Development of molecular-based techniques for the detection, identification and quantification of food-borne pathogens

La presencia de microorganismos patógenos en alimentos es uno de los problemas esenciales en salud pública, y las enfermedades producidas por los mismos es una de las causas más importantes de enfermedad. Por tanto, la aplicación de controles microbiológicos dentro de los programas de aseguramiento de la calidad es una premisa para minimizar el riesgo de infección de los consumidores. Los métodos microbiológicos clásicos requieren, en general, el uso de pre-enriquecimientos no-selectivos, enriquecimientos selectivos, aislamiento en medios selectivos y la confirmación posterior usando pruebas basadas en la morfología, bioquímica y serología propias de cada uno de los microorganismos objeto de estudio. Por lo tanto, estos métodos son laboriosos, requieren un largo proceso para obtener resultados definitivos y, además, no siempre pueden realizarse. Para solucionar estos inconvenientes se han desarrollado diversas metodologías alternativas para la detección identificación y cuantificación de microorganismos patógenos de origen alimentario, entre las que destacan los métodos inmunológicos y moleculares. En esta última categoría, la técnica basada en la reacción en cadena de la polimerasa (PCR) se ha convertido en la técnica diagnóstica más popular en microbiología, y recientemente, la introducción de una mejora de ésta, la PCR a tiempo real, ha producido una segunda revolución en la metodología diagnóstica molecular, como pude observarse por el número creciente de publicaciones científicas y la aparición continua de nuevos kits comerciales. La PCR a tiempo real es una técnica altamente sensible -detección de hasta una molécula- que permite la cuantificación exacta de secuencias de ADN específicas de microorganismos patógenos de origen alimentario. Además, otras ventajas que favorecen su implantación potencial en laboratorios de análisis de alimentos son su rapidez, sencillez y el formato en tubo cerrado que puede evitar contaminaciones post-PCR y favorece la automatización y un alto rendimiento. En este trabajo se han desarrollado técnicas moleculares (PCR y NASBA) sensibles y fiables para la detección, identificación y cuantificación de bacterias patogénicas de origen alimentario (Listeria spp., Mycobacterium avium subsp. paratuberculosis y Salmonella spp.). En concreto, se han diseñado y optimizado métodos basados en la técnica de PCR a tiempo real para cada uno de estos agentes: L. monocytogenes, L. innocua, Listeria spp. M. avium subsp. paratuberculosis, y también se ha optimizado y evaluado en diferentes centros un método previamente desarrollado para Salmonella spp. Además, se ha diseñado y optimizado un método basado en la técnica NASBA para la detección específica de M. avium subsp. paratuberculosis. También se evaluó la aplicación potencial de la técnica NASBA para la detección específica de formas viables de este microorganismo. Todos los métodos presentaron una especificidad del 100 % con una sensibilidad adecuada para su aplicación potencial a muestras reales de alimentos. Además, se han desarrollado y evaluado procedimientos de preparación de las muestras en productos cárnicos, productos pesqueros, leche y agua. De esta manera se han desarrollado métodos basados en la PCR a tiempo real totalmente específicos y altamente sensibles para la determinación cuantitativa de L. monocytogenes en productos cárnicos y en salmón y productos derivados como el salmón ahumado y de M. avium subsp. paratuberculosis en muestras de agua y leche. Además este último método ha sido también aplicado para evaluar la presencia de este microorganismo en el intestino de pacientes con la enfermedad de Crohn's, a partir de biopsias obtenidas de colonoscopia de voluntarios afectados. En conclusión, este estudio presenta ensayos moleculares selectivos y sensibles para la detección de patógenos en alimentos (Listeria spp., Mycobacterium avium subsp. paratuberculosis) y para una rápida e inambigua identificación de Salmonella spp. La exactitud relativa de los ensayos ha sido excelente, si se comparan con los métodos microbiológicos de referencia y pueden serusados para la cuantificación de tanto ADN genómico como de suspensiones celulares. Por otro lado, la combinación con tratamientos de preamplificación ha resultado ser de gran eficiencia para el análisis de las bacterias objeto de estudio. Por tanto, pueden constituir una estrategia útil para la detección rápida y sensible de patógenos en alimentos y deberían ser una herramienta adicional al rango de herramientas diagnósticas disponibles para el estudio de patógenos de origen alimentario.

