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BACKGROUND: Biomarkers play a role in identifying, managing, and predicting cancer outcomes. In lung cancer, they are used at various time points. Doubts remain regarding their accuracy for differential diagnosis and histological subtyping. A diagnostic test study was conducted. It included malignant lesions and controls with benign lesions. Before lung biopsy, all patients had the following biomarkers measured in serum (Pro-GRP,NSE,CYFRA21-1,SCC-Ag,CEA). METHODS: The predictive capacity of serum biomarkers was evaluated to discriminate between lung cancer and benign pathology. The accuracy was also assessed for distinguishing between SCLC and NSCLC and explored their ability to perform histological subtyping. RESULTS: 93 patients were included, 60 with lung cancer, 33 with benign pathology. Pro-GRP and NSE were elevated in SCLC compared with NSCLC or nonmalignant disease. The most accurate for differentiating between malignant and benign pathology were CEA and CYFRA21-1. Pro-GRP had a poor predictive capacity for distinguishing NSCLC from SCLC. However, combined with CEA and CYFRA21-1, performance improved. For SCLC, the diagnostic capacity of Pro-GRP increased by combining with biomarkers, such as NSE/CYFRA21-1. CONCLUSIONS: Biomarkers lacked the sensitivity and specificity for independent differential diagnosis or histological subtyping. However, the observed patterns in biomarker levels associated with specific histological subtypes suggest potential utility in a multi-biomarker approach or in conjunction with other diagnostic tools. This insight could guide future research to improve diagnostic accuracy and personalized treatment strategies in lung cancer.
Biomarkers are crucial for identifying, managing, and predicting outcomes in lung cancer, though they lack accuracy in differentiating histological subtypes.CEA and CYFRA21-1 were the most accurate biomarkers for distinguishing between malignant and benign pathology.Pro-GRP and NSE levels were elevated in SCLC compared to NSCLC. Pro-GRP alone had poor predictive capacity for differentiating NSCLC from SCLC, but combining it with CEA and CYFRA21-1 improved diagnostic performance.Patterns in biomarker levels suggest that a multi-biomarker approach, especially when combined with other diagnostic tools, could improve diagnostic accuracy.
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Antígenos de Neoplasias , Biomarcadores de Tumor , Carcinoma de Pulmón de Células no Pequeñas , Queratina-19 , Neoplasias Pulmonares , Humanos , Carcinoma de Pulmón de Células no Pequeñas/sangre , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico , Biomarcadores de Tumor/sangre , Neoplasias Pulmonares/sangre , Neoplasias Pulmonares/diagnóstico , Diagnóstico Diferencial , Masculino , Femenino , Persona de Mediana Edad , Anciano , Antígenos de Neoplasias/sangre , Queratina-19/sangre , Carcinoma Pulmonar de Células Pequeñas/sangre , Carcinoma Pulmonar de Células Pequeñas/diagnóstico , Antígeno Carcinoembrionario/sangre , Serpinas/sangre , Fosfopiruvato Hidratasa/sangre , Sensibilidad y Especificidad , AdultoRESUMEN
Abstract We subtyped 32 Salmonella enterica strains isolated from carcasses (n = 10), theenvironment (n = 14), head meat (n = 1) and viscera washing and chilling water (n = 7) in provin-cial abattoirs with no Hazard Analysis Critical Control Point (HACCP) system from Buenos Aires,Argentina, before and after implementing improvement actions. Pulsed-field gel electrophore-sis (PFGE) was carried out using the XbaI restriction enzyme. Strains belonged to six serovars,from which 10 restriction patterns were obtained (five unique patterns and five clusters). Wefound different clones of S. enterica serovars in the same abattoir by XbaI-PFGE. In addition topromoting good hygiene practices, the implementation of an HACCP plan is necessary to meetthe zero-tolerance criteria for Salmonella on beef.
Resumen Subtipificamos en total 32 cepas de Salmonella enterica aisladas de carcasas(n = 10), medio ambiente (n = 14), carne de cabeza (n = 1) y agua de lavado y enfriamientode vísceras (n = 7) en frigoríficos provinciales de Buenos Aires (Argentina) sin análisis de peli-gros y puntos críticos de control (hazard analysis critical control point [HACCP]); la toma demuestras se efectuó antes y después de implementar acciones de mejora. Se llevó a cabo elec-troforesis en gel de campo pulsado (PFGE) utilizando la enzima de restricción XbaI. Las cepaspertenecían a 6 serovares y presentaron 10 patrones de restricción (5 patrones únicos y 5 clus-ters). Demostramos la presencia de diferentes serovares de S. enterica en un mismo frigorífico.
