Resumo Enterococcus faecalis, causa comum de infecções nosocomiais, é frequentemente associado a infecções endodônticas. Entretanto, há poucos estudos de caracterização genética das linhagens mais associadas aos canais radiculares. O objetivo deste estudo foi avaliar a relação genética entre isolados de E. faecalis de infecções endodônticas primárias no sudeste do Brasil para testar a hipótese de clones infectando indivíduos não relacionados e examinar o perfil de resistência antimicrobiana. A relação genética de 32 E. faecalis endodônticos foi obtida pela técnica de tipagem de sequências multilocus (MLST). Esses isolados foram coletados de pacientes não relacionados com infeção endodôntica primária tratados no Brasil entre 2010 e 2023. Teste de suscetibilidade antimicrobiana foi realizado utilizando a técnica de difusão em disco de acordo com o Clinical Laboratory Standard Institute (CLSI). Foram detectados 12 tipos de sequência (STs), dos quais 8 STs continham apenas um isolado. Clones de ST 30, ST 40, ST 97 e ST 397 foram encontrados, com uma elevada frequência deste último (15/32). A suscetibilidade aos agentes antimicrobianos testados variou, com a maior percentagem de resistência observada para a clindamicina (100%), tetraciclina (34,4%), azitromicina (31,2%) e ciprofloxacina (19,2%). Um isolado era multirresistente. O MLST de E. faecalis endodônticos revelou clones infectando diferentes indivíduos em diferentes cidades, com até 10 anos de intervalo, com alta ocorrência do ST 397. Portanto, existe uma linhagem predominante de E. faecalis associada a infecções endodônticas no sudeste do Brasil. Estes dados, juntamente com a literatura, levantam a preocupação de que possam existir linhagens especializadas em infecções endodônticas. nosocomiais Entretanto radiculares E 3 MLST. . (MLST) 201 2023 CLSI. CLSI (CLSI) 1 STs, , (STs) 30 40 9 39 encontrados 15/32. 1532 15/32 15 (15/32) variou 100%, 100 100% (100%) 34,4%, 344 34,4% 34 4 (34,4%) 31,2% 312 31 2 (31,2% 19,2%. 192 19,2% 19 (19,2%) multirresistente cidades intervalo Portanto dados literatura (MLST 20 202 (CLSI (STs 153 15/3 (15/32 (100% 34,4 (34,4% 31,2 (31,2 19,2 (19,2% 15/ (15/3 (100 34, (34,4 31, (31, 19, (19,2 (15/ (10 (34, (31 (19, (15 (1 (34 (3 (19 (

Abstract Enterococcus faecalis is a common cause of nosocomial infections and is frequently associated with endodontic infections. However, there is a scarcity of studies addressing the genetic characterization of E. faecalis lineages most commonly associated with root canals. The aim of this study was to assess the genetic relatedness of E. faecalis strains from primary endodontic infections in Southeast Brazil, test the hypothesis of clones infecting unrelated individuals, and examine the antimicrobial resistance profile. The genetic relationship of 32 endodontic E. faecalis isolates was investigated using multilocus sequence typing (MLST). These isolates were collected from unrelated patients with primary endodontic infections treated in Brazil between 2010 and 2023. Antimicrobial susceptibility testing was performed using the disk diffusion method in accordance with the Clinical Laboratory Standards Institute guidelines. Twelve sequence types (STs) were detected, of which eight STs contained only a single strain. Clones of ST 30, ST 40, ST 97, and ST 397 were identified, with a notably high frequency of ST 397 (15/32). Susceptibility to the antimicrobial agents tested varied, with the highest resistance rates observed for clindamycin (100%), tetracycline (34.4%), azithromycin (31.2%), and ciprofloxacin (19.2%). One isolate was found to be multidrug-resistant. MLST analysis of endodontic E. faecalis revealed clones infecting different individuals in various cities over a span of up to 10 years, with a high occurrence of ST 397. Therefore, there appears to be a predominant E. faecalis lineage associated with endodontic infections in Southeast Brazil. These findings, together with existing literature, raise concerns that certain lineages may be specialized in causing endodontic infections. However E canals profile 3 MLST. . (MLST) 201 2023 guidelines (STs detected strain 30 40 97 39 identified 15/32. 1532 15/32 15 (15/32) varied 100%, 100 100% , (100%) 34.4%, 344 34.4% 34 4 (34.4%) 31.2%, 312 31.2% 31 2 (31.2%) 19.2%. 192 19.2% 19 (19.2%) multidrugresistant. multidrugresistant multidrug resistant. resistant multidrug-resistant 1 years Therefore findings literature (MLST 20 202 9 153 15/3 (15/32 (100% 34.4 (34.4% 31.2 (31.2% 19.2 (19.2% 15/ (15/3 (100 34. (34.4 31. (31.2 19. (19.2 (15/ (10 (34. (31. (19. (15 (1 (34 (31 (19 ( (3

