Zoonotic Giardia duodenalis assemblage A in northern sloth from Brazilian Amazon

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.

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

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.

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

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.

Exploring tRNA gene cluster in archaea

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.

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

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.

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

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.

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

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.

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

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 1A complete genome from a fatal case in Brazil

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.

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

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.

Prevalência da infecção pelo HTLV-1, em remanescentes de quilombos no Brasil Central / Prevalence of infection due to HTLV-1 in remnant quilombos in Central Brazil

O presente estudo teve como objetivo estimar a prevalência da infecção pelo HTLV-1 em remanescentes de comunidades de população negra, os quilombos no Brasil Central. 1.837 indivíduos foram avaliados, sendo nove soropositivos para HTLV-1/2 por ELISA. Todos esses foram positivos para HTLV-1 por Western blot e/ou PCR, resultando em uma prevalência de 0,5 por cento (IC 95 por cento: 0,2-1,0). A idade dos indivíduos infectados variou de 11 a 82 anos, sendo a maioria do sexo feminino. Quanto às características de risco, história de aleitamento materno, transfusão de sangue, múltiplos parceiros sexuais e doenças sexualmente transmissíveis foram relatadas por esses indivíduos. Os achados deste estudo evidenciam a importância da identificação dos indivíduos infectados pelo HTLV-1 na estratégia de controle e prevenção dessa infecção em remanescentes de quilombos.

This study aimed to determine the prevalence of HTLV-1 infection among remnant black quilombo communities in Central Brazil. A total of 1,837 individuals were evaluated, among whom nine were HTLV-1/2 seropositive according to ELISA. All of them were positive for HTLV-1 by means of Western blot and/or PCR, thus resulting in a prevalence of 0.5 percent (95 percent CI: 0.2-1.0). The HTLV-1 infected individuals ranged in age from 11 to 82 years. The majority of them were females. Regarding risk characteristics, histories of breastfeeding, blood transfusion, multiple sexual partners and sexually transmitted diseases were reported by these individuals. The findings from this study indicate the importance of identifying HTLV-1 infected individuals, as a strategy for infection control and prevention in these remnant quilombos.

Gastric lesions associated with the presence of Anisakis spp. Dujardin, 1845 (Nematoda: Anisakidae) in Cetaceans stranded on the coast of Ceara, Brazil / Lesões gástricas associadas à presença de Anisakis spp. Dujardin, 1845 (Nematoda: Anisakidae) em Cetáceos encalhados no litoral do Ceará, Brasil

The gastric compartments of ten cetaceans stranded on the coast of Ceará State, Northeast Brazil were analyzed in this study. Gastric Anisakis spp. was diagnosed in all individuals involved in this study. Parasites and tissue samples were collected during necropsy. The presence of Anisakis parasites showed similar distribution across the three gastric compartments and the majority was free within the gastric lumen. Macroscopically, the lesions were predominantly characterized by the presence of ulcers (60 percent, 6/10) within the gastric mucosa, occasionally associated with edema and hemorrhage (30 percent, 3/10). Eight cetaceans (8/10 - 80 percent) presented gastric microscopic alterations and in 75 percent (6/8) of these animals, chronic lymphoplasmocytic gastritis was observed with varying degrees of distribution and severity. Additionally, eosinophilic and granulomatous inflammation with giant cells, hemosiderosis, fibrosis and areas of necrosis were associated with location of parasites within the gastric mucosa. In this study, it was shown that the majority of cetaceans with the presence of Anisakis parasites presented macro and microscopic gastric alterations. These nematodes are probably associated with the development of these alterations; however, more pathological approaches are still required.