Modelling of Johne's disease control options in beef cattle: a decision support approach

Johne's disease in cattle is a contagious wasting disease caused by Mycobacterium avium subspecies paratuberculosis (MAP). Johne's infection is characterised by a long subclinical phase and can therefore go undetected for long periods of time during which substantial production losses can occur. The protracted nature of Johne's infection therefore presents a challenge for both veterinarians and farmers when discussing control options due to a paucity of information and limited test performance when screening for the disease. The objectives were to model Johne's control decisions in suckler beef cattle using a decision support approach, thus implying equal focus on ‘end user’ (veterinarian) participation whilst still focusing on the technical disease modelling aspects during the decision support model development. The model shows how Johne's disease is likely to affect a herd over time both in terms of physical and financial impacts. In addition, the model simulates the effect on production from two different Johne's control strategies; herd management measures and test and cull measures. The article also provides and discusses results from a sensitivity analysis to assess the effects on production from improving the currently available test performance. Output from running the model shows that a combination of management improvements to reduce routes of infection and testing and culling to remove infected and infectious animals is likely to be the least-cost control strategy.

Aspectos epidemiológicos da paratuberculose bovina no Rio Grande do Sul

Descrevem-se os achados clínicos e patológicos da paratuberculose em uma criação intensiva de bovinos de leite no municí pio de Capela de Santana, RS. Os sinais clínicos foram observados em oito de um total de 345 bovinos, consistindo em diarréia crônica refratária aos tratamentos, emagrecimento progressivo e queda na produção de leite. As principais lesões macroscópicas, observadas nos oito animais necropsiados, incluíam intestino delgado com acentuado espessamento da parede e superfície mucosa de aspecto reticulado, semelhante às circunvoluções cerebrais, lesão essa perceptível, através da serosa. A luz intestinal estava preenchida com conteúdo fluido e de aspecto leitoso. Os vasos linfáticos do mesentério mostravam-se mais evidentes sendo que alguns tinham aspecto varicoso. Os linfonodos mesentéricos estavam aumentados de volume e, ao corte, fluía grande quantidade de líquido leitoso. Focos de mineralização foram observados na íntima das artérias, nas válvulas cardíacas e na serosa do rúmen. As principais lesões macroscópicas incluíam enterite, linfadenite e linfangite granulomatosa caracterizada por infiltrado inflamatório com macrófagos, células gigantes de Langhans que continham grande quantidade de bacilos álcool-ácido-resistentes. As lesões vasculares consistiam em degeneração e mineralização das túnicas í ntimas e média das artérias de grande calibre associada a proliferação de colágeno. Havia calcificação da serosa do rúmen atrofia hepatocelular difusa e hepatite granulomatosa multifocal. O M. avium subsp. paratuberculosis (Map) foi isolado em amostras de intestino e linfonodos de 8 vacas Holandesas (3,5%) com doença de Johne, dentre 229 amostras cultivadas provenientes de um rebanho leiteiro. Amostras inoculadas em HEYM com micobactina produziram colônias identificadas como Map, segundo as caracterí sticas fenotí picas próprias como: crescimento lento, coloração álcool-ácido-resistente (A.A.R.) e dependência a micobactina. O laboratório de Referência da OIE confirmou a amostra isolada. O M. avium subsp. paratuberculosis (Map) foi isolado em amostras de intestino e linfonodos de 8 vacas Holandesas (3,5%) com doença de Johne, dentre 229 amostras cultivadas provenientes de um rebanho leiteiro Amostras inoculadas em HEYM com micobactina produziram colônias identificadas como Map, segundo as caracterí sticas fenotí picas próprias como: crescimento lento, coloração álcool-ácido-resistente (A.A.R.) e dependência a micobactina. O laboratório de Referência da OIE confirmou a amostra isolada. Não houve isolamento do agente em 221 amostras intestinais quando processadas, após 2 anos de sua colheita. O teste de IDGA aplicado como “screening”, detectou 26 vacas (11,4%) positivas, dentre 228 animais testados e sacrificados em matadouro. O teste de ELISA adsorvido, utilizando o antí geno PPA-3 detectou 125 (39,8%) amostras positivas. O ELISA não adsorvido detectou mais 32 (10,1%) reagentes positivos, dentre os 314 bovinos testados. A prevalência da infecção causada pelo Map em 36 rebanhos leiteiros procedentes de 25 municí pios do Rio Grande do Sul foi estimada em 44,6% das 1316 amostras testadas. A infecção foi identificada em 35 (97,2%) dos 36 rebanhos testados e presentes em todos os municí pios incluí dos. A ocorrência da doença de Johne foi enfatizada, tanto a forma clí nica quanto a infecção subclí nica no Rio Grande do Sul, sugerindo a adoção de medidas de controle sejam aplicadas na proteção dos rebanhos leiteiros nacionais.