RESUMO Os primatas que habitam a floresta tropical ao redor da cidade de Manaus (Amazonas, Brasil) há muito são reconhecidos como reservatórios potencialmente importantes de doenças infecciosas emergentes e reemergentes. Sequências de DNA de parasitas filariais detectadas por PCR em amostras de Simulium oyapockense foram usadas para demonstrar que eles haviam se alimentado anteriormente de primatas não humanos e, dessa maneira, incriminar vetores-ponte da região amazônica. O uso mais amplo de detecção de parasitas filariais para a incriminação de vetores-ponte é limitado por uma escassez de sequências referência de parasitas filarias obtidas de hospedeiros. Aqui nós usamos o sequenciamento tipo shotgun para obter dados de referência de um parasita adulto Dipetalonema gracile encontrado infectando um sauim-de-coleira, Saguinus bicolor no entorno de Manaus. Relatamos o genoma mitocondrial completo do parasita (que tem 13.647 pares de bases de comprimento), 894.846 pares de bases de seu genoma de Wolbachia e 6.426 pares de bases de seu locus de DNA ribossômico (desde o início de sua subunidade 18S até o final de sua subunidade 28S). Apesar de criticamente ameaçado, S. bicolor é comumente encontrado no entorno de Manaus e em fragmentos florestais urbanos. As sequências relatadas podem ser uma ferramenta de referência útil para identificar vetores ponte e potencialmente fornecer algumas informações sobre o contato entre reservatórios de patógenos de primatas e os moradores de Manaus. Amazonas, Amazonas (Amazonas Brasil reemergentes maneira vetoresponte amazônica hospedeiros sauimdecoleira, sauimdecoleira sauim coleira, coleira sauim-de-coleira 13647 13 647 13.64 comprimento, comprimento , comprimento) 894846 894 846 894.84 6426 6 426 6.42 desde S 28S. 28S . 28S) ameaçado urbanos 1364 1 64 13.6 89484 89 84 894.8 642 42 6.4 136 13. 8948 8 894. 4 6.

ABSTRACT The primates that inhabit the rainforest surrounding the city of Manaus (Amazonas, Brazil) have long been recognised as potentially important reservoirs of emerging and re-emerging infectious diseases (ERIDs). PCR amplification of filarial sequences from wild-caught Simulium oyapockense has been used to incriminate potentially important Amazon-region ERID bridge vectors by showing they had previously fed on non-human primates. The broader use of filarial parasite sequences for the incrimination of biting insects as potentially important zoonotic disease vectors is limited by a paucity of primate-derived filarial parasite reference sequences which can be matched to the PCR amplified sequences obtained from insect-vector vectors. Here we have used shotgun sequencing to obtain reference data from an adult Dipetalonema gracile parasite which was found infecting a wild pied tamarin (Saguinus bicolor) in a peripheral region of Manaus. We report the parasite´s complete mitochondrial genome (which is 13,647 base pairs in length), 894,846 base pairs of its Wolbachia genome and 6,426 base pairs of its ribosomal DNA locus (spanning from the start of its 18S subunit to the end of its 28S subunit). Despite being critically endangered, S. bicolor is commonly encountered around the periphery of Manaus and in urban forest fragments. The reported sequences may be a useful reference tool for identifying ERID bridge vectors and potentially provide some insights into the amount and the nature of contact between primate pathogen reservoirs and the residents of Manaus. Amazonas, Amazonas (Amazonas Brazil reemerging re ERIDs. ERIDs . (ERIDs) wildcaught caught Amazonregion Amazon nonhuman non human primatederived derived insectvector insect vector Saguinus parasites s 13647 13 647 13,64 length, length , length) 894846 894 846 894,84 6426 6 426 6,42 spanning S subunit. subunit) endangered fragments (ERIDs 1364 1 64 13,6 89484 89 84 894,8 642 42 6,4 136 13, 8948 8 894, 4 6,

