Investigation of antimicrobial susceptibility and genetic diversity among Staphylococcus pseudintermedius isolated from dogs in Rio de Janeiro.

Staphylococcus pseudintermedius is an opportunistic pathogen causing a variety of infections that are difficult to treat, especially because of the development of antimicrobial resistance. It has a clonal distribution around the world. To have a better understanding of the MRSP population, we search the presence of MRSP in colonized or infected dogs. Samples from 99 dogs with infections and 35 from asymptomatic dogs were collected. Isolates were identified by mass spectrometry and Multiplex-PCR. The mecA gene was confirmed by conventional PCR. MRSP strains were analyzed by whole-genome sequencing. 75 S. pseudintermedius were identified, most from infection cases. The species were isolated from 70 out of the 135 dogs. Penicillin and Trimethoprim/Sulfamethoxazole presented higher resistance rates. Forty-seven strains were classified as multi-drug resistant (MDR), and were more isolated from dogs with infection (P < 0.05). Eighteen samples were classified as MRSP, representing 24.0% of the population. Six of 16 MRSP sequenced samples belonged to the world spread clone ST71; others belonged to unknown clones. Most samples carried the SCCmec type IIIA. Twenty-one different genetic resistance determinants were found among MRPS strains. MRSP is circulating among infected and colonized dogs in Rio de Janeiro, Brazil.

A molecular and morphological study of Ascaris suum in a human-pig contact scenario in northeastern Brazil.

The aim of the present study was to assess morphologic and genetic data on ascariasis in swine (Sus scrofa domesticus) and humans in low-resource rural and periurban communities in the state of Piauí, Brazil. Our cross-sectional survey included 100 fecal samples obtained from swine and 682 samples from humans. Fifteen pigs were necropsied. Human and porcine fecal samples were examined to identify Ascaris eggs. Parasites obtained in the swine necropsies were studied using scanning electron microscopy (SEM), and the mitochondrial gene encoding the cytochrome oxidase 1 (cox1) enzyme was partially amplified and sequenced for molecular taxonomy and phylogenetic analyses. The overall prevalence of Ascaris eggs in the swine fecal samples was 16/100 (16%). No Ascaris eggs were identified in the human fecal samples. SEM of six worms recovered from pigs demonstrated morphological characteristics of A. suum. Cox1 sequences were compatible with A. suum reference sequences. Original and reference (GenBank) nucleotide sequences were organized into clusters that did not segregate the parasites by host species or and region. The largest haplogroups were dominated by haplotypes H01, H02 and H31. In the communities studied, there was no epidemiological evidence of the zoonotic transmission of ascariasis at the human-swine interface.

The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil.

The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic increases the viscosity of clinical samples collected for diagnosis. Coinciding with the arrival of the Omicron variant, we observed a failure in control gene expression in our laboratory. In this report, we have optimized a rapid nucleic acid extraction step to restore gene expression and detect the presence of the SARS-CoV-2 virus. We reevaluated 3000 samples, compared variant types occurring in different time periods, and confirmed that the presence of the Omicron variant was responsible for changes observed in the characteristics of these clinical samples. For samples with large amounts of mucus, such as those containing the Omicron variant, a modification to the nucleic acid extraction step was sufficient to restore the quality of RT-qPCR results.

A molecular and morphological study of Ascaris suum in a human-pig contact scenario in northeastern Brazil / Estudo molecular e morfológico de Ascaris suum em um cenário de contato entre suínos e humanos no nordeste brasileiro

The aim of the present study was to assess morphologic and genetic data on ascariasis in swine (Sus scrofa domesticus) and humans in low-resource rural and periurban communities in the state of Piauí, Brazil. Our cross-sectional survey included 100 fecal samples obtained from swine and 682 samples from humans. Fifteen pigs were necropsied. Human and porcine fecal samples were examined to identify Ascaris eggs. Parasites obtained in the swine necropsies were studied using scanning electron microscopy (SEM), and the mitochondrial gene encoding the cytochrome oxidase 1 (cox1) enzyme was partially amplified and sequenced for molecular taxonomy and phylogenetic analyses. The overall prevalence of Ascaris eggs in the swine fecal samples was 16/100 (16%). No Ascaris eggs were identified in the human fecal samples. SEM of six worms recovered from pigs demonstrated morphological characteristics of A. suum. Cox1 sequences were compatible with A. suum reference sequences. Original and reference (GenBank) nucleotide sequences were organized into clusters that did not segregate the parasites by host species or and region. The largest haplogroups were dominated by haplotypes H01, H02 and H31. In the communities studied, there was no epidemiological evidence of the zoonotic transmission of ascariasis at the human-swine interface.(AU)