Diagnóstico da paratuberculose em bovinos de corte do estado do Pará - Brasil

514 amostras de sangue bovino foram analisadas para detecção de anticorpos anti-Mycobacterium avium (subsp.) paratuberculosis, utilizando um kit comercial do teste ELISA indireto. Os animais eram todos mestiços, machos e fêmeas, classificados em dois grupos, de acordo com a idade, menores ou iguais a 36 meses e maiores de 36 meses, provenientes de 23 municípios do Estado do Pará. Além deste teste, também foram colhidas 100 amostras de fragmentos de intestino delgado e de linfonodo mesentérico para análise bacteriológicaatravés da coloração de Ziehl-Neelsen, a fim de identificar o Mycobacterium avium (subsp.) paratuberculosis. As amostras foram colhidas aleatoriamente em matadouro da região metropolitana de Belém. No teste ELISA indireto, das 514 amostras de sangue bovino 182 (35,4%) foram reagentes para anticorpos anti-Mycobacterium avium (subsp.) paratuberculosis e 332 (64,6%) foram não-reagentes. Em todas as mesorregiões encontraramse animais soropositivos. As fêmeas com idade superior a 36 meses mostraram maior respostas ao teste , 92,06% de animais soropositivos. Entre os machos, a maior prevalência (76,79%), foi obtida nos mais novos, com idade abaixo de 36 meses. Das 100 lâminas coradas através do método de Ziehl-Neelsen, nenhum Mycobacterium sp. foi identificado. Conclui-se assim, que o elevado número de animais com anticorpos anti-Mycobacterium avium (subsp.) paratuberculosis indica a presença da doença em todas as mesorregiões estudadas, devendo-se atentar aos riscos desta enfermidade, através de pesquisas mais abrangentes sobre a Paratuberculose, com aplicação de métodos diagnósticos diretos e indiretos.

Epidemiological studies of Johne’s Disease in cattle from Scottish farms, with a focus on slaughterhouse investigations

The PARABAN project has been a Scotland-wide initiative to develop and deliver farm-specific ‘best practice’ for the control of Mycobacterium avium ssp. paratuberculosis (MAP) in cattle using ‘Knowledge Exchange’. A range of partners have been involved, including nine ‘Champion Farms’. With input from the farmer, his/her vet and PARABAN advisors, a tailored monitoring and control programme was devised for each ‘Champion Farm’, taking into account the history of the disease on the farm, the physical facilities available and farmer objectives. Culling decisions based on live animal test results were incorporated into each farm-specific programme to complement the management programme already in place to maintain each herd. Results were analysed and discussed with all the partners throughout the project and then offered for wider scrutiny at farm open days. Feedback and questions from these open days have been used to complete the ‘Knowledge Exchange’ cycle. As a major component of the PARABAN project the author collected samples from all adult animals culled from ‘Champion Farms’ at slaughter or as fallen stock, irrespective of in-life MAP test status. These were then subjected to histopathological examination by experienced veterinary pathologists and the results compared with the results from in-life MAP testing. This was intended to evaluate the contribution slaughterhouse sampling could make towards decision making for disease control on farm and formed the main aim of this thesis. In total, samples of terminal ileum and draining lymph node were collected from three-hundred and fifty-two animals. A positive result on histopathology was defined as the presence of lesions typical of MAP and also the presence of acid-fast bacteria within the sections. There was found to be fair agreement between the overall results from histopathology and serum ELISA (Kappa = 0.33), though there appeared to be some variation in agreement between the tests on the individual ‘Champion Farms’. The presence of MAP was confirmed in seven of the eight farms which contributed animals to this study, despite sometimes prolonged efforts at controlling the disease. A separate study was undertaken to make use of the archives of the Scottish Centre for Production Animal Health and Food Safety at the Veterinary School, University of Glasgow. The archive contained records of cases from across southern Scotland and northern England. Analysis of the data generated from examination of these records suggested that MAP is widespread within the Scottish cattle herd and may well be increasing

