São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.
Carbapenem resistance in Acinetobacter baumannii is a public health issue globally, mainly due to the production of carbapenem hydrolyzing class D ß-lactamases (CHDLs). In Brazil, OXA-23 and OXA-143 CHDLs have been prevalent in A. baumannii from clinical settings, with some OXA-23 reports in the environmental samples, whereas OXA-72 has begun to be increasingly reported. This study aims to perform the genomic and microbiological characterization of carbapenem-resistant A. baumannii isolates recovered from migratory birds and captive birds inhabiting a lake within a Brazilian Zoo. Four hundred and eighty-one gram-negative bacilli were recovered from choanal and cloacal swabs obtained from 50 migratory birds and 37 captive birds present at the zoo’s lake between July and August of 2012. Among all GNB, nine OXA-72-producing A. baumannii were detected from the microbiota of four migratory and five captive aquatic birds. The OXA-72-producing A. baumannii isolates were submitted to antimicrobial susceptibility test and PFGE, exhibiting a multidrug-resistant profile and clonal relatedness with OXA-72-positive human isolates circulating for eighteen years in a hospital setting. MLST, plasmid analysis and whole-genome sequencing revealed which all carbapenem-resistant A. baumannii from bird and human hosts belonged to clonal complex 79, and harboured a small plasmid (~16.6-kb in size), named pAC1-BRL, which carried blaOXA-72 gene, macrolide resistance genes msrE and mphE, and the toxinantitoxin system AbkAB. To determine the impact of pAC1-BRL acquisition in the the capacity of a microorganism to survive in a competitive environment (in the following called fitness), the laboratory strain A. baumannii ATCC 19606 was used in the fitness experiments and suggested an increase of its relative fitness after the pAC1-BRL acquisition. In summary, the detection of OXA-72-producing A. baumannii strains belonging to CC79 in aquatic birds is a piece of epidemiological evidence demonstrating that dissemination of high-risk bacteria is extending beyond the hospital.
Cães e seres humanos compartilham os mesmos caminhos por pelo menos 14-100 mil anos e, atualmente, o cão doméstico (Canis lupus familiaris) e a espécie de carnívoro mais abundante e difundida do planeta, está presente em todos os continentes, exceto Antártida. Como consequência, cães representam um desafio global tanto para conservação da biodiversidade como para saúde pública, e esta problemática e ainda mais grave entre cães mantidos soltos e cães ferais em áreas rurais. No entanto, apesar da abrangência e da gravidade do problema, tanto a intensidade dos impactos causados por cães domésticos, como a eficácia de estratégias de manejo, ainda são incertas. Isso ocorre, pois estudos raramente quantificam aspectos básicos da ecologia dos cães. Aspectos que são cruciais tanto para compreensão dos processos de invasão biológica, como para elaboração de modelos epidemiológicos de dispersão de doenças. E nesta lacuna de conhecimento que buscamos nos aprofundar na presente tese de doutorado. Utilizando como modelo a população de cães de um agroecossistema de Cerrado no Brasil Central, realizamos um estudo longitudinal buscando elucidar como e a estrutura e a dinâmica populacional dos cães; de que forma eles utilizam o espaço e que fatores determinam seus caminhos; e como a população e o movimento dos cães podem ser modulados pelas pessoas. Com os estudos aqui apresentados, trouxemos avanços metodológicos, e reflexões de manejo, que contribuirão de forma substancial para aprofundar nossa compreensão de uma problemática comum a todas as partes do planeta. Vimos que, mesmo em uma população de tamanho estável, a estrutura populacional pode ser extremamente dinâmica, e este fluxo de indivíduos e regido essencialmente pelas pessoas. Observamos também que os cães têm um uso considerável da paisagem, ainda que eles permaneçam a maior parte do tempo ao redor de suas casas. Além disso, constatamos que os padrões de uso do espaço variam substancialmente a depender das características do indivíduo, do manejo e do papel social do cão na comunidade. Por fim, propomos estratégias de manejo que possam simultaneamente mitigar os impactos causados por cães e aprimorar o desempenho de suas funções na comunidade.