O presente estudo teve como objetivo acessar dados morfológicos e genéticos sobre a ascaridíase em suínos (Sus scrofa domesticus) e humanos, em comunidades rurais e periurbanas no estado do Piauí. O estudo transversal incluiu 100 amostras fecais de suínos e 682 amostras obtidas de humanos. Quinze suínos foram necropsiados. Amostras fecais suínas e humanas foram examinadas para detecção de ovos de Ascaris. Os parasitas adultos, obtidos nas necropsias, foram estudados através de microscopia eletrônica de varredura (MEV), e o gene mitocondrial codificante da enzima citocromo oxidase 1 (cox1) foi parcialmente amplificado e sequenciado para análises filogenéticas e de taxonomia molecular. A prevalência de Ascaris em amostras fecais de suínos foi 16/100 (16%), não sendo identificado nenhum caso de infecção por este parasita em humanos. A análise por MEV de parasitas recuperados de suínos demonstrou características morfológicas de Ascaris suum. As sequências nucleotídicas de cox1 foram compatíveis com A. suum. As sequências originais e de referência (obtidas no GeneBank) foram organizadas em clusters que não segregaram os parasitas por hospedeiro ou região geográfica. Os maiores haplogrupos foram dominados pelos haplótipos H01, H02 e H31. Nas comunidades estudadas, não foi evidenciada transmissão zoonótica de A. suum na interface suíno-humana.(AU)

Cytochrome c oxidase subunit 1 gene reveals species composition and phylogenetic relationships of Oesophagostomum spp. infecting pigs in northeastern Brazil.

Helminths of the genus Oesophagostomum cause enteric diseases and affect domestic animals such as pigs. The aim of this study was to explore the species composition and genetic diversity of Oesophagostomum spp. infecting pigs in close contact with humans in the state of Piauí, Brazil. Eighty-seven fecal samples were collected for parasitological tests and molecular analysis. Through microscopy, the overall positivity rate for strongyliform eggs was 81.6% among the pigs studied. Forty-two strongyliform egg samples were subjected to PCR and six cox1 sequences (637 bp) were identified for the genus Oesophagostomum. The sequences were identified as Oesophagostomum dentatum, O. quadrispinulatum and O. columbianum. In the phylogenetic tree and haplotype network, 89 sequences were separated into seven clusters, which also included reference sequences from GenBank. Oesophagostomum dentatum and O. quadrispinulatum were seen to be closely related species and formed a monophyletic group related to O. aculeatum. Oesophagostomum columbianum showed similarity with sequences from parasites infecting small ruminants and the clade was positioned closer to O. bifurcum. High interspecific diversity was found and intraspecific diversity varied according to the species. This was the first study to characterize Oesophagostomum DNA sequences obtained from pigs in Brazil.

Epidemiology, species composition and genetic diversity of tetra- and octonucleated Entamoeba spp. in different Brazilian biomes.

