Pattern recognition

Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex.

Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge.

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Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii: An Atlas of the Molecular Types.

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(05)67145-0.pdf

Effect of BCG revaccination on incidence of tuberculosis in school-aged children in Brazil: the BCG-REVAC cluster-randomised trial

During the last two decades, the resurgence of tuberculosis (TB) has been documented in both developed and developing nations, and much of this increase in TB burden coincided with human immunodeficiency virus (HIV) epidemics. Since then, the disease pattern has changed with a higher incidence of extrapulmonary tuberculosis (EPTB) as well as disseminated TB. EPTB cases include TB lymphadenitis, pleural TB, TB meningitis, osteoarticular TB, genitourinary TB, abdominal TB, cutaneous TB, ocular TB, TB pericarditis and breast TB, although any organ can be involved. Diagnosis of EPTB can be baffling, compelling a high index of suspicion owing to paucibacillary load in the biological specimens. A negative smear for acid-fast bacilli, lack of granulomas on histopathology and failure to culture Mycobacterium tuberculosis do not exclude the diagnosis of EPTB. Novel diagnostic modalities such as nucleic acid amplification (NAA) can be useful in varied forms of EPTB. This review is primarily focused on the diagnosis of several clinical forms of EPTB by polymerase chain reaction (PCR) using different gene targets.

Diagnosis of extrapulmonary tuberculosis by PCR.

This article presents an automatic identification method of mycobacterium tuberculosis with conventional microscopy images based on Red and Green color channels using global adaptive threshold segmentation. Differing from fluorescence microscopy, in the conventional microscopy the bacilli are not easily distinguished from the background. The key to the bacilli segmentation method employed in this work is the use of Red minus Green (R-G) images from RGB color format. In this image, the bacilli appear as white regions on a dark background. Some artifacts are present in the (R-G) segmented image. To remove them we used morphological, color and size filters. The best sensitivity achieved was about 76.65%. The main contribution of this work was the proposal of the first automatic identification method of tuberculosis bacilli for conventional light microscopy.

Automatic identification of mycobacterium tuberculosis with conventional light microscopy

The Brazilian State of Amazonas has a high incidence of Tuberculosis, 91.4 in 10,000 habitants (SESAU, 1994) and resistant strains of Mycobacterium tuberculosis are frequently being found in the region (SALEM et.al, 1990). These problems have been associated with side effects caused by the antibiotics used to treat Tuberculosis, which have in rum been associated with treatment non-compliance (PATTISAPU, 1984). To resolve this problem a cost effective alternative treatment for Tuberculosis with few or no side effects, needs to be found. Amazonas has an abundance of plants, many of which are used by the lay population for medicinal purposes. A survey was carried out in five towns of the region, interviewing patients receiving treatment for Tuberculosis, to find out whether and which plants have been used to treat Tuberculosis. Results showed that the majority of patients in the sample had used medicinal plants before or after diagnosis of Tuberculoses. Thirteen different plants were recorded for this purpose. Chenopodium ambrosioides L, popularly known as Mastruz, was the most commonly used, followed by Caesalpinia ferrea Mart. Juca and Spilanthes acmella DC. Jambu. This study concentrates on Mastruz as it was used more frequently than the other medicinal plants. No significant effects on baciloscopy test results were found when Mastruz was used before diagnosis. ln-vitro laboratory tests have also not shown any tuberculocidal effects for Mastruz. Further tests are being carried out on the other medicinal plants.

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Lay use of amazonian plants for the treatment of tuberculosis

As there are four major molecular types of Cryptococcus neoformans (VNI, VNII, VNIII and VNIV) and four molecular types of Cryptococcus gattii (VGI, VGII, VGIII and VGIV), it is important to identify the specific groups causing cryptococcosis in different geographical regions. Here, we investigated the molecular types of 57 cryptococcal isolates from patients in a tertiary care hospital in the state of Amazonas, Brazil, between 2006 and 2010. The isolates were characterised by PCR fingerprinting using the M13 minisatellite and confirmed by URA5-RFLP analysis, and the presence of specific genes from the mating type locus (MATα and MATa) of these species was analysed by PCR. Most of the patients were male (66.7%), between 16 and 30 years of age (51.7%), and HIV-positive (75.0%). Most isolates were collected from cerebrospinal fluid samples (71.7%). Most of the C. neoformans isolates (n=40) were characterised as members of the VNI molecular group (n=39), a unique isolate was characterised as VNII whereas all isolates of C. gattii (n=17) were members of the VGII molecular group. With regard to mating types, 55 isolates were type 'α', and only two were type 'a'. This study revealed the prevalence of the VNI molecular group and provides the first reported observation of the VNII molecular group in the northern region of Brazil.

