The performance of an in-house nested-PCR technique for pleural tuberculosis diagnoses

Introduction This study evaluated the performance of an in-house nested-PCR system for the detection of the Mycobacterium tuberculosis complex in pleural fluid, blood and urine samples from pleural effusion tuberculosis patients by health services physicians in Pernambuco, Brazil. Methods A prospective double-blind study with 37 hospitalized patients of both sexes, aged over 15, was used to investigate the diagnosis of pleural effusion. The criteria used to define the cases included the demonstration of bacillus in biological samples by smear or culture or by a granulomatous finding in the histopathological examination, associated with an evident response to specific treatments to each clinical situation. Pleural fluid, blood and urine samples were collected and subjected to routine tests and the nested PCR technique to assess for M. tuberculosis amplification. Results In total, 37 pleural effusion patients took part in the study, of whom 19 (51.3%) had tubercular etiologies and 18 (48.7%) had etiologies from other causes. When the pleural fluid, blood and/or urine sample in-house nested-PCR sensitivities were evaluated simultaneously, the results were positive regardless of the biological specimen (the sensitivity was 84.2%); however, when the blood and/or urine samples were analyzed together, the sensitivity was 72.2%. When the pleural fluid samples were evaluated alone, the sensitivity was only 33.3%. Conclusions The performance of the diagnostic pleural tuberculosis nested-PCR was directly related to the diversity of the samples collected from the same patient. Additionally, this study may identify a need to prioritize non-invasive blood and urine collection for this diagnosis.

Minimum detection limit of an in-house nested-PCR assay for herpes simplex virus and varicella zoster virus

Introduction Herpes simplex virus (HSV) and varicella zoster virus (VZV) are responsible for a variety of human diseases, including central nervous system diseases. The use of polymerase chain reaction (PCR) techniques on cerebrospinal fluid samples has allowed the detection of viral DNA with high sensitivity and specificity. Methods Serial dilutions of quantified commercial controls of each virus were subjected to an in-house nested-PCR technique. Results The minimum detection limits for HSV and VZV were 5 and 10 copies/µL, respectively. Conclusions The detection limit of nested-PCR for HSV and VZV in this study was similar to the limits found in previous studies.

Single-tube nested PCR assay with in-house DNA extraction for Mycobacterium tuberculosis detection in blood and urine

Abstract: INTRODUCTION : Molecular analyses are auxiliary tools for detecting Koch's bacilli in clinical specimens from patients with suspected tuberculosis (TB). However, there are still no efficient diagnostic tests that combine high sensitivity and specificity and yield rapid results in the detection of TB. This study evaluated single-tube nested polymerase chain reaction (STNPCR) as a molecular diagnostic test with low risk of cross contamination for detecting Mycobacterium tuberculosis in clinical samples. METHODS: Mycobacterium tuberculosis deoxyribonucleic acid (DNA) was detected in blood and urine samples by STNPCR followed by agarose gel electrophoresis. In this system, reaction tubes were not opened between the two stages of PCR (simple and nested). RESULTS: STNPCR demonstrated good accuracy in clinical samples with no cross contamination between microtubes. Sensitivity in blood and urine, analyzed in parallel, was 35%-62% for pulmonary and 41%-72% for extrapulmonary TB. The specificity of STNPCR was 100% in most analyses, depending on the type of clinical sample (blood or urine) and clinical form of disease (pulmonary or extrapulmonary). CONCLUSIONS: STNPCR was effective in detecting TB, especially the extrapulmonary form for which sensitivity was higher, and had the advantage of less invasive sample collection from patients for whom a spontaneous sputum sample was unavailable. With low risk of cross contamination, the STNPCR can be used as an adjunct to conventional methods for diagnosing TB.

Helminths of introduced house sparrows (Passer domesticus) in Brazil: does population age affect parasite richness?

