An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

An online scheme to assign Stenotrophomonas isolates to genomic groups was developed using the multilocus sequence analysis (MLSA), which is based on the DNA sequencing of selected fragments of the housekeeping genes ATP synthase alpha subunit (atpA), the recombination repair protein (recA), the RNA polymerase alpha subunit (rpoA) and the excision repair beta subunit (uvrB). This MLSA-based scheme was validated using eight of the 10 Stenotrophomonas species that have been previously described. The environmental and nosocomial Stenotrophomonas strains were characterised using MLSA, 16S rRNA sequencing and DNA-DNA hybridisation (DDH) analyses. Strains of the same species were found to have greater than 95% concatenated sequence similarity and specific strains formed cohesive readily recognisable phylogenetic groups. Therefore, MLSA appeared to be an effective alternative methodology to amplified fragment length polymorphism fingerprint and DDH techniques. Strains of Stenotrophomonas can be readily assigned through the open database resource that was developed in the current study (www.steno.lncc.br/)

Taxonomy of Stenotrophomonas genus by means of Multi Locus Sequence Analysis (MLSA).

As Stenotrophomonas são comumente encontradas no trato respiratório de pacientes com doenças pulmonares crônicas e também na rizosfera de plantas. Esse gênero apresenta resistência a diversos antibióticos, promove o crescimento de plantas e algumas espécies apresentam a capacidade de fixar o nitrogênio atmosférico. O Multi Locus Sequence Analysis (MLSA) é uma metodologia baseada em genes constitutivos para definição e alocação taxonômica de novas espécies. O objetivo geral do presente trabalho foi caracterizar taxonomicamente uma coleção ampla de Stenotrophomonas composta por isolados endófitos, linhagens-tipo e de referência. Para tanto, foi estabelecido um sistema de classificação e identificação de Stenotrophomonas por meio de MLSA. Foi possível através da metodologia de MLSA definir 9 novas espécies, detectar a presença de um novo gênero e estabelecer um sistema online de taxonomia para Stenotrophomonas.The genus Stenotrophomonas is found in the respiratory treatment of patients with chronic pulmonary and also in the rizhosfera of plants. It presents resistance to several antibiotics, promotes the growth of plants and some species present the ability to fix atmospheric nitrogen. The Multi Locus Sequence Analysis (MLSA) is a methodology based on constitutive genes for definition and taxonomic allocation of new species. The general objective of the present work was to characterize a wide collection constituted by Stenotrophomonas from isolated endophytic, type and reference strains. In such a way, a system of classification and identification of Stenotrophomonas by means of MLSA was established. It was possible through the MLSA methodology to define 9 new species, to detect the presence of a new genus and to establish an online system for Stenotrophomonas taxonomy

Taxonomy of Stenotrophomonas genus by means of Multi Locus Sequence Analysis (MLSA).

As Stenotrophomonas são comumente encontradas no trato respiratório de pacientes com doenças pulmonares crônicas e também na rizosfera de plantas. Esse gênero apresenta resistência a diversos antibióticos, promove o crescimento de plantas e algumas espécies apresentam a capacidade de fixar o nitrogênio atmosférico. O Multi Locus Sequence Analysis (MLSA) é uma metodologia baseada em genes constitutivos para definição e alocação taxonômica de novas espécies. O objetivo geral do presente trabalho foi caracterizar taxonomicamente uma coleção ampla de Stenotrophomonas composta por isolados endófitos, linhagens-tipo e de referência. Para tanto, foi estabelecido um sistema de classificação e identificação de Stenotrophomonas por meio de MLSA. Foi possível através da metodologia de MLSA definir 9 novas espécies, detectar a presença de um novo gênero e estabelecer um sistema online de taxonomia para Stenotrophomonas.The genus Stenotrophomonas is found in the respiratory treatment of patients with chronic pulmonary and also in the rizhosfera of plants. It presents resistance to several antibiotics, promotes the growth of plants and some species present the ability to fix atmospheric nitrogen. The Multi Locus Sequence Analysis (MLSA) is a methodology based on constitutive genes for definition and taxonomic allocation of new species. The general objective of the present work was to characterize a wide collection constituted by Stenotrophomonas from isolated endophytic, type and reference strains. In such a way, a system of classification and identification of Stenotrophomonas by means of MLSA was established. It was possible through the MLSA methodology to define 9 new species, to detect the presence of a new genus and to establish an online system for Stenotrophomonas taxonomy

Parasitological surveillance in a rat (Rattus norvegicus) colony in Sao Paulo Zoo animal house