Genetic diversity of Mycobacterium avium isolates recovered from clinical samples and from the environment: molecular characterization for diagnostic purposes

Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR for detection of IS1245 and IS901, sequencing of the hsp65 gene, and pulsed-field gel electrophoresis) were evaluated. The same strain was found in all the environmental isolates, 21 out of 23 (91.3%) of the isolates cultured from urine samples, and 5 out of 19 (26.3%) isolates from respiratory specimens. This strain did not cause disease in the patients. Testing best characterized the strain as M. avium subsp. hominissuis, with the unusual feature that 81.4% of these isolates lacked the IS1245 element. Contamination of certain clinical samples with an environmental strain was the most likely event; therefore, characterization of the environmental mycobacteria present in health care facilities should be performed to discard false-positive isolations in nonsterile samples, mainly urine samples. Molecular techniques applied in this study demonstrated their usefulness for this purpose.

Caracterização da resistência a quinolonas em Mycobacterium abscessus subsp. bolletii e outras micobactérias de crescimento rápido relacionadas

Em diversos estados do Brasil, foram relatadas epidemias de infecções causadas por micobactérias de crescimento rápido (MCR) desde o ano 2000. A maioria dos casos foi principalmente associada ao clone BRA100 de Mycobacterium massiliense, recentemente renomeada para Mycobacterium abscessus subsp. bolletii, isolado de pacientes submetidos a procedimentos invasivos nos quais os instrumentos médicos não foram adequadamente esterilizados e/ou desinfetados. Sendo as quinolonas uma opção no tratamento de infecções por MCR e sugerida para esquemas terapêuticos para esses surtos, foram avaliadas nesse trabalho as atividades in vitro de quatro gerações de quinolonas para cepas clinicas e de referência de MCR através da microdiluição em caldo. Também foram analisadas as sequências peptídicas das regiões determinantes da resistência a quinolonas (RDRQ) das subunidades A e B da DNA gyrase (GyrA e GyrB) após o seqüenciamento de DNA seguido pela tradução da sequência de aminoácidos. Cinquenta e quatro cepas de M. abscessus subsp bolletii, incluindo o clone BRA100, isoladas em diferentes estados do Brasil, e 19 cepas de referência de MCR foram caracterizadas. Todas as 54 cepas clínicas de M. abscessus subsp. bolletii foram resistentes a todas as gerações de quinolonas e mostraram o mesmo resíduo nas RDRQ, incluindo Ala-83 em GyrA, Arg-447 e Asp-464 em GyrB, descritos como sendo responsáveis por gerar um baixo nível de resistência a quinolonas em micobactérias. Porém, outras espécies de MCR apresentaram diferentes susceptibilidade e padrões de mutações contrários aos classicamente já definidos, sugerindo que outros mecanismos de resistência, diferentes de mutações em gyrA e gyrB também possam estar envolvidos na alta resistência a quinolonas.

Estudios sobre la actividad antibacteriana del macrófago en contra del complejo Mycobacterium avium-M. intracellulare

Tesis (Doctorado en Ciencias con Especialidad en Microbiología) UANL

Exposure to Mycobacterium avium Decreases the Protective Effect of the DNA Vaccine pVAXhsp65 Against Mycobacterium tuberculosis-Induced Inflammation of the Pulmonary Parenchyma

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of environmental mycobacteria (Mycobacterium avium) on immunity induced by a DNA vaccine (DNAhsp65) against tuberculosis

