro, RJ, Brazil / Institute of Tropical Medicine. Mycobacterium Unit. Antwerp, Belgium. Universidade Federal do Par?. Instituto de Ci?ncias Biol?gicas. Laborat?rio de Polimorfismo de DNA. Bel?m, PA, Brazil. Universidade Federal do Par?. N?cleo de Medicina Tropical. Bel?m, PA, Brazil. Univ. Paris-Sud. Institut de Biologie Int?grative de la Cellule. Univ. Paris-Saclay, France. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil. Universidade Federal do Rio de Janeiro. Instituto de Microbiologia. Rio de Janeiro, RJ, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade do Estado do Par?. Programa de P?s-gradua??o em Biologia Parasit?ria na Amaz?nia. Bel?m, PA, Brazil. There is only scarce information available on genotypic diversity of the Mycobacterium tuberculosis complex (MTBC) clinical isolates circulating in the Northern part of Brazil, a relatively neglected region regarding research on tuberculosis. We therefore characterized 980 MTBC clinical isolates from the state of Par?, by spoligotyping and data was compared with patterns from around the world, besides analyzing drug susceptibility, and collecting sociodemographic data. We also performed 24 loci MIRU-VNTR typing to evaluate phylogenetic inferences among the East-African-India (EAI) lineage strains. The Geographic Information System analyses were performed to generate a descriptive visualization of MTBC strain distribution in the region. A total of 249 different spoligopatterns primarily belonging to evolutionary recent Euro-American lineages, as well as Central-Asian, Manu and ancestral EAI lineages, were identified, in addition to strains with reportedly unknown lineage signatures. The most frequent lineages were Latin American Mediterranean, T and Haarlem. Interestingly, EAI lineage strains were found in a higher proportion in a significantly higher proportion in comparison with previous studies from South America. Regarding EAI lineage, the absence of spacers 4?9 and 23?24 co-related to 24 loci MIRU-VNTRs may suggest a close evolutionary relationship between such strains in Par? and those prevalent in Mozambique, which might have contributed to the genetic diversity of MTBC strains in this region.