BACKGROUND Pandrug-resistant (PDR) Klebsiella pneumoniae has been reported sporadically in many countries and remains rare in Brazil. OBJECTIVES This study unravelled the genetic determinants involved with the PDR background of a clinical ST11 K. pneumoniae recovered in the Brazilian Amazon Region, where K. pneumoniae genomic and epidemiological information is scarce. METHODS Kp196 was submitted to the antimicrobial susceptibility test by the disk-diffusion method and minimum inhibitory concentration (MIC) determination. The whole genome sequencing was obtained and the sequence type was determined by core genome multilocus sequence typing (cgMLST). Its intrinsic and acquired resistome was assessed by Comprehensive Antibiotic Resistance Database (CARD) and comparison with wild-type genes. FINDINGS The analyses revealed that Kp196 belonged to the pandemic ST11 and presented the PDR phenotype. Its acquired resistome was composed of a huge set of clinically relevant resistance determinants, including bla CTX-M-15 and bla NDM-1, all found in the vicinity of mobile platforms. Considering its intrinsic resistome, the multidrug resistance, especially to colistin, tigecycline and fluoroquinolones, was multifactorial and attributed to modifications (indels, missense mutations, and gene disruption) in several housekeeping genes (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37). The Kp196 intrinsic resistome was also observed in a ST11 environmental strain, although harbouring distinct acquired resistomes. CONCLUSIONS An accumulation of different resistance mechanisms regarding the intrinsic resistome accounts for a more stable resistome, strongly contributing to the Kp196 PDR phenotype. Pandrugresistant Pandrug resistant (PDR Brazil ST ST1 K Region scarce Kp Kp19 diskdiffusion disk diffusion MIC (MIC determination cgMLST. cgMLST . (cgMLST) CARD (CARD wildtype wild phenotype CTXM15 CTXM CTX M 15 CTX-M-1 NDM1, NDM1 NDM 1, 1 NDM-1 platforms colistin fluoroquinolones indels, indels (indels mutations disruption arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK353637. arnTphoQmgrBramRacrBgyrAparCompK353637 arnTphoQmgrBramRacrBgyrAparCompK arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35 36 37 arnT phoQ mgrB ramR acrB gyrA parC ompK35 ompK (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37) strain resistomes Kp1 (cgMLST CTXM1 CTX-M- NDM- ompK353637 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK353637 arnTphoQmgrBramRacrBgyrAparCompK35363 arnTphoQmgrBramRacrBgyrAparCompK35 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK3 3 ompK3 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37 CTX-M ompK35363 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35363 arnTphoQmgrBramRacrBgyrAparCompK3536 arnTphoQmgrBramRacrBgyrAparCompK3 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-3 ompK3536 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK3536 arnTphoQmgrBramRacrBgyrAparCompK353 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36- ompK353 arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK353 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-3 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35- (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK3 (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK

BACKGROUND The parasite Giardia duodenalis infects a wide range of vertebrate hosts, including domestic and wild animals as well as humans. Giardia is genotyped into eight assemblages (A-H). Zoonotic assemblages A and B have already been identified in humans and wild and domestic animals (non-human primates and cats) from Brazilian Amazon and in the world. Due to its zoonotic/zooanthroponotic nature, surveillance initiatives and the definition of Giardia assemblages are important in order to characterise the epidemiological scenario and to implement further control measures. OBJECTIVES Determine assemblages of G. duodenalis in sloths from the Brazilian Amazon Region. METHODS Faecal parasitological examination of sloths from Amazonas State. Polymerase chain reaction (PCR) targeting the beta giardin (BG), and genes from multilocus sequence typing (MLST) scheme, amplicon sequencing and phylogenetic analysis. FINDINGS Here, we identified, by microscopy, Giardia in two northern sloths (Bradypus tridactylus). These two samples were submitted to molecular assays and it was revealed that both were infected by G. duodenalis assemblage A. Phylogenetic analysis showed that they belong to assemblage A within sequences from humans and wild and domestic animals. CONCLUSION Therefore, besides showing, by the first time, the current presence of this parasite in sloths, our findings reveals that this wild animal species would be part of the zoonotic/zooanthroponotic scenario of this parasite in the Brazilian Amazon. hosts AH. AH H . (A-H) nonhuman non human cats world zoonoticzooanthroponotic zoonotic zooanthroponotic nature measures G Region State PCR (PCR BG, BG , (BG) MLST (MLST scheme Here microscopy Bradypus tridactylus. tridactylus tridactylus) Therefore showing time (A-H (BG

BACKGROUND Giardia duodenalis is a protozoan parasite that infects humans and other mammals and causes giardiasis worldwide. Giardia is genotyped into eight assemblages (A-H), with assemblages A and B considered zoonotic. OBJECTIVES The aim of this study was to determine the assemblages of G. duodenalis from individuals living in rural and urban areas of the Amazonas State. METHODS 103 human faecal specimens microscopically positive for the presence of Giardia obtained from four municipalities in Amazonas and four animal faecal specimens were genotyped based on the sequences of two genes, triosephosphate isomerase (TPI) and β-giardin (BG). FINDINGS In humans, assemblage A was the most represented with the identification of sub-assemblages AI, AII and AIII based on BG and sub-assemblages AI and AII based on TPI. Similarly, there is a diversity of sub-assemblage B considering BG (B and BIII) and TPI (B, BIII and BIV). In addition, we characterised homogeneous and heterogeneous genotypes comprising assemblages/sub-assemblages A and B in individuals from urban and rural areas. Here, for the first time, it was genotyped Giardia that infects animals from the Brazilian Amazon region. We identified sub-assemblage AI in one Ateles paniscus and two Felis catus and sub-assemblage BIV in one Lagothrix cana. MAIN CONCLUSIONS Therefore, humans and animals from the urban and rural Amazon share Giardia genotypes belonging to assemblages A and B, which are found in cosmopolitan regions around the world.

The presence of tRNA array, a region with high tRNA gene number and density, has been demonstrated in Mycobacterium genus. However, a recent phylogenomic study revealed the existence of five distinct monophyletic groups (genera) within this genus. Considering this new scenario, and based on in-silico analyses, we have identified and characterised the abundance and diversity of tRNA array units within Mycobacterium, Mycolicibacterium gen. nov., Mycolicibacillus gen. nov., and Mycobacteroides gen. nov. The occurrence and prevalence of tRNA arrays among the genera belonging to Actinobacteria indicate their possible role in the organismal fitness.

BACKGROUND Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE Explore the occurrence of tRNA gene clusters in archaea. METHODS In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.

ABSTRACT Human T cell lymphotropic virus type 1 (HTLV-1) was the first retrovirus discovered in humans and is endemic in several parts of the world. Because of risk behaviors, mainly sexual, men who have sex with men (MSM) are at high risk of acquiring HTLV-1 infection. A cross-sectional study was performed to estimate the prevalence of HTLV-1 infection, to characterize genetically HTLV-1 sequences and to identify risk behaviors associated with this infection among MSM in Central Brazil. A total of 430 MSM were enrolled in this study and three were shown to be HTLV-1 infected, prevalence of 0.7% (95% confidence interval: 0.4-0.9). Phylogenetic analysis showed that all HTLV-1 positive samples belonged to Cosmopolitan subtype Transcontinental subgroup A. Although the prevalence rate of HTLV-1 infection found in this study was similar to that observed among Brazilian blood donors, additional HTLV-1 preventive interventions need to be further implemented because this population is engaged in high-risk sexual behavior.