Species introductions have altered host and parasite diversity throughout the world. In the case of introduced hosts, population age appears to be a good predictor of parasite richness. Habitat alteration is another variable that may impact host-parasite interactions by affecting the availability of intermediate hosts. The house sparrow (Passer domesticus (Linnaeus, 1758)) is a good model to test these predictions. It was introduced in several parts of the world and can be found across rural-urban gradients. A total of 160 house sparrows from Porto Alegre, state of Rio Grande do Sul, Brazil, were necropsied. Thirty house sparrows (19 %) were parasitized with at least one out of five helminth species (Digenea: Tamerlania inopina Freitas, 1951 and Eumegacetes sp.; Eucestoda: Choanotaenia passerina (Fuhrmann, 1907) Fuhrmann, 1932; Nematoda: Dispharynx nasuta (Rudolphi, 1819) Stiles & Hassall, 1920 and Cardiofilaria pavlovskyi Strom, 1937). Overall, there was no difference in prevalence and intensity of infection of any parasite species, parasite richness and community diversity between adult males and females and adults and juveniles. The number of infected sparrows among seasons, the richness of helminths and the abundance of species were also similar between rural and urban landscapes. Only the prevalence of C. passerina varied seasonally (p=0.0007). A decrease in the number of parasite species from the original range of P. domesticus (13) to its port of entrance in Brazil, the city of Rio de Janeiro (nine), to Porto Alegre (five) is compatible with the hypothesis that host population age is a good predictor of parasite richness.

Dispersive flight and house invasion by Triatoma guasayana and Triatoma sordida in Argentina

Flight activity and invasion of houses by Triatoma sordida and T. guasayana were studied in the Province of Santiago del Estero, Argentina. Spontaneous findings of both species in houses were recorded from 1982 to 1989. Light trap collections were performed in 1982, 1983 and 1984, at the woods surrounding the settlements of Amamá (43 houses) and Trinidad (19 houses). Most of the 101 triatomines collected, were unfed and negative for Trypanosoma cruzi. T. guasayana predominated over T. sordida, and both appeared on the lighted screens between 19-31 min (mean 24) after dusk and the catch time was 30-45 min. Although entomological evaluation of 41 houses at Amamá performed in September 1985, just before insecticidal spraying, showed that Triatoma infestans predominated, adults of T. guasayana were collected in sleeping places, in 7 houses (17%). Most triatomines invading houses from then up to 1990 were flying T. guasayana (20/27) and females outnumbered males. Three non infected T. guasayana females were fed on man and two T. guasayana males positive for "T. cruzi like" trypanosomes were unfed. Therefore, visiting hungry adults could transmit T. cruzi to people and introduce wild parasites to the domestic cycle. T. guasayana stands as the main potential substitute of T. infestans in the studied area, and it might play there the same role as T. sordida in Brazil.

House dust mites in Brazil - an annotated bibliography

House dust mites have been reported to be the most important allergen in human dwellings. Several articles had already shown the presence of different mite species at homes in Brazil, being Pyroglyphidae, Glycyphagidae and Cheyletidae the most important families found. This paper is an annotated bibliography that will lead to a better knowledge of house dust mite fauna in Brazil.

Standardization of in-house polymerase chain reaction for the identification of Mycobacterium tuberculosis at the reference tropical disease hospital in the State of Goiás, Brazil

This study compares smear, growth in Lowenstein-Jensen medium, and in-house polymerase chain reaction (PCR) techniques for the detection of Mycobacterium tuberculosis. A total of 72 specimens from 72 patients with clinical symptoms of tuberculosis, including 70 sputum and two bronchial aspirate samples, were tested in parallel by smear, culture, and in-house PCR techniques. From these, 48 (66.6%) were negative by the 3 methods, 2 (2.8%) were smear positive and negative by culture and in-house PCR, 11 (15.3%) were both smear and culture negative, and in-house PCR positive, 7 (9.7%) were positive by the 3 methods, 2 (2.8%) were positive by smear and culture, and negative by PCR, 2 (2.8%) were positive by culture and PCR, but smear negative. After the resolution of discrepancies in PCR results, the sensitivity and specificity for in-house PCR technique to M. tuberculosis relative to the culture, were 81.8% and 81.9%, respectively. These results confirm that this method, in-house PCR, may be a sensitive and specific technique for M. tuberculosis detection, occurring in both positive and negative smear and negative cultures.

