Evaluation of three qPCR for the detection of pathogenic leptospires in domestic animals in Nicaragua / [Evaluación de tres PCR cuantitativas para la detección de leptospiras patógenas en animales domésticos en Nicaragua].

Introduction: Molecular biology diagnostic methods such as real-time PCR should be used in Nicaragua to improve the diagnosis of leptospirosis in humans and animals. Objective: To evaluate three qPCR methods for pathogenic Leptospira detection in domestic animals. Materials and methods: Real-time PCR primers were designed for the amplification of specific regions from the Lip 32 gene of Leptospira in SYBER Green (SYBER Green-A) and TaqMan, as well in SYBER Green-B as previously published. The sequences of 12 strains obtained from the database of the National Center for Biotechnology Information (NCBI) were aligned to select probes and primers. The analytical sensitivity was determined by calculating the detectable genomic equivalent while 18 pathogenic references strains and 28 negative controls were used to evaluate the sensitivity and specificity of each one of the three sets in 129 urine samples of domestic animals. Results: The detection limit of four genomic equivalents per reaction was obtained from SYBR Green-A. The specificities were 94.4% (95% CI: 81.1-100.0) for TaqMan, 77.8% (95% CI: 55.8-99.8) for SYBR Green-A, while for SYBR Green-B it was 61.1% (95% CI: 35.8-86.4). In the three tests, we obtained a specificity of 100% (95% CI: 98.2-100.0). In the field samples, 26.4% were positive with SYBR Green-A and 6.1% with SYBR Green-B. Conclusion: SYBR Green-A presented the lowest detection limit while the three techniques under evaluation showed high specificity while TaqMan was the most sensitive.

Introducción. En Nicaragua es necesario estandarizar pruebas moleculares como la PCR en tiempo real (quantitative Polymerase Chain Reaction, qPCR) que mejoren el diagnóstico de leptospirosis en humanos y animales. Objetivo. Evaluar tres qPCR para la detección de leptospiras patógenas en animales domésticos de Nicaragua. Materiales y métodos. Se diseñaron cebadores para la amplificación del gen LipL32 en SYBR Green (SYBR Green-A) y TaqMan, y en otros descritos previamente (SYBR Green-B). Las secuencias de 12 cepas obtenidas de la base de datos del National Center for Biotechnology Information (NCBI) se alinearon para la búsqueda de sondas y cebadores. La sensibilidad analítica se determinó calculando el equivalente genómico detectable, se utilizaron 18 cepas de referencia para la sensibilidad diagnóstica y 28 controles negativos para la especificidad. Los métodos se aplicaron en 129 muestras de orina de animales domésticos. Resultados. En SYBR Green-A se obtuvo un límite de detección de cuatro equivalentes genómicos; en TaqMan, la sensibilidad fue del 94,4 % (IC95% 81,1-100,0). Con SYBR Green-A, se obtuvo una sensibilidad del 77,8 % (IC95% 55,8-99,8), en tanto que con SYBR Green-B fue del 61,1 % (IC95% 35,8-86,4). En las tres pruebas se logró una especificidad del 100 % (IC95% 98,2-100,0). El 26,4 % de las muestras de animales domésticos fueron positivas con SYBR Green-A y el 6,2 % con SYBR Green-B. Conclusiones. El SYBR Green-A presentó un límite de detección bajo, en tanto que las tres técnicas evaluadas mostraron alta especificidad, en tanto que la TaqMan tuvo la mayor sensibilidad.

Evaluación de tres PCR cuantitativas para la detección de leptospiras patógenas en animales domésticos en Nicaragua / Evaluation of three qPCR for the detection of pathogenic leptospires in domestic animals in Nicaragua