Neste estudo, foram analisados os compartimentos gástricos de dez cetáceos encalhados na costa do Ceará, região nordeste do Brasil. Parasitos do gênero Anisakis foram diagnosticados em todos os indivíduos estudados. As amostras parasitárias e teciduais foram coletadas durante o procedimento de necropsia. A presença de Anisakis demonstrou distribuição similar nos três compartimentos gástricos, estando a maior parte dos parasitos livre na mucosa gástrica. Macroscopicamente, as lesões se caracterizaram principalmente pela presença de úlceras (60 por cento, 6/10) gástricas, associadas ocasionalmente a edema e hemorragia (30 por cento, 3/10). Oito cetáceos (8/10 - 80 por cento) apresentaram alterações gástricas microscópicas e em 75 por cento (6/8) destes animais, foi observada uma gastrite crônica linfoplasmocitária com vários graus de distribuição e severidade. Foram constatados ainda, focos de inflamação granulomatosa com a presença de eosinófilos, células gigantes e a formação de hemossiderose, fibrose e de necrose em torno dos parasitos. Neste estudo, a maioria dos cetáceos com a presença de parasitos do gênero Anisakis apresentaram alterações gástricas macro e microscópicas. Estes nematóides estão provavelmente associados ao desenvolvimento destas alterações, entretanto, mais estudos são ainda necessários.

Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times

Paleoparasitological studies using microscopy showed that Ascarisand Trichuris trichiura are the human intestinal parasites most found in archaeological sites. However, in pre-Columbian South American archaeological sites, Ascaris is rare. In this work we standardized a molecular methodology for Ascaris diagnosis directly from ancient DNA retrieved from coprolites. Using cythochrome b gene (142 bp) target, ancient DNA sequences were retrieved from South American samples, negative by microscopy. Moreover, the methodology applied was sensitive enough to detect ancient DNA extracted from 30 Ascaris eggs from an European coprolite. These results revealed a new scenery for the paleodistribution of Ascaris in South America.

Evolutionary control of infectious disease: prospects for vectorborne and waterborne pathogens

Evolutionary theory may contribute to practical solutions for control of disease by identifying interventions that may cause pathogens to evolve to reduce virulence. Theory predicts, for example, that pathogens transmitted by water or arthropod vectors should evolve to relatively high levels of virulence because such pathogens can gain the evolutionary benefits of relatively high levels of host exploitation while paying little price from host illness. The entrance of Vibrio cholerae into South America in 1991 has generated a natural experiment that allows testing of this idea by determining whether geographic and temporal variations in toxigenicity correspond to variation in the potencial for waterborne transmission. Preliminary studies show such correspondences: toxigenicity is negatively associated with access to uncontaminated water in Brazil; and in Chile, where the potential for waterborne transmission is particularly low, toxigenicity of strains declined between 1991 and 1998. In theory vector-proofing of houses should be similarly associated with benignity of vectorborne pathogens, such as the agents of dengue, malaria, and Chagas'disease. These preliminary studies draw attention to the need for definitive prospective experiments to determine whether interventions such as provisioning of uncontaminated water and vector -proofing of houses cause evolutionary reductions in virulence.

The Amazonia variant of Vibrio cholerae: molecular identification and study of virulence genes

The pathogenic O1 Amazonia variant of Vibrio cholerae has been shown previously to have a cytotoxin acting on cultured Vero and Y-1 cells, and to lack important virulence factors such as the cholera toxin (Coelho et al. 1995a). This study extends the molecular analysis of the Amazonia strains, detecting the presence to the toxR gene, with a very similar sequence to that of the El Tor and classical biotypes. The outer membrane proteins are analysed, detecting a variation among the group of Amazonia strains, with three different patterns found. As a by-product of this work a polymerase chain reation fragment was sequenced, reading part of the sequence of the Lon protease of the Amazonia strains. The gene was not previously described in V. cholerae, but its sequences is present in the TIGR database specific for this species.

Coleformes fecais em águas de esgoto: II- transferência de marcadores e presença de plasmidial / Fecal coliforms in sewage treatment: II. Genetic tranfer and plasmids

Investigou-se a transferência de marcadores genéticos e a presença de DNA plasmidial em 240 culturas de Escherichia coli originárias de água de esgoto (afluente e fluentes) da Estaçäo de Tratamento da Ilha do Governador, na cidade do Rio de Janeiro, RJ. Experimentos de conjugaçäo com E. coli K 12 permitiram o isolamento de transconjugantes com resistência a antibióticos (Su, Sm, Tc, Cm e Ap); a metais pesados (Cu, Hg e Zn) e fatores colicinogênicos (Col Ia, Ib e V) principalmente para os coliformes isolados nos setores terminais da estaçäo de tratamento. A distribuiçäo de plasmídeos foi prevalente nas culturas de E. coli advindas dos efluentes, com percentuais superiores a 65