BACKGROUND: Entamoeba species harbored by humans have different degrees of pathogenicity. The present study explores the intra- and interspecific diversity, phylogenetic relationships, prevalence and distribution of tetra- and octonucleated cyst-producing Entamoeba in different Brazilian regions. METHODS: Cross-sectional studies were performed to collect fecal samples (n = 1728) and sociodemographic data in communities located in four Brazilian biomes: Atlantic Forest, Caatinga, Cerrado, and Amazon. Fecal samples were subjected to molecular analysis by partial small subunit ribosomal DNA sequencing (SSU rDNA) and phylogenetic analysis. RESULTS: Light microscopy analysis revealed that tetranucleated cysts were found in all the studied biomes. The highest positivity rates were observed in the age group 6-10 years (23.21%). For octonucleated cysts, positivity rates ranged from 1 to 55.1%. Sixty SSU rDNA Entamoeba sequences were obtained, and four different species were identified: the octonucleated E. coli, and the tetranucleated E. histolytica, E. dispar, and E. hartmanni. Novel haplotypes (n = 32) were characterized; however, new ribosomal lineages were not identified. The Entamoeba coli ST1 subtype predominated in Atlantic Forest and Caatinga, and the ST2 subtype was predominant in the Amazon biome. E. histolytica was detected only in the Amazon biome. In phylogenetic trees, sequences were grouped in two groups, the first containing uni- and tetranucleated and the second containing uni- and octonucleated cyst-producing Entamoeba species. Molecular diversity indexes revealed a high interspecific diversity for tetra- and octonucleated Entamoeba spp. (H ± SD = 0.9625 ± 0.0126). The intraspecific diversity varied according to species or subtype: E. dispar and E. histolytica showed lower diversity than E. coli subtypes ST1 and ST2 and E. hartmanni. CONCLUSIONS: Tetra- and octonucleated cyst-producing Entamoeba are endemic in the studied communities; E. histolytica was found in a low proportion and only in the Amazon biome. With regard to E. coli, subtype ST2 was predominant in the Amazon biome. The molecular epidemiology of Entamoeba spp. is a field to be further explored and provides information with important implications for public health.

Adjusting RT-qPCR conditions to avoid unspecific amplification in SARS-CoV-2 diagnosis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 and quickly spread around the world, forcing global health authorities to develop protocols for its diagnosis. Here we report dimer formation in the N2 primers-probe set (CDC 2019-nCoV Real-Time RT-PCR) used in the diagnostic routine, and propose alternatives to reduce dimerization events. Late unspecific amplifications were visualized in 56.4% of negative samples and 57.1% of no-template control, but not in positive samples or positive control. In silico analysis and gel electrophoresis confirmed the dimer formation. The RT-qPCR parameters were optimized and the late unspecific amplifications decreased to 11.5% in negative samples and no-template control. The adjustment of PCR parameters was essential to reduce the risk of false-positives results and to avoid inclusive results requiring repeat testing, which increases the costs and generates delays in results or even unnecessary requests for new samples.

Mitochondrial DNA reveals species composition and phylogenetic relationships of hookworms in northeastern Brazil.

Hookworm infection persists focally in rural communities in Brazil. In this study, we analyze the mitochondrial nucleotide sequences obtained from hookworms infecting humans in order to characterize species composition and assess their genetic diversity and phylogenetic relationships. Field expeditions and cross-sectional surveys were carried out in three Brazilian municipalities from 2013 to 2017: Nossa Senhora de Nazaré (n = 605) and Teresina (n = 297), in the state of Piauí, and Russas (n = 213) in the State of Ceará. Parasitological methods were used to evaluate fecal samples. Hookworm-positive samples had a partial mtDNA cox1 amplified and sequenced. Maximum-likelihood and Bayesian analysis demonstrated two strongly-supported clades, including Group A, corresponding to Necator americanus, and Groups B and C, corresponding to Necator sp. Group A was divided into three main clusters: A1 grouped with Asian sequences, A2 grouped with African sequences, and A3 had only Asian sequences. Group B was closely related to Necator sp., showing a sequence similarity of 98%-99% with African samples circulating zoonotically among humans and non-human primates. Twenty three N. americanus haplotypes were identified. N. americanus Median-Joining network revealed three distinct groups, designated again as A1, A2, and A3. Group A1 presented a star-like shape, with one dominant haplotype. The molecular dating suggested that the two clades dividing N. americanus and Necator sp. began to diverge during the middle Pleistocene. The most recent common ancestor among N. americanus groups was dated to the late Pleistocene. Hookworms circulating in the studied communities are structured in well-defined subpopulations presenting both Asian and African genetic backgrounds. This reveals a double origin for hookworms in northeastern Brazil and opens up new possibilities in phylogeographic, evolutionary, and molecular epidemiological studies in regions where hookworms persists focally, despite control efforts. The presence of potentially zoonotic species and the specific identification of Necator sp. should be further investigated.

Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara.

Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.

Characterization of the clonal subpopulation Fiocruz L1-130 of Leptospira interrogans in rats and dogs from Brazil.

