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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.

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.

https://doi.org/10.1590/1809-4392202201741

Unveiling the genome of a high-risk pandrug-resistant Klebsiella pneumoniae emerging in the Brazilian Amazon Region, 2022
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Fonseca, Érica Lourenço

; Morgado, Sérgio M

; Freitas, Fernanda S

; Bighi, Nathalia S

; Cipriano, Rosângela

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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2023, Volume 118 elocation e230081

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760230081

Zoonotic Giardia duodenalis assemblage A in northern sloth from Brazilian Amazon
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dos Reis, Lisiane Lappe

; de Souza, Lirna Salvioni Silva

; Braga, Francisco Carlos de Oliveira

; Lima, Dayane Costa de Souza

; Lima, Natália Aparecida de Souza

; Padinha, Jessica da Silva

; Nava, Alessandra Ferreira Dales

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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2023, Volume 118 elocation e230088

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760230088

Giardiasis in urban and rural Amazonas, Brazil is driven by zoonotic and cosmopolitan A and B assemblages
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dos Reis, Lisiane Lappe

; da Silva, Túllio Romão Ribeiro

; Braga, Francisco Carlos de Oliveira

; do Nascimento, Naara Macedo

; de Menezes, Katia Maria Lima

; Nava, Alessandra Ferreira Dales

; Lima, Natália Aparecida de Souza

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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2021, Volume 116 elocation e210280

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760210280

Increasing awareness of human T-lymphotropic virus type-1 infection: a serious, invisible, and neglected health problem in Brazil
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Puccioni-Sohler, Marzia

; Grassi, Maria Fernanda Rios

; Galvão-Castro, Bernardo

; Caterino, Adele

; Proietti, Anna Bárbara de Freitas Carneiro

; Vicente, Ana Carolina Paulo

; Galvão-Castro, Ana Verena

; Vallinoto, Antonio Carlos

; Paiva, Arthur

; Penalva, Augusto

; Rosadas, Carolina

; Miyashiro, Denis

; Barbosa, Edel Figueiredo

; Carvalho, Edgar Marcelino de

; Batista, Everton da Silva

; Smid, Jerusa

; Casseb, Jorge

; Vidal, Jose

; Sousa, Maisa Silva

; Viana, Maria Graça de Castro

; Bastos, Michele de Souza

; Lírio, Monique

; Boa-Sorte, Ney

; Ferreira Jr, Orlando C.

; Takayanagui, Osvaldo

; Moura, Patrícia

; Rocco, Regina

; Cunha, Rodrigo Guimaraes

; Haddad, Simone Kashima

; Assone, Tatiane

; Araújo, Thessika Hialla Almeida

Revista da Sociedade Brasileira de Medicina Tropical

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2019, Volume 52 elocation e20190343

Resumo: En | Texto: En | PDF: En

https://doi.org/10.1590/0037-8682-0343-2019 953 downloads

Exploring tRNA gene cluster in archaea
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Morgado, Sergio Mascarenhas

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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2019, Volume 114 elocation e180348

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760180348 1206 downloads

Mycobacterium genus and tRNA arrays
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Morgado, Sergio Mascarenhas

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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2019, Volume 114 elocation e180443

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760180443 1102 downloads

Human T cell lymphotropic virus type 1 infection among men who have sex with men in Central Brazil
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Castro, Lisie Souza

; Rezende, Grazielli Rocha de

; Fernandes, Fernanda Rodas Pires

; Bandeira, Larissa Melo

; Puga, Marco Antonio Moreira

; Tanaka, Tayana Serpa Ortiz

; Weis-Torres, Sabrina Moreira dos Santos

; Vicente, Ana Carolina Paulo

; Otsuki, Koko

; Motta-Castro, Ana Rita Coimbra

Brazilian Journal of Infectious Diseases

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Nov 2018, Volume 22 Nº 6 Páginas 472 - 476

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1016/j.bjid.2018.11.003 557 downloads

Complete plasmid sequence carrying type IV-like and type VII secretion systems from an atypical mycobacteria strain
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Morgado, Sergio Mascarenhas

; Marín, Michel Abanto

; Freitas, Fernanda S

; Fonseca, Erica Lourenço

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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Jul 2017, Volume 112 Nº 7 Páginas 514 - 516

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760160546 911 downloads

10.

Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan
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David, Mariana Rocha

; Santos, Lilha Maria Barbosa dos

; Vicente, Ana Carolina Paulo

; Maciel-de-Freitas, Rafael

Memórias do Instituto Oswaldo Cruz

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Set 2016, Volume 111 Nº 9 Páginas 577 - 587

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760160238 2337 downloads

11.

Phylogenetic analyses of chikungunya virus among travelers in Rio de Janeiro, Brazil, 2014-2015
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Conteville, Liliane Costa

; Zanella, Louise

; Marín, Michel Abanto

; Filippis, Ana Maria Bispo de

; Nogueira, Rita Maria Ribeiro

; Vicente, Ana Carolina Paulo

; Mendonça, Marcos César Lima de

Memórias do Instituto Oswaldo Cruz

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Mai 2016, Volume 111 Nº 5 Páginas 347 - 348

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760160004 1688 downloads

12.

Parvovirus B19 1A complete genome from a fatal case in Brazil
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Conteville, Liliane Costa

; Zanella, Louise

; Marín, Michel Abanto

; Filippis, Ana Maria Bispo de

; Nogueira, Rita Maria Ribeiro

; Vicente, Ana Carolina Paulo

; Mendonça, Marcos César Lima de

Memórias do Instituto Oswaldo Cruz

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Set 2015, Volume 110 Nº 6 Páginas 820 - 821

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-02760150261 1680 downloads

13.

Prevalence and genetic characterisation of HTLV-1 and 2 dual infections in patients with pulmonary tuberculosis in Central-West Brazil
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Kozlowski, Aline Garcia

; Carneiro, Megmar Aparecida dos Santos

; Matos, Márcia Alves Dias de

; Teles, Sheila Araújo

; Araújo Filho, João Alves

; Otsuki, Koko

; Vicente, Ana Carolina Paulo

; Martins, Regina Maria Bringel

Memórias do Instituto Oswaldo Cruz

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Fev 2014, Volume 109 Nº 1 Páginas 118 - 121

Resumo: En | Texto: En | PDF: En

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.

https://doi.org/10.1590/0074-0276130230 2064 downloads

14.

Foreword
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Carvalho, Omar dos Santos

; Grault, Carlos Eduardo

; Machado, Marcelo Pelajo

; Pieri, Otávio

; Vicente, Ana Carolina Paulo

; Cupolillo, Elisa

Memórias do Instituto Oswaldo Cruz

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Nov 2011, Volume 106 Nº 7 Páginas 783 - 783

Resumo: En | Texto: En | PDF: En

1172 downloads

15.

Occurrence and composition of class 1 and class 2 integrons in clinical and environmental O1 and non-O1/non-O139 Vibrio cholerae strains from the Brazilian Amazon
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Sá, Lena Lillian Canto de

; Fonseca, Érica Lourenço da

; Pellegrini, Maíra

; Freitas, Fernanda

; Loureiro, Edvaldo Carlos Brito

; Vicente, Ana Carolina Paulo

Memórias do Instituto Oswaldo Cruz

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Mar 2010, Volume 105 Nº 2 Páginas 229 - 232

Resumo: En | Texto: En | PDF: En

This study identified and characterised class 1 and 2 integrons in clinical and environmental Vibrio cholerae O1 and non-O1/non-O139 strains isolated from the Brazilian Amazon. The aadA2 and aadA7 gene cassettes were found in class 1 integrons in two genotypes of environmental V. cholerae non-O1/non-O139. Empty integrons were found in strains from the Brazilian cholera epidemic. A class 2 integron was detected in one strain from the V. cholerae Amazonia lineage harbouring sat1 and aadA1 genes. All isolates were resistant to aminoglycosides, indicating aadA functionality. These findings suggest that environmental bacteria act as cassette reservoirs that favour the emergence of resistant pathogens.

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