The efficacy of BCG vaccine (attenuated Mycobacterium bovis) against pulmonary tuberculosis varies enormously among different populations. The prevailing hypothesis attributes this variation to interactions between the vaccine and mycobacteria common in the environment. Studies have revealed that most protective antigens expressed by the antituberculous vaccine are conserved in M. avium, supporting the hypothesis that exposure to environmental mycobacteria generates a cross-reactive immune response that interferes with BCG efficacy. In this study we investigated the effect of a prior exposure to heat-killed M. avium on the immune response and the protective efficacy induced by a genetic vaccine pVAXhsp65 (hsp65 gene from M. leprae inserted in pVAX vector) against experimental tuberculosis. To evaluate the effect on the immune response, female BALB/c mice were initially injected with distinct doses (0.08×106, 4×106, and 200×10 6) of heat-killed M. avium by subcutaneous route. Three weeks later, the animals were immunized with 3 doses of DNAhsp65 by intramuscular route (100μg/15 days apart). Control groups received only M. avium, vaccine (pVAXhsp65), vector (pVAX) or saline solution. Cytokine production and antibody levels were determined by ELISA. To evaluate the effect on the protective efficacy, animals were initially sensitized with 200×106 heat-killed CFU of M. avium by subcutaneous route and then immunized with 3 doses of pVAXhsp65 (100μg/15 days apart) by intramuscular route. Control groups were injected with saline, pVAX (4 doses), pVAXhsp65 (4 doses), M. avium or M. avium plus pVAX (3 doses). Fifteen days after last DNA dose, the animals were infected with 1×104 viable CFU of H37Rv M. tuberculosis by intratracheal route. Thirty days after challenge, the animals were sacrificed and the bacterial burden was determined by counting the number of CFU in the lungs. Lung histological sections were also analyzed. Splenic cells from primed animals produced more IL-5 but less IFN-gamma than non-primed ones. Also, prior contact with M. avium determined higher production of IgG1 and IgG2a anti-hsp65 antibodies in comparison to control groups. However, this higher immune response did not decrease the bacterial burden in the lungs. In addition, prior sensitization with M. avium decreased the parenchyma preservation observed in the group immunized only with pVaxhsp65. These results indicate that environmental mycobacteria can interfere with immunity and protective efficacy induced by DNAhsp65.

A photoelectrocatalytic process that disinfects water contaminated with Mycobacterium kansasii and Mycobacterium avium

Nontuberculous mycobacteria are resistant to conventional water treatment; indeed, they have been recovered from a wide variety of environmental sources. Here, we applied the photoelectrocatalytic technique using a Ti/TiO2-Ag photoanode to inactivate mycobacteria. For a mycobacteria population of 5 × 108 CFU mL-1, we achieved 99.9 and 99.8% inactivation of Mycobacterium kansasii and Mycobacterium avium with rate constant of 6.2 × 10-3 and 4.2 × 10-3 min-1, respectively, after 240 min. We compared the proposed method with the photolytic and photocatalytic methods. Using a mycobacteria population of 7.5 × 104 CFU mL-1, the proposed Ti/TiO2-Ag photoanode elicited total mycobacteria inactivation within 3 min of treatment; the presence of Ag nanoparticles in the electrode provided 1.5 larger degradation rate constant as compared with the Ti/TiO2 anode (1.75 × 10-2 for M. kansassi and 1.98 × 10-2 for M. avium). We monitored the degradation of the metabolites released during cellular lysis by TOC removal, sugar release, chromatography, and mass spectrometry measurements; photoelectrocatalysis and Ti/TiO2-Ag photoanodes furnished the best results. © 2013 Elsevier Ltd. All rights reserved.