The genus Mycobacterium is highly diverse and ubiquitous in nature, comprehending fast- and slow-growing species with distinct impact in public health. The plasmid-mediated horizontal gene transfer represents one of the major events in bacteria evolution. Here, we report the complete sequence of a 160,489 bp circular plasmid (pCBMA213_2) from an atypical and fast-growing environmental mycobacteria. This is a unique plasmid, in comparison with the characterised mycobacteria plasmids, harboring a type IV-like and ESX-P2 type VII secretion systems. pCBMA213_2 can be further explored for evolutionary and conjugation studies as well as a tool to manipulate DNA within this bacteria genus.

Abstract Mosquito midgut microbiota is a key component of vector competence, as gut bacteria can disturb pathogen development. In this study, we addressed the microbiota composition of Aedes aegypti during its lifespan, under field conditions. We also investigated the possible effects of environment, dietary regime and ageing on the gut community composition. We employed culture independent and dependent approaches to characterise vector microbiota. There was evidence of a lifelong stable core microbiota after mosquitoes were released into an urban settlement, where they presumably fed on a range of vertebrate hosts and carbohydrate sources. This core was formed mainly of bacteria belonging to the genera Pseudomonas, Acinetobacter, Aeromonas and Stenotrophomonas and to the families Oxalobacteraceae, Enterobacteriaceae and Comamonadaceae. We showed that both dietary regime and age were associated with the abundance of some bacterial groups in the Ae. aegypti microbiota. The majority of the bacterial groups we identified have been detected in the midgut of Ae. aegypti from laboratory and wild populations, indicating a possible core microbiota associated with this mosquito species. Our findings suggest that Ae. aegypti harbours a stable bacterial community during its adult life, similar to mosquito populations from distinct geographic areas, which may be further explored for arbovirus biocontrol strategies.

Chikungunya virus (CHIKV) is a mosquito-borne pathogen that emerged in Brazil by late 2014. In the country, two CHIKV foci characterized by the East/Central/South Africa and Asian genotypes, were established in North and Northeast regions. We characterized, by phylogenetic analyses of full and partial genomes, CHIKV from Rio de Janeiro state (2014-2015). These CHIKV strains belong to the Asian genotype, which is the determinant of the current Northern Brazilian focus, even though the genome sequence presents particular single nucleotide variations. This study provides the first genetic characterisation of CHIKV in Rio de Janeiro and highlights the potential impact of human mobility in the spread of an arthropod-borne virus.

Parvovirus B19 (B19V) infects individuals worldwide and is associated with an ample range of pathologies and clinical manifestations. B19V is classified into three distinct genotypes, all identified in Brazil. Here, we report a complete sequence of a B19V genotype 1A that was obtained by high-throughput metagenomic sequencing. This genome provides information that will contribute to the studies on B19V epidemiology and evolution.

Human T-cell lymphotropic virus (HTLV) may impact the clinical course of tuberculosis (TB). Both infections are highly endemic in Brazil. The aim of this study was to assess the prevalence of HTLV-1/2 in TB patients in Central-West Brazil and to perform a genetic characterisation of the respective isolates. Of the 402 patients, six (1.49%) were positive for anti-HTLV and five (1.24%; 95% confidence interval: 0.46-3.05) were infected with HTLV-1/2. Genetic characterisation demonstrated that the four HTLV-1 isolates belonged to the Transcontinental subgroup A of the Cosmopolitan subtype a and that the HTLV-2 isolate belonged to subtype a (HTLV-2a/c). The prevalence of HTLV infection observed in this study is higher than that observed in local blood donors and the HTLV-1 and 2 subtypes identified are consistent with those circulating in Brazil.