The increase of contact between natural and rural areas is prominent in Brazil, due to agricultural activities and concern with the environmental conservation. In this context, domestic animals, wild fauna and humans are exposed to mutual exchange of parasites, microorganisms and diseases. We studied tick parasitism of wild carnivores and domestic dogs, and the environmental of questing ticks, in extensive cattle ranch areas intermingled with natural vegetation, and in a natural reserve, both in a region of Cerrado biome, Midwestern Brazil. From 2008 to 2015, we inspected 119 wild carnivores from nine species, and collected six tick species (Amblyomma sculptum, Amblyomma ovale, Amblyomma dubitatum, Amblyomma tigrinum, Dermacentor nitens and Rhipicephalus microplus). The most numerous and infested hosts were Cerdocyon thous, Lycalopex vetulus, Chrysocyon brachyurus, Puma concolor and Conepatus amazonicus. From 139 domestic dogs, we collected A. sculptum, Rhipicephalus sanguineus and R. microplus. From vegetation, samplings resulted in A. sculptum, A. dubitatum, A. ovale, Amblyomma rotundatum and R. microplus, with dominance of A. sculptum. Domestics and wild animals presented high overlapping of infestations by A. sculptum, a generalist and anthropophilic tick species. This tick is the most important vector of the Brazilian spotted fever, a lethal human disease. This fact elicits attention and requires efforts to monitor the presence of pathogens vectored by ticks circulating in this type of agroecosystem, including in other regions of the Brazil, because the most of the natural vegetation remaining have been increasingly immersed in pastures and agricultural matrix.
Trypanosoma cruzi and Leishmania spp. are parasites that infect multiple hosts including canids, considered bioaccumulators of parasites. Deforestation in the Cerrado biome has resulted in the exposure of wild canids to anthropized areas, where they may establish ecological and epidemiological relationships with domestic dogs. We evaluated the infection by trypanosomatids in canids from a Cerrado agroecosystem between 2013 and 2017. Samples of wild canids (blood, bone marrow and skin) and dogs (blood) were collected for parasitological, serological and molecular diagnosis. A total of 414 samples from wild (n = 131) and domestic (n = 283) canids were collected, including recaptures. We obtained five positive hemocultures from Lycalopex vetulus (n = 2), Cerdocyon thous (n = 1) and dogs (n = 2), all characterized as T. cruzi TcIII/V (18S rDNA) and TcIII/V/VI (gGAPDH); one positive skin fragment for Leishmania sp. (C. thous), one positive skin culture (Chrysocyon brachyurus) and one positive fresh blood examination from a dog. Infection by T. cruzi and Leishmania spp. was serologically confirmed in 18% and 4% of the canids, respectively. Active transmission was attested by seroconversion events and occurred despite the low rate of positive parasitological assays. Wild and domestic canids infected by both parasites were detected sharing the same areas, pointing to a possible spillover of parasites among them.
Reproduction is key to species survival, and reproductive physiology represents a high priority investigative area for conservation biology, as it provides a basic understanding of critical life-history traits, information that is helpful for the establishment of management strategies. Here, we generated knowledge about the reproductive endocrinology of the hoary fox (Lycalopex vetulus), a small canid (2.5–4 kg) endemic to open areas of the Brazilian Cerrado and listed in the Brazilian National List of Endangered species. Specifically, we utilized non-invasive hormone monitoring methods to assess oestrogen and progestagen metabolites from eight female hoary foxes housed in five zoological institutions in the state of Sao Paulo–Brazil. We observed the elevations of oestrogen and progestagen metabolites between July and September in six of the eight females. No significant evidence of ovarian activity was observed during other months. Two females, who shared the same enclosure, did not show a pattern of reproductive cyclicity. Based on these characteristics, we concluded that captive hoary foxes are seasonal monoestric, with the beginning of the oestrus cycle occurring mainly in July followed by 2 months of the luteal phase when conception does not occur. We suggest the dosage of faecal metabolites of estradiol and progesterone could be used to differentiate the reproductive period from a non-reproductive period in Lycalopex vetulus females, providing relevant information about their reproductive biology that may contribute to species conservation and management strategies, such as increased ex situ reproductive success.