Resumen: Introducción. En Nicaragua es necesario estandarizar pruebas moleculares como la PCR en tiempo real (quantitative Polymerase Chain Reaction, qPCR) que mejoren el diagnóstico de leptospirosis en humanos y animales. Objetivo. Evaluar tres qPCR para la detección de leptospiras patógenas en animales domésticos de Nicaragua. Materiales y métodos. Se diseñaron cebadores para la amplificación del gen LipL32 en SYBR Green (SYBR Green-A) y TaqMan, y en otros descritos previamente (SYBR Green-B). Las secuencias de 12 cepas obtenidas de la base de datos del National Center for Biotechnology Information (NCBI) se alinearon para la búsqueda de sondas y cebadores. La sensibilidad analítica se determinó calculando el equivalente genómico detectable, se utilizaron 18 cepas de referencia para la sensibilidad diagnóstica y 28 controles negativos para la especificidad. Los métodos se aplicaron en 129 muestras de orina de animales domésticos. Resultados. En SYBR Green-A se obtuvo un límite de detección de cuatro equivalentes genómicos; en TaqMan, la sensibilidad fue del 94,4 % (IC95% 81,1-100,0). Con SYBR Green-A, se obtuvo una sensibilidad del 77,8 % (IC95% 55,8-99,8), en tanto que con SYBR Green-B fue del 61,1 % (IC95% 35,8-86,4). En las tres pruebas se logró una especificidad del 100 % (IC95% 98,2-100,0). El 26,4 % de las muestras de animales domésticos fueron positivas con SYBR Green-A y el 6,2 % con SYBR Green-B. Conclusiones. El SYBR Green-A presentó un límite de detección bajo, en tanto que las tres técnicas evaluadas mostraron alta especificidad, en tanto que la TaqMan tuvo la mayor sensibilidad.

Abstract: Introduction: Molecular biology diagnostic methods such as real-time PCR should be used in Nicaragua to improve the diagnosis of leptospirosis in humans and animals. Objective: To evaluate three qPCR methods for pathogenic Leptospira detection in domestic animals. Materials and methods: Real-time PCR primers were designed for the amplification of specific regions from the Lip 32 gene of Leptospira in SYBER Green (SYBER Green-A) and TaqMan, as well in SYBER Green-B as previously published. The sequences of 12 strains obtained from the database of the National Center for Biotechnology Information (NCBI) were aligned to select probes and primers. The analytical sensitivity was determined by calculating the detectable genomic equivalent while 18 pathogenic references strains and 28 negative controls were used to evaluate the sensitivity and specificity of each one of the three sets in 129 urine samples of domestic animals. Results: The detection limit of four genomic equivalents per reaction was obtained from SYBR Green-A. The specificities were 94.4% (95% CI: 81.1-100.0) for TaqMan, 77.8% (95% CI: 55.8-99.8) for SYBR Green-A, while for SYBR Green-B it was 61.1% (95% CI: 35.886.4). In the three tests, we obtained a specificity of 100% (95% CI: 98.2-100.0). In the field samples, 26.4% were positive with SYBR Green-A and 6.1% with SYBR Green-B. Conclusion: SYBR Green-A presented the lowest detection limit while the three techniques under evaluation showed high specificity while TaqMan was the most sensitive.

Detection of Pathogenic Leptospires in Water and Soil in Areas Endemic to Leptospirosis in Nicaragua.

In Nicaragua, there are ideal environmental conditions for leptospirosis. The objective of this investigation was to detect pathogenic and saprophytic leptospires in water and soil samples from leptospirosis-endemic areas in Nicaragua. Seventy-eight water and 42 soil samples were collected from houses and rivers close to confirmed human cases. Leptospira spp was isolated in Ellinghausen-McCullough-Johnson-Harris (EMJH) culture medium with 5-fluororacil and positive samples were analyzed through PCR for the LipL32 gene, specific for pathogenic leptospires (P1 clade). There were 73 positive cultures from 120 samples, however only six of these (5% of all collected samples) were confirmed to be pathogenic, based on the presence of the LipL32 gene (P1 clade). Of these six pathogenic isolates, four were from Leon and two from Chinandega. Four pathogenic isolates were obtained from water and two from soil. This study proved the contamination of water and soil with pathogenic leptospires, which represents a potential risk for public health.