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We subtyped 32 Salmonella enterica strains isolated from carcasses (n=10), the environment (n=14), head meat (n=1) and viscera washing and chilling water (n=7) in provincial abattoirs with no Hazard Analysis Critical Control Point (HACCP) system from Buenos Aires, Argentina, before and after implementing improvement actions. Pulsed-field gel electrophoresis (PFGE) was carried out using the XbaI restriction enzyme. Strains belonged to six serovars, from which 10 restriction patterns were obtained (five unique patterns and five clusters). We found different clones of S. enterica serovars in the same abattoir by XbaI-PFGE. In addition to promoting good hygiene practices, the implementation of an HACCP plan is necessary to meet the zero-tolerance criteria for Salmonella on beef.
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Mataderos , Salmonella enterica , Bovinos , Animales , Análisis de Peligros y Puntos de Control Críticos , Argentina , Salmonella/genética , Salmonella enterica/genética , Electroforesis en Gel de Campo Pulsado/métodosRESUMEN
PURPOSE: Multiomics cancer subtyping is becoming increasingly popular for directing state-of-the-art therapeutics. However, these methods have never been systematically assessed for their ability to capture cancer prognosis for identified subtypes, which is essential to effectively treat patients. METHODS: We systematically searched PubMed, The Cancer Genome Atlas, and Pan-Cancer Atlas for multiomics cancer subtyping studies from 2010 through 2019. Studies comprising at least 50 patients and examining survival were included. Pooled Cox and logistic mixed-effects models were used to compare the ability of multiomics subtyping methods to identify clinically prognostic subtypes, and a structural equation model was used to examine causal paths underlying subtyping method and mortality. RESULTS: A total of 31 studies comprising 10,848 unique patients across 32 cancers were analyzed. Latent-variable subtyping was significantly associated with overall survival (adjusted hazard ratio, 2.81; 95% CI, 1.16-6.83; P = .023) and vital status (1 year adjusted odds ratio, 4.71; 95% CI, 1.34-16.49; P = .015; 5 year adjusted odds ratio, 7.69; 95% CI, 1.83-32.29; P = .005); latent-variable-identified subtypes had greater associations with mortality across models (adjusted hazard ratio, 1.19; 95% CI, 1.01-1.42; P = .050). Our structural equation model confirmed the path from subtyping method through multiomics subtype (ßË = 0.66; P = .048) on survival (ßË = 0.37; P = .008). CONCLUSION: Multiomics methods have different abilities to define clinically prognostic cancer subtypes, which should be considered before administration of personalized therapy; preliminary evidence suggests that latent-variable methods better identify clinically prognostic biomarkers and subtypes.
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Biomarcadores de Tumor , Neoplasias , Biomarcadores de Tumor/genética , Humanos , Neoplasias/diagnóstico , Neoplasias/genética , Neoplasias/terapia , Pronóstico , Modelos de Riesgos ProporcionalesRESUMEN
We aimed to compare the genetic diversity existing in VTEC O157:H7 strains isolated from cases of human disease from Argentina and Chile. For it, 76 strains were studied in relation to the distribution of genes encoding virulence factors and subtyped by lineage-specific polymorphisms (LSPA-6), and phylogroups assignment. Our results show the almost exclusive circulation of VTEC O157:H7 isolates belonging to lineage I/II, associated with hypervirulent strains, and to the phylogroup E and, on the other hand, genetic diversity present among Argentinean and Chilean strains analyzed, mainly in relation to putative virulence determinants and nle profiles.