A polinização e uma relação mutualística bem-sucedida entre morcegos e angiospermas. Apesar disso, pouco se conhece sobre a diversidade polínica presente na pelagem de espécies de morcegos fitófagos. O objetivo deste estudo foi registrar os tipos polínicos encontrados na pelagem de morcegos Phyllostomidae, a fim de identificar possíveis interações entre esses animais e as plantas. Para a captura dos quirópteros no Parque Estadual Fontes do Ipiranga, localizado na cidade de São Paulo, foram utilizadas redes de neblina entre outubro de 2015 e setembro de 2016. Os grãos de pólen foram coletados com pincel e água destilada e submetidos a análise em laboratório. Setenta e dois tipos polínicos foram registrados, sendo que os mais frequentes foram Alchornea (9,3%, n=20), Eucalyptus (5,6%, n=12) e Euterpe (4,6%, n=10). Foram amostrados 267 morcegos pertencentes a cinco espécies, sendo que Artibeus lituratus, Stunira lilium e Artibeus fimbriatus apresentaram as maiores diversidades polínicas em seus corpos. Neste trabalho, foram identificadas interações inéditas entre morcegos e plantas.
Captive animals commonly have infections by direct life cycle parasites, since they are easily transmitted between individuals. However, diagnosing these infections in the laboratory is challenging due to the wide variety of parasite, their life stages and to the variety of available diagnose techniques, being difficult to choose the best one. The present study sampled a group of captive Indian peafowl (Pavo cristatus) from Sao Paulo Zoological Park Foundation, Sao Paulo, Brazil, to test and compare different coproscopical techniques commonly applied in veterinarian clinical analysis laboratories: direct smear, concentrations by sodium chlorite, sucrose, zinc sulphate, faecal sedimentation and formalin-ether followed by modified Ziehl-Neelsen staining. Sensitivity, specificity, predictive values (positive and negative) and Cohen’s kappa index were calculated. In total 108 samples were processed and parasites found were: nonsporulated coccidian oocysts (91.7%), Capillarinae eggs (89.8%), unidentified nematode larvae (75%), Ascarididae eggs (63%), unidentified nematode adults (60.2%), unidentified nematode eggs (42.6%), strongylid-like eggs (42.6%), Cryptosporidium spp. (28.7%), flagellated (15.7%) and ciliated (10.2%) protozoans, trematode eggs (0.9%), Acanthocephala eggs (0.9%), Adeleidae oocysts (0.9%) and Cruzia sp. eggs (0.9%). Sensitivity and specificity varied considerably between parasite groups. Cohen’s Kappa index reinforces the recommendation of applying more than one technique to diagnose enteroparasites infections.
Multiple interlinked factors are associated with the global resistome, whereas multidrug-resistant (MDR) pathogens have been related to increased mortality rates in humans and animals. CTX-M-type is the most prevalent extended-spectrum -lactamase (ESBL) among Enterobacteriaceae, which raises concern worldwide. Zoological gardens have a high density of animals that live very close to each other and to humans. Therefore, this study aimed to investigate through the whole-genome sequencing (WGS) MDR Escherichia coli lineages obtained from captivity wild animals in a zoo. Genetic background showed a wide resistome for antimicrobials (e.g., blaCTX-M-65, blaCTX-M-8, blaCMY-2, qnrB19), metals (e.g., pcoABCDERS, silABCEP, merACDEPRT), and antibacterial biocides (e.g., sugE, mdfA) among MDR CTX-M-producing E. coli belonging to CC155 and CC156. Mobilome analysis revealed several plasmids, and eight of them were completely characterized, which showed different backbone-encoding genes. Comparative analysis of plasmids blaCTX-M-65/IncHI2-ST3, blaCTX-M-8/IncI1-ST113, and IncQ1 showed a high identity among plasmids obtained from humans and animals worldwide distributed. Besides, several virulence genes, CRISPR, and prophage-related sequences were also detected. The occurrence of MDR E. coli belonging to CCs closely related to humans and food-producing animals and the high similarity among the plasmids from MDR E. coli carrying clinically significant antimicrobial resistance genes may indicate intercontinental dissemination of these lineages and plasmids. Therefore, these findings contribute to the monitoring of antimicrobial resistance and the human-animal-environment interface worldwide.