Detección de Leptospira spp. en animales y muestras ambientales de áreas peridomésticas en Nicaragua

[RESUMEN]. Objetivo. El objetivo de este estudio fue conocer las características epidemiológicas de la leptospirosis en animales domésticos y en los casos de leptospirosis humana en áreas peridomésticas en Nicaragua entre 2014 y 2016. Métodos. Las muestras se extrajeron en áreas donde se confirmaron casos en humanos utilizando un muestreo no probabilístico en 10 de los 17 departamentos del país. Se incluyeron 112 muestras de orina de animales domésticos, 129 muestras de agua y 69 de tierra para aislar leptospiras en medio Ellinghausen-McCullough-Johnson-Harris (EMJH). Además, se aplicó la prueba de microaglutinación (MAT) en 263 muestras de suero de animales y 88 aislados se analizaron mediante PCR. Resultados. En 32,6% (101/310) de las muestras se aislaron espiroquetas, 23,2% (26/112) se aislaron en la orina de animales domésticos, 47,3% (61/129), en las muestras de agua y 20,3 % (14/69), en las de tierra. El análisis de aislamiento mostró diferencias significativas (P < 0,05) entre los departamentos para los diferentes tipos de muestras, y el aislamiento fue más frecuente en agua que en tierra (OR = 3,49; IC95%: 1,56-7,80). El 14,1% (37/263) de los animales fueron reactores en la prueba de microaglutinación. El serogrupo más frecuente fue Icterohaemorrhagiae (40%). En el análisis con la PCR para identificar leptospiras de las especies patógenas 10,2% (9/88) de los aislamientos fueron positivos. Conclusiones. Esta investigación demuestra que los animales domésticos y el ambiente desempeñan un papel importante en la aparición de brotes de la leptospirosis y confirma el comportamiento endémico de la enfermedad en Nicaragua.

[ABSTRACT]. Objective. The objective of this study was to determine the epidemiological characteristics of leptospirosis in pets and in humans in peridomestic settings in Nicaragua between 2014 and 2016. Methods. The samples were taken in areas where cases were confirmed in humans using non-probabilistic sampling in 10 of the country’s 17 departments. This included 112 urine samples from pets, 129 water samples, and 69 soil samples in order to isolate leptospires in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium. Furthermore, the microscopic agglutination test (MAT) was applied to 263 samples of animal serum, and 88 isolates were analyzed using PCR. Results. In 32.6% (101/310) of the samples, spirochetes were isolated: 23.2% (26/112) in the pet urine, 47.3% (61/129) in water samples, and 20.3% (14/69) in soil samples. Isolation analysis showed significant differences (p<0.05) between departments for the different types of samples, and isolation was more frequent in water than in soil (OR = 3.49; CI95%: 1.56-7.80). In total, 14.1% (37/263) of the animals were reactors in the microscopic agglutination test. The most frequent serogroup was Icterohaemorrhagiae (40%). PCR analysis to identify pathogenic species of leptospires resulted in 10.2% (9/88) positive isolations. Conclusions. This research demonstrates that pets and environment conditions play an important role in the emergence of outbreaks of leptospirosis, and confirms the endemic behavior of the disease in Nicaragua.

[RESUMO]. Objetivo. Descrever as características epidemiológicas da leptospirose em animais domésticos e em casos de leptospirose humana em áreas peridomiciliares na Nicarágua entre 2014 e 2016. Métodos. As amostras foram coletadas por amostragem não probabilística em áreas com casos confirmados de leptospirose humana em 10 das 17 províncias do país. Foram analisadas 112 amostras de urina de animais domésticos, 129 amostras de água e 69 amostras de solo com o uso do meio de cultura padrão para o isolamento de leptospiras (Ellinghausen-McCullough-Johnson-Harris, EMJH). Além disso, foi realizado o teste de aglutinação microscópica em 263 amostras séricas de animais e 88 isolados foram analisados com a técnica de PCR. Resultados. Em 32,6% (101/310) das amostras foram isoladas espiroquetas, sendo 23,2% (26/112) isoladas na urina de animais domésticos, 47,3% (61/129) nas amostras de água e 20,3% (14/69) nas amostras de solo. Houve diferença significativa (P < 0,05) entre as províncias no isolamento nos diferentes tipos de amostras analisadas, sendo o isolamento mais frequente nas amostras de água que de solo (OR = 3,49; IC95%: 1, 56–7,80). Reatividade no teste de aglutinação microscópica foi observada em 14,1% (37/263) das amostras de animais. O sorogrupo mais frequentemente isolado foi Icterohaemorrhagiae (40%). A técnica de PCR demonstrou que 10,2% (9/88) dos isolados eram positivos para espécies patogênicas de leptospiras. Conclusões. Esta pesquisa demonstra que os animais domésticos e o entorno têm papel importante no surgimento de surtos de leptospirose e confirma o comportamento endêmico da doença na Nicarágua.