Pyrethroid insecticide evaluation on different house structures in a Chagas disease endemic area of the Paraguayan Chaco

Insecticide effects of deltamethrin 2.5% SC (flowable solution) on different substrates and triatomine infestation rates in two indigenous villages (Estancia Salzar and Nueva Promesa) of the Paraguayan Chaco are reported. This field study was carried out to determine the extent to which variability in spray penetration may affect residual action of the insecticide. A total of 117 houses in the two villages were sprayed. Filter papers discs were placed on aluminium foil pinned to walls and roofs in selected houses and the applied insecticide concentration was determined by high pressure liquid chromatography (HPLC). The target dose rate was 25 mg a.i./m². The mean actual applied dose in Estancia Salazar was 11.2 ± 3.1 mg a.i./m² in walls and 11.9 ± 5.6 mg a.i./m² in roofs while in Nueva Promesa, where duplicates were carried out, the mean values were 19.9 ± 6.9 mg a.i./m² and 34.7 ± 10.4 mg a.i./m² in walls and 28.8 ± 19.2 mg a.i./m² and 24.9 ± 21.8 mg a.i./m² in roofs. This shows the unevenness and variability of applied doses during spraying campaigns, and also the reduced coverage over roof surfaces. However, wall bioassays with Triatoma infestans nymphs in a 72 h exposure test showed that deposits of deltamethrin persisted in quantities sufficient to kill triatomines until three months post spraying. Knockdown by deltamethrin on both types of surfaces resulted in 100% final mortality. A lower insecticidal effect was observed on mud walls. However, three months after treatment, sprayed lime-coated mud surfaces displayed a twofold greater capacity (57.5%) to kill triatomines than mud sprayed surfaces (25%). Re-infestation was detected by manual capture only in one locality, six months after spraying,

The number of families of Triatoma dimidiata in a Guatemalan house

Triatoma dimidiata is an important vector of Chagas disease in Guatemala. To help understand the biology and population dynamics of the insect, we estimated the number of full sibling families living in one house. Forty one families with an average size of 2.17 individuals were detected using random amplification of polymorphic DNA-polymerase chain reaction genetic markers. This result suggests high levels of migration of the vector, polyandry, and a significant capability for spreading the disease.

Triatoma mexicana (Hemiptera: Reduviidae) in Guanajuato, Mexico: house infestation and seasonal variation

Triatoma mexicana was described by Herrich-Schaeffer in 1848. In 1940, a male specimen was found in Hidalgo. In 1970, this species was recorded in the state of Queretaro. Later, it was registered in Guanajuato and San Luis Potosi. In the present paper we performed an investigation in 545 dwellings from three counties in the state of Guanajuato, Mexico, from March 2003 to May 2004. The search and capture of triatomines were seasonally performed indoors and outdoors. Entomological indexes were calculated. The risk and no risk relations between triatomine presence and housing construction materials were analyzed. Fourteen triatomines were collected indoors and 151 outdoors. The vectors were collected in houses built with either risky and non-risky materials. Adults go indoors but do not settle there, hence, no relationship was found between the building materials and infestation of houses. Conventional interventions like house improvement or insecticide spraying are not efficient for the control of T. mexicana, because its developmental cycle is accomplished outdoors in the area surrounding the houses.

Use of in-house PCR for identification of Mycobacterium tuberculosis in BACTEC broth cultures of respiratory specimens

We evaluated the ability of a PCR assay to identify Mycobacterium tuberculosis complex (MTBC) from positive BACTEC® 12B broth cultures. A total of 107 sputum samples were processed and inoculated into Ogawa slants and BACTEC® 12B vials. At a growth index (GI) > 30, 1.0 ml of the 12B broth was removed, stored, and assayed with PCR. Molecular results were compared to those obtained by phenotypic identification methods, including the BACTEC® NAP method. The average times required to perform PCR and NAP were compared. Of the 107 broth cultures evaluated, 90 were NAP positive, while 91 were PCR positive for MTBC. Of particular interest were three contaminated BACTEC® 12B broth cultures yielding microorganisms other than acid-fast bacilli growth with a MTBC that were successfully identified by PCR, resulting in a mean time of 14 days to identify MTBC before NAP identification. These results suggest that PCR could be used as an alternative to the NAP test for the rapid identification of MTBC in BACTEC® 12B cultures, particularly in those that contained both MTBC and nontuberculous mycobacteria.