PURPOSE: Leptospira interrogans serogroup Icterohaemorrhagiae strains have been described as causing disease in both humans and animals and as being present worldwide. Icterohaemorrhagiae and Copenhageni serovars are known to cause severe disease in their hosts, and zoonotic outbreaks have been described. The genetic similarity among the strains of these serovars is known. However, it has not yet been demonstrated whether major clonal subpopulation in humans, strain Fiocruz L1-130-like, can circulate among other hosts. METHODOLOGY: We performed genetic characterization of Brazilian serogroup Icterohaemorrhagiae strains of dog and rat origin by secY sequencing, variable-number tandem-repeat, multilocus sequence type and multi-spacer typing analysis. RESULTS: The strains were found to be identical among themselves and to strain Fiocruz L1-130. We suggest that the major strain of L. interrogans serogroup Icterohaemorrhagiae, Fiocruz L1-130, is widely distributed in Brazil in different hosts with substantial zoonotic potential. CONCLUSION: Understanding the circulation of strain Fiocruz L1-130 is important for the implementation of appropriate control measures. Its circulation highlights the need to treat leptospirosis caused by L. interrogans serogroup Icterohaemorrhagiae as a zoonosis that acts in the human-animal-environment interface, as per the One Health approach.

Focal persistence of soil-transmitted helminthiases in impoverished areas in the State of Piaui, Northeastern Brazil.

This study aims to describe the prevalence, distribution, and factors associated with soil-transmitted helminthiases (STHs) in rural localities in Piaui, Brazil. Two cross-sectional surveys (n=605 subjects; 172 families) were carried out in order to obtain socio-demographic, anthropometric, spatial and parasitological data. Parasites were evaluated using Kato-Katz and centrifugal sedimentation techniques. Eggs were measured to assess infection with zoonotic Strongylida parasites. Kernel maps were constructed with Q-GIS. The prevalence of hookworm infection was 12.4% (75/605). Other helminthes found were Trichuris trichiura (n=1; 0.2%) and Hymenolepis nana (n=1; 0.2%). The hookworm positivity rate was significantly lower among subjects who had used albendazole when compared with individuals who had not used anthelmintics or had used antiprotozoal drugs in the last 6 months (8/134 [6.0%] vs. 59/415 [14.2%]; p=0.009). A total of 39/172 (22.7%) families had at least one infected member. The association between the number of dwellers and hookworm positivity in the family was present in a logistic regression multivariate model. Assessment of worm burdens showed 92.2% light, 6.2% moderate, and 1.6% heavy infections. Hookworm eggs (n=34) measured 57.2 - 75.4 µm in length and 36.4 - 44.2 µm in width (mean ± SD = 65.86 ± 4.66 µm L and 40.05 ± 1.99 µm W), commensurate with human hookworms. Hotspots suggest that transmission has a focal pattern. STHs persist in impoverished rural areas in Northeastern Brazil where currently available control strategies (mass drug administration) apparently do not allow the elimination of the infection.

Genetic diversity of Giardia duodenalis circulating in three Brazilian biomes.

Giardia duodenalis has a wide genetic variety, and its characterization helps in the understanding of its transmission dynamics and in the development control strategies. This study aimed to assess the genetic diversity of G. duodenalis obtained in different Brazilian biomes and estimate their phylogenetic relationships. Three surveys including 944 participants were carried out in the municipalities of Russas (RSS, Caatinga semiarid biome), Santa Isabel do Rio Negro (SIRN, Amazon rainforest biome) and Nossa Senhora de Nazaré (NSN, Cerrado-Caatinga transition biome). G. duodenalis-positive fecal samples were submitted to amplification of gene fragments encoding ß-giardin (ßG, N = 71), glutamate dehydrogenase (GDH, N = 42), and triosephosphate isomerase (TPI, N = 27). Overall detection rates of assemblage A in G. duodenalis-positive samples through ßG, GDH and TPI were 22/71 (31%), 13/42 (31%), and 13/27 (48.1%), respectively. Concerning assemblage B, rates with distinct genetic markers were 49/71 (69%), 29/42 (69%), and 14/27 (51.9%), respectively. In the Amazon, assemblage B was more prevalent (77.8%, 71.8% and 65% through ßG, GDH and TPI, respectively), while in the Cerrado biome assemblage A predominated (50%, 66.6%, and 85.7%, through ßG, GDH and TPI, respectively). In Caatinga biome assemblage A also predominated (71.4%, through ßG). Thirty new sub-assemblages are described for assemblage B (24 ßG and six TPI), as well as three new sub-assemblages are described for assemblage A (one GDH and 2 TPI). Higher genetic diversity of assemblage B in the Amazon may be related to demographic concentration leading to a more complex transmission network within a poorer sanitation background. The high genetic divergence between assemblages A and B (5.5-6.3%) support the proposal of taxon separation in distinct species.