[Detection of Leptospire spp. in animals and in environmental samples from peridomestic areas in NicaraguaDetecção de Leptospira spp. em animais e em amostras ambientais de áreas peridomiciliares na Nicarágua]. / Detección de Leptospira spp. en animales y muestras ambientales de áreas peridomésticas en Nicaragua.

OBJECTIVE: The objective of this study was to determine the epidemiological characteristics of leptospirosis in pets and in humans in peridomestic settings in Nicaragua between 2014 and 2016. METHODS: The samples were taken in areas where cases were confirmed in humans using non-probabilistic sampling in 10 of the country's 17 departments. This included 112 urine samples from pets, 129 water samples, and 69 soil samples in order to isolate leptospires in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium. Furthermore, the microscopic agglutination test (MAT) was applied to 263 samples of animal serum, and 88 isolates were analyzed using PCR. RESULTS: In 32.6% (101/310) of the samples, spirochetes were isolated: 23.2% (26/112) in the pet urine, 47.3% (61/129) in water samples, and 20.3% (14/69) in soil samples. Isolation analysis showed significant differences (p<0.05) between departments for the different types of samples, and isolation was more frequent in water than in soil (OR = 3.49; CI95%: 1.56-7.80). In total, 14.1% (37/263) of the animals were reactors in the microscopic agglutination test. The most frequent serogroup was Icterohaemorrhagiae (40%). PCR analysis to identify pathogenic species of leptospires resulted in 10.2% (9/88) positive isolations. CONCLUSIONS: This research demonstrates that pets and environment conditions play an important role in the emergence of outbreaks of leptospirosis, and confirms the endemic behavior of the disease in Nicaragua.

OBJETIVO: Descrever as características epidemiológicas da leptospirose em animais domésticos e em casos de leptospirose humana em áreas peridomiciliares na Nicarágua entre 2014 e 2016. MÉTODOS: As amostras foram coletadas por amostragem não probabilística em áreas com casos confirmados de leptospirose humana em 10 das 17 províncias do país. Foram analisadas 112 amostras de urina de animais domésticos, 129 amostras de água e 69 amostras de solo com o uso do meio de cultura padrão para o isolamento de leptospiras (Ellinghausen-McCullough-Johnson-Harris, EMJH). Além disso, foi realizado o teste de aglutinação microscópica em 263 amostras séricas de animais e 88 isolados foram analisados com a técnica de PCR. RESULTADOS: Em 32,6% (101/310) das amostras foram isoladas espiroquetas, sendo 23,2% (26/112) isoladas na urina de animais domésticos, 47,3% (61/129) nas amostras de água e 20,3% (14/69) nas amostras de solo. Houve diferença significativa (P < 0,05) entre as províncias no isolamento nos diferentes tipos de amostras analisadas, sendo o isolamento mais frequente nas amostras de água que de solo (OR = 3,49; IC95%: 1,56­7,80). Reatividade no teste de aglutinação microscópica foi observada em 14,1% (37/263) das amostras de animais. O sorogrupo mais frequentemente isolado foi Icterohaemorrhagiae (40%). A técnica de PCR demonstrou que 10,2% (9/88) dos isolados eram positivos para espécies patogênicas de leptospiras. CONCLUSÕES: Esta pesquisa demonstra que os animais domésticos e o entorno têm papel importante no surgimento de surtos de leptospirose e confirma o comportamento endêmico da doença na Nicarágua.