In house colorimetric reverse hybridisation assay for detection of the mutation most frequently associated with resistance to isoniazid in Mycobacterium tuberculosis

Mutations in the katG gene have been identified and correlated with isoniazid (INH) resistance in Mycobacterium tuberculosis isolates. The mutation AGC→ACC (Ser→Thr) at katG315 has been reported to be the most frequent and is associated with transmission and multidrug resistance. Rapid detection of this mutation could therefore improve the choice of an adequate anti-tuberculosis regimen, the epidemiological monitoring of INH resistance and, possibly, the tracking of transmission of resistant strains. An in house reverse hybridisation assay was designed in our laboratory and evaluated with 180 isolates of M. tuberculosis. It could successfully characterise the katG315 mutation in 100% of the samples as compared to DNA sequencing. The test is efficient and is a promising alternative for the rapid identification of INH resistance in regions with a high prevalence of katG315 mutants.

The peri-urban interface and house infestation with Triatoma infestans in the Argentine Chaco: an underreported process?

Peri-urban infestations with triatomine bugs, their sources and their dynamics have rarely been investigated. Here, we corroborated the reported occurrence of Triatoma infestans in a peri-urban area and in neighbouring rural houses in Pampa del Indio, in the Argentine Chaco, and identified its putative sources using spatial analysis and demographic questionnaires. Peri-urban householders reported that 10% of their premises had triatomines, whereas T. infestans was collected by timed manual searches or community-based surveillance in only nine (3%) houses. Trypanosoma cruzi-infected T. infestans and Triatoma sordida were collected indoors only in peri-urban houses and were infected with TcV and TcI, respectively. The triatomines fed on chickens, cats and humans. Peri-urban infestations were most frequent in a squatter settlement and particularly within the recently built mud houses of rural immigrants, with large-sized households, more dogs and cats and more crowding. Several of the observed infestations were most likely associated with passive bug transport from other sources and with active bug dispersal from neighbouring foci. Thus, the households in the squatter settlement were at a greater risk of bug invasion and colonisation. In sum, the incipient process of domestic colonisation and transmission, along with persistent rural-to-urban migratory flows and unplanned urbanisation, indicate the need for active vector surveillance and control actions at the peri-urban interface of the Gran Chaco.

An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Incidental enchondromas at knee magnetic resonance imaging: intraobserver and interobserver agreement and prevalence of imaging findings

Objective To evaluate intra- and interobserver agreement in the identification of incidental enchondromas at knee magnetic resonance imaging, and to assess the prevalence of imaging findings. Materials and Methods Retrospective study reviewing 326 knee magnetic resonance images acquired in the period between November 2009 and September 2010. The images were independently and blindly analyzed by two specialists in musculoskeletal radiology, with the objective of identifying incidental enchondromas, presence of foci with signal similar to bone marrow and foci of signal absence suggestive of calcifications within the enchondromas. Inter- and intraobserver agreements were analyzed. Results Eleven lesions compatible with enchondromas (3.3%) were identified. The interobserver agreement for the presence of enchondroma was high. Prevalence of foci of bone marrow signal inside the enchondromas was of 54.55%, and foci suggestive of calcification corresponded to 36.36%. The intraobserver agreement for foci of bone marrow signal in enchondromas was perfect, and interobserver agreement was high. Conclusion The prevalence of incidental enchondromas in the current study was compatible with data in the literature. Excellent agreement was observed in the identification of enchondromas and in the assessment of imaging findings. A higher prevalence of fat signal foci was observed as compared with signal absence suggestive of calcifications.