Occurrence of uterine carriers for Leptospira interrogans on slaughtered cows.

Reproductive tract is an important site of infection for chronic leptospirosis and cooperate in pathogenesis of reproductive failure, leading to economic losses. Since serology techniques cannot detect chronic carriers, the molecular analysis of clinical samples is an alternative to detect these animals on livestock. The aim of the present study was to perform a retrospective study in order to detect leptospiral uterine carriers in slaughtered cows. Tissue samples were collected from 50 post-pubertal, nonpregnant cows. These samples were fixed in 10% buffered formalin, paraffin-embedded and stored. PCR targeting lipL32 gene and molecular characterization by secY sequence was performed. Leptospiral DNA was identified in 18% (9/50) examined blocks. Two sequences were characterized as L. interrogans. These findings suggest that the presence of infectious leptospires in uterus is associated with the physiopathogenesis of the reproductive failure.

Status of benzimidazole resistance in intestinal nematode populations of livestock in Brazil: a systematic review.

BACKGROUND: Benzimidazoles (BZ) are a class of drugs widely used in veterinary and human medicine, creating a great selection pressure and the emergence of BZ resistance. We conducted a systematic review to assess the status of resistance and/or effectiveness reduction of BZ drugs in animal nematodes in Brazil, and make information accessible to the scientific community, as many studies are published in Portuguese. PubMed, SciELO Brasil, LILACS/Bireme, GNTD database, and Google Scholar were searched with no language restrictions. RESULTS: A total of 40 studies met our eligibility criteria (from the year 1989 forward). Sheep was the host most frequently analysed, and albendazole was the most frequently drug studied. The majority of studies (75.7%) showed that BZ drugs are insufficiently active (FECRT <80%) against nematode parasites of livestock. The mean FECRT for fenbendazole, thiabendazole, albendazole, mebendazole, oxfendazole, and ricobendazole were 71.8%, 71.8%, 58.6%, 53.9%, 46.9%, and 41.5%, respectively. It was observed through linear regression that FECRT is significantly reduced over time between 2007 and 2014 (R = -0.653 p = 0.021) for the treatment of cattle with BZ, suggesting progressive loss of effectiveness and increased resistance for these hosts. CONCLUSIONS: The scenario of BZ resistance in nematode populations in Brazil is not favourable. Given the high cost of drug discovery and development, it is urgent to implement control measures and to monitor the effectiveness/resistance to nematodes in livestock in Brazil.

Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations.

The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status.

Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains.

Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples.

Análise paleogenética da tuberculose e perfil paleoparasitológico de populações do período histórico do Rio de Janeiro / Paleogenetic analysis of tuberculosis and paleoparasitological profile of populations of the historical period of Rio de Janeiro

A cidade do Rio de Janeiro foi o principal centro comercial e capital do país durante o período colonial brasileiro. A chegada de centenas de milhares de colonizadores europeus e escravos africanos à cidade desencadeou um crescimento urbano e populacional desenfreado. O objetivo do trabalho é avaliar o cenário paleoepidemiológico da tuberculose na população do Rio de Janeiro entre os séculos XVII e XIX através da análise paleogenética do complexo Mycobacteriumtuberculosis (MTC), bem como da análise do perfil paleoparasitológico e da ancestralidade humana. A infecção por bactérias do MTC foi identificada na população enterrada nos sítios arqueológicos analisados. A frequência de infecção observada foi de 53 por cento e 25 por cento em cemitérios europeu e africano, respectivamente. Os parasitos Trichuris trichiura, Ascaris sp., Taenia sp. e Enterobius vermicularis foram detectados através de técnicas paleoparasitológicas e paleoparasitológicas moleculares. O nematoide T. trichiura foi o mais comumente encontrado nos sítios arqueológicos estudados, demonstrando uma frequência de infecção de até 70 por cento.Estes dois últimos representam o registro mais antigo dessas infecções no país. A ancestralidade humana revelou uma proeminente contribuição da população europeia na dispersão da tuberculose na cidade, e confirmou a presença da infecçãoem escravos africanos recém – chegados ao país. O cenário de infecção portuberculose na cidade, assim como por parasitos intestinais, é discutido...