Detección de Leptospira spp. en animales y muestras ambientales de áreas peridomésticas en Nicaragua / Detection of Leptospire spp. in animals and in environmental samples from peridomestic areas in Nicaragua / Detecção de Leptospira spp. em animais e em amostras ambientais de áreas peridomiciliares na Nicarágua

RESUMEN Objetivo El objetivo de este estudio fue conocer las características epidemiológicas de la leptospirosis en animales domésticos y en los casos de leptospirosis humana en áreas peridomésticas en Nicaragua entre 2014 y 2016. Métodos Las muestras se extrajeron en áreas donde se confirmaron casos en humanos utilizando un muestreo no probabilístico en 10 de los 17 departamentos del país. Se incluyeron 112 muestras de orina de animales domésticos, 129 muestras de agua y 69 de tierra para aislar leptospiras en medio Ellinghausen-McCullough-Johnson-Harris (EMJH). Además, se aplicó la prueba de microaglutinación (MAT) en 263 muestras de suero de animales y 88 aislados se analizaron mediante PCR. Resultados En 32,6% (101/310) de las muestras se aislaron espiroquetas, 23,2% (26/112) se aislaron en la orina de animales domésticos, 47,3% (61/129), en las muestras de agua y 20,3 % (14/69), en las de tierra. El análisis de aislamiento mostró diferencias significativas (P < 0,05) entre los departamentos para los diferentes tipos de muestras, y el aislamiento fue más frecuente en agua que en tierra (OR = 3,49; IC95%: 1,56-7,80). El 14,1% (37/263) de los animales fueron reactores en la prueba de microaglutinación. El serogrupo más frecuente fue Icterohaemorrhagiae (40%). En el análisis con la PCR para identificar leptospiras de las especies patógenas 10,2% (9/88) de los aislamientos fueron positivos. Conclusiones Esta investigación demuestra que los animales domésticos y el ambiente desempeñan un papel importante en la aparición de brotes de la leptospirosis y confirma el comportamiento endémico de la enfermedad en Nicaragua.

ABSTRACT Objective The objective of this study was to determine the epidemiological characteristics of leptospirosis in pets and in humans in peridomestic settings in Nicaragua between 2014 and 2016. Methods The samples were taken in areas where cases were confirmed in humans using non-probabilistic sampling in 10 of the country's 17 departments. This included 112 urine samples from pets, 129 water samples, and 69 soil samples in order to isolate leptospires in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium. Furthermore, the microscopic agglutination test (MAT) was applied to 263 samples of animal serum, and 88 isolates were analyzed using PCR. Results In 32.6% (101/310) of the samples, spirochetes were isolated: 23.2% (26/112) in the pet urine, 47.3% (61/129) in water samples, and 20.3% (14/69) in soil samples. Isolation analysis showed significant differences (p<0.05) between departments for the different types of samples, and isolation was more frequent in water than in soil (OR = 3.49; CI95%: 1.56-7.80). In total, 14.1% (37/263) of the animals were reactors in the microscopic agglutination test. The most frequent serogroup was Icterohaemorrhagiae (40%). PCR analysis to identify pathogenic species of leptospires resulted in 10.2% (9/88) positive isolations. Conclusions This research demonstrates that pets and environment conditions play an important role in the emergence of outbreaks of leptospirosis, and confirms the endemic behavior of the disease in Nicaragua.

RESUMO Objetivo Descrever as características epidemiológicas da leptospirose em animais domésticos e em casos de leptospirose humana em áreas peridomiciliares na Nicarágua entre 2014 e 2016. Métodos As amostras foram coletadas por amostragem não probabilística em áreas com casos confirmados de leptospirose humana em 10 das 17 províncias do país. Foram analisadas 112 amostras de urina de animais domésticos, 129 amostras de água e 69 amostras de solo com o uso do meio de cultura padrão para o isolamento de leptospiras (Ellinghausen-McCullough-Johnson-Harris, EMJH). Além disso, foi realizado o teste de aglutinação microscópica em 263 amostras séricas de animais e 88 isolados foram analisados com a técnica de PCR. Resultados Em 32,6% (101/310) das amostras foram isoladas espiroquetas, sendo 23,2% (26/112) isoladas na urina de animais domésticos, 47,3% (61/129) nas amostras de água e 20,3% (14/69) nas amostras de solo. Houve diferença significativa (P < 0,05) entre as províncias no isolamento nos diferentes tipos de amostras analisadas, sendo o isolamento mais frequente nas amostras de água que de solo (OR = 3,49; IC95%: 1,56-7,80). Reatividade no teste de aglutinação microscópica foi observada em 14,1% (37/263) das amostras de animais. O sorogrupo mais frequentemente isolado foi Icterohaemorrhagiae (40%). A técnica de PCR demonstrou que 10,2% (9/88) dos isolados eram positivos para espécies patogênicas de leptospiras. Conclusões Esta pesquisa demonstra que os animais domésticos e o entorno têm papel importante no surgimento de surtos de leptospirose e confirma o comportamento endêmico da doença na Nicarágua.