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Infecciones por Escherichia coli , Escherichia coli O157 , Argentina , Chile , Infecciones por Escherichia coli/epidemiología , Escherichia coli O157/genética , Humanos , Factores de Virulencia/genéticaRESUMEN
The present study was aimed at subtyping of Stx1 and Stx2 genes and characterization of antimicrobial resistance in 106 Shiga toxin-producing Escherichia coli (STEC) strains isolated from cattle and sheep feces. PCR was used to determine the subtypes, and the disk-diffusion method was used to evaluate the antimicrobial resistance. Ten antibiotics from five different classes were tested. Among the isolates of bovine origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2d) were identified. In isolates of sheep origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2 g) were identified. The results obtained suggest the presence of high diversity in Stx1 and Stx2 genes. Further, 96.6% (57/59) of bovine fecal strains and 89.4% (42/47) of sheep fecal strains showed resistance to at least one tested antibiotic. In both animal species, most strains were multidrug-resistant (MDR) (67.8% in cattle and 59.6% in sheep), with no significant difference between host animals. Adult animals were eight times more likely to have STEC with greater pathogenic potential. STEC with the highest pathogenic potential were three times more likely to be multidrug-resistant than STEC with the lowest pathogenic potential. The data reported in this study suggests the occurrence of strains with high potential pathogenicity in the region studied. Therefore, the ruminants of this region are carriers of strains that can cause infections in humans.(AU)
O presente estudo teve como objetivo subtipar os genes Stx1 e Stx2 e caracterizar a resistência antimicrobiana em 106 isolados de Escherichia coli produtoras de toxinas Shiga (STEC) isoladas de fezes de bovinos e ovinos. A PCR foi utilizada para determinar os subtipos e o método de difusão em disco foi utilizado para avaliar a resistência antimicrobiana. Dez antibióticos de cinco classes diferentes foram testados. Entre os isolados de origem bovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2d). Nos isolados de origem ovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2g). Os resultados obtidos sugerem a presença de alta variabilidade nos genes Stx1 e Stx2. Além disso, 96,6% (57/59) dos isolados fecais de bovinos e 89,4% (42/47) dos isolados de ovinos mostraram resistência a pelo menos um antibiótico testado. Em ambas as espécies animais, a maioria das cepas foi multirresistente (MDR) (67,8% em bovinos e 59,6% em ovinos), sem diferença significativa entre as espécies animais do reservatório. Os animais adultos tiveram oito vezes mais chances de apresentar STEC com maior potencial patogênico. STEC com o maior potencial patogênico teve três vezes mais chances de ser multirresistente do que o STEC com o menor potencial patogênico. Os dados relatados neste estudo sugerem a ocorrência de cepas com alto potencial de patogenicidade na região estudada. Portanto, os ruminantes dessa região são hospedeiros de isolados que podem causar infecções em humanos.(AU)
Asunto(s)
Animales , Bovinos , Bovinos/microbiología , Ovinos/microbiología , Toxinas Shiga , Escherichia coli/aislamiento & purificación , Escherichia coli Shiga-Toxigénica , Antiinfecciosos , Reacción en Cadena de la PolimerasaRESUMEN
The present study was aimed at subtyping of Stx1 and Stx2 genes and characterization of antimicrobial resistance in 106 Shiga toxin-producing Escherichia coli (STEC) strains isolated from cattle and sheep feces. PCR was used to determine the subtypes, and the disk-diffusion method was used to evaluate the antimicrobial resistance. Ten antibiotics from five different classes were tested. Among the isolates of bovine origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2d) were identified. In isolates of sheep origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2 g) were identified. The results obtained suggest the presence of high diversity in Stx1 and Stx2 genes. Further, 96.6% (57/59) of bovine fecal strains and 89.4% (42/47) of sheep fecal strains showed resistance to at least one tested antibiotic. In both animal species, most strains were multidrug-resistant (MDR) (67.8% in cattle and 59.6% in sheep), with no significant difference between host animals. Adult animals were eight times more likely to have STEC with greater pathogenic potential. STEC with the highest pathogenic potential were three times more likely to be multidrug-resistant than STEC with the lowest pathogenic potential. The data reported in this study suggests the occurrence of strains with high potential pathogenicity in the region studied. Therefore, the ruminants of this region are carriers of strains that can cause infections in humans.(AU)