The city of Rio de Janeiro was the main commercial center and capital of thecountry during the Brazilian colonial period. The arrival of hundreds of thousands ofEuropean settlers and African slaves to the city triggered unbridled population andurban growth. This study aims to evaluate the paleoepidemiologic scenario oftuberculosis in Rio de Janeiro population between the seventeenth and nineteenthcenturies through paleogenetic analysis of Mycobacterium tuberculosis complex(MTC), as well as examining the paleoparasitologic profile and human ancestry. TheTB infection was identified in the individuals buried in archaeological sites. Thefrequency of infection was observed in 53 percent and 25 percent in European and Africancemeteries, respectively. The parasite Trichuris trichiura, Ascaris sp., Taenia sp. andEnterobius vermicularis were detected by paleoparasitolgical and moleculartechniques. The latter two represent the earliest record of these infections in thecountry. The nematode T. trichiura was the most commonly found in archaeologicalsites studied, showing an infection rate of up to 70 percent. The human ancestry revealed aprominent contribution of the European population in the dispersion of tuberculosis inthe city, and confirmed the presence of infection in African slaves. The scenario ofTB infection in the city, as well as intestinal parasites, is discussed...

Paleoparasitological analysis of human remains from a European cemetery of the 17th-19th century in Rio de Janeiro, Brazil.

Most paleoparasitological studies based on archeological sites in the New World are from pre-Columbian times. However, understanding of the introduction and spread of parasites with the arrival of European settlers and African slaves in America remains a topic for investigation. This study evaluated the presence of intestinal parasites in human remains from an archeological site of the colonial period, and compared the sensitivity of three parasitological techniques for paleoparasitological study. Samples were collected from the archeological site Nossa Senhora do Carmo Church, Rio de Janeiro, Brazil. Paleoparasitological examination revealed intestinal helminths in 2/17 (11.8%) individuals. Trichuris trichiura and Ascaris sp. eggs were found. The spontaneous sedimentation technique showed a greater numerical recovery of parasites, while the flotation techniques were superior in retrieving more parasite types. The study demonstrated that combining the three techniques improves the recovery of parasites in terms of number and diversity. Similar diversity of parasites to that of a previous historical archeological site suggests that the distribution of intestinal parasites was widespread in Rio de Janeiro, regardless of social status.

Paleoparasitological results from XVIII century human remains from Rio de Janeiro, Brazil.

Paleoparasitological studies of the Brazilian colonial period are scarce. A paleoparasitological analysis was performed on human remains from the archeological site Praça XV Cemetery in Rio de Janeiro, dating from the early 18th to 19th Centuries. The samples were obtained from the Institute of the Brazilian Archaeology collection, and showed evidence of washing and brushing. Sediments were extracted from sacral foramina by scraping. Sediments from skulls were used as negative paleoparasitological controls. Spontaneous sedimentation method was performed prior to microscopic analysis. The results revealed that 8 of 10 individuals were infected with intestinal helminths and/or protozoa. Eggs of the nematodes Trichuris sp. and Ascaris sp. as well as a single taeniid egg were found. Protozoa cysts suggestive of Entamoeba sp. were also observed. Trichuris sp. was the most frequent and abundant parasite, found in 70% of individuals (26 eggs). The study showed the importance of analysis of sediment from human remains preserved in museum or scientific collections, even those subjected to a curating procedure. The levels of infection revealed here should be considered underestimations. This is the first paleoparasitological study from Rio de Janeiro city for the Brazilian colonial period and the first report of human Taenia sp. in the New World.

Mycobacterium tuberculosis complex detection in human remains: tuberculosis spread since the 17th century in Rio de Janeiro, Brazil.

Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World.