/pdf/molecular-characterisation-of-the-causative-agents-of-594hq6p57f.pdf

Molecular characterisation of the causative agents of Cryptococcosis in patients of a tertiary healthcare facility in the state of Amazonas‐Brazil

This paper presents a new method for segmentation of tuberculosis bacillus in conventional sputum smear microscopy. The method comprises three main steps. In the first step, a scalar selection are made for characteristics from the following color spaces: RGB, HSI, YCbCr and Lab. The features used for pixel classification in the segmentation step were the components and subtraction of components of these color spaces. In the second step, a feedforward neural network pixel classifier, using selected characteristics as inputs, is applied to segment pixels that belong to bacilli from the background. In third step geometric characteristics, especially the eccentricity, and a new proposed color characteristic, the color ratio, are used to noise filtering. The best sensitivity achieved in bacilli detection was 91.5%.

Mycobacterium tuberculosis recognition with conventional microscopy

INTRODUCAO: Ha diferentes primers sendo testados para a deteccao do DNA do Mycobacterium tuberculosis. A acuidade da reacao em cadeia da polimerase (PCR) depende da existencia da sequencia alvo no bacilo e de os testes serem realizados em cepas isoladas ou em amostras clinicas. OBJETIVO: Verificar a presenca das sequencias de DNA alvo mais relatadas na literatura para o diagnostico da tuberculose em amostras clinicas usando como controle positivo as respectivas cepas de M. tuberculosis isoladas. METODO: Oitenta e uma amostras clinicas de pacientes com suspeita de tuberculose foram submetidas a baciloscopia e cultivo. A tecnica de PCR foi realizada nas amostras clinicas e cepas isoladas com primers especificos para os seguintes alvos: IS6110, 65 kDa, 38 kDa e MPB64. RESULTADOS: Em 24 amostras com baciloscopia e cultivo negativos, a PCR tambem foi negativa com todos os primers testados. Em 19 amostras com baciloscopia positiva e nas cepas isoladas obteve-se 100% de resultados positivos nas PCR, exceto nas PCR em amostras clinicas com os primers para a sequencia MPB64 (89,4%). Em 38 amostras com baciloscopia negativa e cultivo positivo, as PCR tiveram resultados variaveis, sendo que os primers especificos que amplificam o fragmento de 123 pb da sequencia IS6110 foram os que forneceram os maiores percentuais de positividade (92,1%), concordância diagnostica (0,9143), co-positividade (94,7%) e co-negatividade (100%). CONCLUSAO: As sequencias IS6110, 38 kDa, MPB64 e 65 kDa foram encontradas no genoma de todas as cepas de M. tuberculosis isoladas desses pacientes do Estado do Amazonas. O protocolo utilizado no processamento das amostras clinicas e os primers especificos utilizados para amplificacao do fragmento de 123 pb da sequencia IS6110 demonstraram maior eficiencia no diagnostico da tuberculose pulmonar (paucibacilar) em comparacao com a literatura.

http://www.scielo.br/pdf/jbpneu/v30n4/en_v30n4a08.pdf

Julia Ignez Salem

Papers

Automatic identification of mycobacterium tuberculosis with conventional light microscopy

Lay use of amazonian plants for the treatment of tuberculosis

Molecular characterisation of the causative agents of Cryptococcosis in patients of a tertiary healthcare facility in the state of Amazonas‐Brazil

Mycobacterium tuberculosis recognition with conventional microscopy

Análise de diferentes primers utilizados na PCR visando ao diagnóstico da tuberculose no Estado do Amazonas