Rattus norvegicus (Mammalia: Rodentia) is a widespread and synanthropic rodent, broadly used in medical experiments. It can also be used for feeding captive animals in zoos. Parasitological surveys are important to guarantee the health of both the animals and the staff responsible for their management. The aim of this study was to identify intestinal parasites of Rattus norvegicus offered as food to captive animals from São Paulo Zoo, and demonstrate the importance of sanitary hurdling, disease control and biosecurity. The identified protozoan parasites were Eimeria sp., Entamoeba sp., Spironucleus sp., Giardia sp., Tritrichomonas sp., Chilomastix sp., unidentified cysts and non-sporulated coccidians oocysts (Isospora/Eimeria). The following helminths were found: Syphacia muris, Rodentolepis nana and Aspiculuris tetraptera

Molecular and morphological characterization of Hepatozoon spp. in Brazilian snakes

The genus Hepatozoon represents one of six genera in the hemogregarine group. Some studies in snakes indicated effects in the host, from slight influences on fitness to severe effects on growth rate, reproduction and offspring survival rates. Diagnosis and identification are usually through blood smear analyses; but not all infected animals show parasitemia. Based on this, the present study established an adapted molecular protocol to identify Hepatozoon spp. to be used as a complementary test for routine diagnoses at the Clinical Analysis Laboratory at São Paulo Zoological Park Foundation. The study was conducted with 113 individuals. Microscopical analysis and molecular techniques were used to identify the parasite. Microscopic analyses showed 13.3% of the samples to be positive. The first pair of primers, targeting 18S rRNA gene, amplified parasite DNA in 6.3% of the samples. The second pair of primers, targeting Apicoplast fragment, were used only on samples that were identified microscopically as being positive, detecting the presence of parasite DNA in 93.3% of these. Phylogenetic analysis of the resulting sequences found five clusters for the 18S gene and five clusters for the Apicoplast fragment. Studies involving Hepatozoon spp. are still scarce and limited, mainly in snakes and the impacts of this parasite on the vertebrate host, so diagnostic studies are essential for wildlife conservation, especially in ex situ work

Feral cats: Parasitic reservoirs in our Zoos?

Up until the recent past, zoos served limited function, primarily existing for entertainment value. Today’s zoos, however, are serving many roles, chief among them: species conservation of captive animals. The biggest zoo in Brazil, S?o Paulo Zoological Park Foundation, has among its 2000 animals and many species of wild cats. The presence of domestic cats living freely in zoos is common and can be a source of spreading disease. The aim of this study was to verify the variety and prevalence of parasites found in the feces of felids (feral and wild) living in the S?o Paulo Zoo. The results of this parasitological analysis have been obtained from the laboratory of clinical analysis and correspond to the 4-year period beginning January/2009 and ending December/2012. Eight species of parasites were identified in the feces of captive wild cats and three in the feces of feral cats. For those captives, Toxocara cati (7.95%) had the highest prevalence, followed by Toxascaris leonina (7.58%), Isospora sp. (2.03%), Hymenolepis nana (0.92%), Eimeria sp., Giardia sp. and Blastocystis sp. (0.37% each) and Ascaris sp. (0.18%). Among the feral cats, we found Toxocara cati (59.26%), Giardia sp. (22.22%) and Isospora sp. (11.11%). For the captive group, we also distinguished natives from exotic species, finding native species to be more frequently parasitized than the exotic ones. Key to our findings, though, was the fact that a few parasite species were found among all groups of felids, specifically (Toxocara cati, Giardia sp. and Isospora sp). Further research is needed, however, to confirm that transmission of these parasites is occurring between and among these groups

Comparative analyses of coproscopical techniques to diagnose enteroparasites in a group of captive Indian peafowl (Pavo cristatus)

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 São Paulo Zoological Park Foundation, São 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

An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

An online scheme to assign Stenotrophomonas isolates to genomic groups was developed using the multilocus sequence analysis (MLSA), which is based on the DNA sequencing of selected fragments of the housekeeping genes ATP synthase alpha subunit (atpA), the recombination repair protein (recA), the RNA polymerase alpha subunit (rpoA) and the excision repair beta subunit (uvrB). This MLSA-based scheme was validated using eight of the 10 Stenotrophomonas species that have been previously described. The environmental and nosocomial Stenotrophomonas strains were characterised using MLSA, 16S rRNA sequencing and DNA-DNA hybridisation (DDH) analyses. Strains of the same species were found to have greater than 95% concatenated sequence similarity and specific strains formed cohesive readily recognisable phylogenetic groups. Therefore, MLSA appeared to be an effective alternative methodology to amplified fragment length polymorphism fingerprint and DDH techniques. Strains of Stenotrophomonas can be readily assigned through the open database resource that was developed in the current study (www.steno.lncc.br/)