A field study of the microbiological quality of fresh produce of domestic and Mexican origin.

Produce is responsible for an increasingly larger proportion of foodborne disease outbreaks. In particular, the globalization of the food supply may introduce new food safety risks and allow widespread distribution of contaminated food, particularly produce. The objectives of this study were to: (i) compare the overall quality of domestic and Mexican produce throughout the packing process; (ii) examine changes in microbiological quality of both domestic and Mexican produce at each stage of production and processing; and (iii) evaluate the prevalence of select pathogens on fresh produce, including leafy green, herbs, melons, and vegetables. Furthermore, we also sought to characterize the antibiotic resistance profiles of Enterococcus faecium and Enterococcus faecalis strains isolated from fresh produce. A total of 466 produce and matching environmental swab samples was collected from various locations in packing sheds in the southern US from November 2002 through December 2003. These samples were assayed by enumerative tests for total aerobic bacteria (APC), total coliforms, total Enterococcus, and E. coli. Produce samples were also analyzed for the presence of Salmonella, Listeria monocytogenes, Shigella, and E. coli O157:H7. A total of 112 E. faecium and E. faecalis isolates were further screened for antibiotic resistance using a panel of seventeen antibiotics. Overall, the microbiological quality of fresh produce ranged from 4.0 to 7.9 log(10) CFU/g (APC); less than 1.0 log(10) to 4.5 log(10) CFU/g (coliforms); less than 1.0 log(10) to 4.0 log(10) CFU/g (E. coli); and less than 1.0 log(10) to 5.4 log(10) CFU/g (Enterococcus). No Salmonella, Shigella, or E. coli O157:H7 were detected from the 466 25-g produce samples tested. However, three domestic cabbage samples were found to be positive for L. monocytogenes. Of the Enterococcus isolates, E. faecium had a higher degree of resistance to antibiotics in general, while Enterococcus spp. isolated from Mexican produce had a higher degree of antibiotic resistance when compared to strains isolated from produce samples of domestic origin. Despite increased attention to the role of imported produce in foodborne disease, this study does not support the assumption that domestic produce is of higher microbial quality than Mexican produce.

A field study of the microbiological quality of fresh produce.

The Centers for Disease Control and Prevention has reported that foodborne disease outbreaks associated with fruits and vegetables increased during the past decade. This study was conducted to characterize the routes of microbial contamination in produce and to identify areas of potential contamination from production through postharvest handling. We report here the levels of bacterial indicator organisms and the prevalence of selected pathogens in produce samples collected from the southern United States. A total of 398 produce samples (leafy greens, herbs, and cantaloupe) were collected through production and the packing shed and assayed by enumerative tests for total aerobic bacteria, total coliforms, total Enterococcus, and Escherichia coli. These samples also were analyzed for Salmonella, Listeria monocytogenes, and E. coli O157:H7. Microbiological methods were based on methods recommended by the U.S. Food and Drug Administration. For all leafy greens and herbs, geometric mean indicator levels ranged from 4.5 to 6.2 log CFU/g (aerobic plate count); less than 1 to 4.3 log CFU/g (coliforms and Enterococcus); and less than 1 to 1.5 log CFU/g (E. coli). In many cases, indicator levels remained relatively constant throughout the packing shed, particularly for mustard greens. However, for cilantro and parsley, total coliform levels increased during the packing process. For cantaloupe, microbial levels significantly increased from field through packing, with ranges of 6.4 to 7.0 log CFU/g (aerobic plate count); 2.1 to 4.3 log CFU/g (coliforms); 3.5 to 5.2 log CFU/g (Enterococcus); and less than 1 to 2.5 log CFU/g (E. coli). The prevalence of pathogens for all samples was 0, 0, and 0.7% (3 of 398) for L. monocytogenes, E. coli O157:H7, and Salmonella, respectively. This study demonstrates that each step from production to consumption may affect the microbial load of produce and reinforces government recommendations for ensuring a high-quality product.