Efeito de micobactéria ambiental (Mycobacterium avium) na imunidade induzida pela vacina gênica para tuberculose (pVAXhsp65)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Evaluation of Mycobacterium avium complex lung disease in women

Mycobacterium avium complex (MAC) is a ubiquitous organism responsible for most pulmonary and disseminated disease caused by non-tuberculosis (NTM) mycobacteria. Though MAC lung disease without predisposing factors is uncommon, in recent years it has been increasingly described in middle-aged and elderly women. Recognition and correct diagnosis, is often delayed due to the indolent nature of the disease. It is unclear if these women have significant clinical disease as or if their airways are simply colonized by the bacterium. This study describes the clinical presentation, identifies risk factors, and describes the clinical significance of MAC lung disease in HIV-negative women aged 50 or greater. ^ A hybrid study design utilizing both cross-sectional and case-control methodologies was used. A comparison population was selected from previously identified tuberculosis suspects found throughout Harris County. The study population had at least one acid fast bacillus pulmonary culture performed between 1/1/1998 and 12/31/2000 from a pulmonary source. Clinical presentation and symptoms were analyzed using a cross-sectional design. Past medical history and other risk factors were evaluated using a traditional case-control study design. Differences in categorical variables were estimated with the Chi Square or Fisher's Exact test as appropriate. Odds ratios and 95% confidence intervals were utilized to evaluate associations. Multivariate logistic regression was used to identify predictive factors for MAC. All statistical tests were two-sided and P-values <0.05 were considered statistically significant. ^ Culture confirmed MAC pulmonary cases were more likely to be white, have bronchiectasis, scoliosis, evidence of cavitation and pleural changes on chest radiography and granulomas on histopathologic examination than women whose pulmonary cultures were AFB negative. After controlling for selected risk factors, white race continued to be significantly associated with MAC lung disease (OR = 4.6, 95% CI = 2.3, 9.2). In addition, asthma history, smoking history and alcohol use were less likely to be evident among MAC cases in a multivariate analysis. Right upper and right middle lobe disease was further noted among clinically significant cases. Based on population data, MAC lung disease appears to represent a significant clinical syndrome in HIV-negative women thus supporting the theory of the Lady Windermere Syndrome. ^

Role of {\it Mycobacterium avium-intracellulare\/} complex infection in AIDS mortality

Disseminated MAC (dMAC) is the third most prevalent opportunistic infection in AIDS patients. In order to understand the role MAC infection plays in affecting survival of AIDS patients, a cohort of 203 suspected dMAC veterans seen at the Houston Veterans Affairs Medical Center between August 14, 1987 and December 31, 1991 were analyzed. The criteria for suspected dMAC infection was HIV+ men having a CD4+ level $\le$200 cells/mm$\sp3,$ on zidovudine treatment $\ge$1 month and who had any of the following: (a) a confirmed respiratory MAC infection, (b) fever $\ge$101$\sp\circ\rm F$ for $\ge$48 hours, (c) unexplained weight loss of 10 lbs or $\ge$10% BW over 3 months or (d) Hgb $\le$7.5 g/dl or decrease in Hgb $\ge$3.0 g/dl, while on 500-600 mg/day AZT. The study was conducted before the commencement of an effective MAC anti-mycobacterial therapy, so the true course of MAC infection was seen without the confounder of a therapeutic regimen. Kaplan-Meier and Cox regression survival analysis was used to compare 45 MAC culture positive and 118 MAC culture negative veterans. The 1 year survival rate of veterans with documented dMAC infection was 0.37 compared to 0.50 for veterans not acquiring dMAC infection. Significant differences between subgroups were also seen with the variables: PCP prophylaxis, the AIDS indicator disease Candida esophagitis, CD4+ lymphocyte level, CD4 percent lymphocyte level, WBC level, Hgb and Hct levels. Using multivariate modeling, it was determined that PCP prophylaxis (RR = 6.12, CI 2.24-16.68) was a predictor of survival and both CD4% lymphocytes $\le$6.0% (RR = 0.33, CI 0.17-0.68) and WBC level $\le$3000 cells/mm$\sp3$ (RR = 0.60, CI 0.39-0.93) were predictors of mortality. CD4+ level $\le$50 cells/mm$\sp3$ was not a significant predictor of mortality. Although MAC culture status was a significant predictor of mortality in the univariate model, a positive dMAC culture was not a significant predictor of AIDS mortality in the multivariate model. A positive dMAC culture, however, did affect mortality in a stratified analysis when baseline laboratory values were: CD8+ lymphocytes $>$600 cells/mm$\sp3,$ Hgb $>$11.0 g/dl, Hct $>$31.0% and WBC level $>$3000 cells/mm$\sp3.$ ^