O presente estudo teve como objetivo subtipar os genes Stx1 e Stx2 e caracterizar a resistência antimicrobiana em 106 isolados de Escherichia coli produtoras de toxinas Shiga (STEC) isoladas de fezes de bovinos e ovinos. A PCR foi utilizada para determinar os subtipos e o método de difusão em disco foi utilizado para avaliar a resistência antimicrobiana. Dez antibióticos de cinco classes diferentes foram testados. Entre os isolados de origem bovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2d). Nos isolados de origem ovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2g). Os resultados obtidos sugerem a presença de alta variabilidade nos genes Stx1 e Stx2. Além disso, 96,6% (57/59) dos isolados fecais de bovinos e 89,4% (42/47) dos isolados de ovinos mostraram resistência a pelo menos um antibiótico testado. Em ambas as espécies animais, a maioria das cepas foi multirresistente (MDR) (67,8% em bovinos e 59,6% em ovinos), sem diferença significativa entre as espécies animais do reservatório. Os animais adultos tiveram oito vezes mais chances de apresentar STEC com maior potencial patogênico. STEC com o maior potencial patogênico teve três vezes mais chances de ser multirresistente do que o STEC com o menor potencial patogênico. Os dados relatados neste estudo sugerem a ocorrência de cepas com alto potencial de patogenicidade na região estudada. Portanto, os ruminantes dessa região são hospedeiros de isolados que podem causar infecções em humanos.(AU)
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Animales , Bovinos , Bovinos/microbiología , Ovinos/microbiología , Toxinas Shiga , Escherichia coli/aislamiento & purificación , Escherichia coli Shiga-Toxigénica , Antiinfecciosos , Reacción en Cadena de la PolimerasaRESUMEN
ABSTRACT: The present study was aimed at subtyping of Stx1 and Stx2 genes and characterization of antimicrobial resistance in 106 Shiga toxin-producing Escherichia coli (STEC) strains isolated from cattle and sheep feces. PCR was used to determine the subtypes, and the disk-diffusion method was used to evaluate the antimicrobial resistance. Ten antibiotics from five different classes were tested. Among the isolates of bovine origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2d) were identified. In isolates of sheep origin, two subtypes of Stx1 (Stx1a and Stx1c), and four subtypes of Stx2 (Stx2a, Stx2b, Stx2c, and Stx2 g) were identified. The results obtained suggest the presence of high diversity in Stx1 and Stx2 genes. Further, 96.6% (57/59) of bovine fecal strains and 89.4% (42/47) of sheep fecal strains showed resistance to at least one tested antibiotic. In both animal species, most strains were multidrug-resistant (MDR) (67.8% in cattle and 59.6% in sheep), with no significant difference between host animals. Adult animals were eight times more likely to have STEC with greater pathogenic potential. STEC with the highest pathogenic potential were three times more likely to be multidrug-resistant than STEC with the lowest pathogenic potential. The data reported in this study suggests the occurrence of strains with high potential pathogenicity in the region studied. Therefore, the ruminants of this region are carriers of strains that can cause infections in humans.
RESUMO: O presente estudo teve como objetivo subtipar os genes Stx1 e Stx2 e caracterizar a resistência antimicrobiana em 106 isolados de Escherichia coli produtoras de toxinas Shiga (STEC) isoladas de fezes de bovinos e ovinos. A PCR foi utilizada para determinar os subtipos e o método de difusão em disco foi utilizado para avaliar a resistência antimicrobiana. Dez antibióticos de cinco classes diferentes foram testados. Entre os isolados de origem bovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2d). Nos isolados de origem ovina, foram identificados dois subtipos de Stx1 (Stx1a e Stx1c) e quatro subtipos de Stx2 (Stx2a, Stx2b, Stx2c e Stx2g). Os resultados obtidos sugerem a presença de alta variabilidade nos genes Stx1 e Stx2. Além disso, 96,6% (57/59) dos isolados fecais de bovinos e 89,4% (42/47) dos isolados de ovinos mostraram resistência a pelo menos um antibiótico testado. Em ambas as espécies animais, a maioria das cepas foi multirresistente (MDR) (67,8% em bovinos e 59,6% em ovinos), sem diferença significativa entre as espécies animais do reservatório. Os animais adultos tiveram oito vezes mais chances de apresentar STEC com maior potencial patogênico. STEC com o maior potencial patogênico teve três vezes mais chances de ser multirresistente do que o STEC com o menor potencial patogênico. Os dados relatados neste estudo sugerem a ocorrência de cepas com alto potencial de patogenicidade na região estudada. Portanto, os ruminantes dessa região são hospedeiros de isolados que podem causar infecções em humanos.
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We characterized Shiga toxin-producing Escherichia coli (STEC) O157 (n = 20) and non-O157 (n = 68) isolated from carcasses (n = 54), the environment (n = 20), head meat (n = 3) and viscera washing and chilling water (n = 11) in provincial abattoirs before and after implementing improvement actions. The strains were tested for eae, saa, ehxA and fliCH7 genes. Variants stx1 and stx2 were also determined. Pulsed-field gel electrophoresis (PFGE) was carried out with restriction enzymes XbaI and BlnI. All twenty O157 STEC strains [H7; H21; HNM] carried genes rfbO157 and ehxA; 90.0 % were positive for eae and 15.0 % were negative for fliCH7 and positive for saa. Results of PFGE showed 17 XbaI patterns, of which 14 were unique and three formed clusters. From the 68 non-O157 STEC strains, 66.2 %, 55.9 % and 2.9 % were positive for ehxA, saa and eae genes, respectively. Fifty-three XbaI patterns were obtained (49 unique and four forming clusters). Cross-contamination between products and between the environment and products was confirmed in all abattoirs. While the proposed improvements reduced the risk of contamination, Good Hygiene Practices and Good Manufacturing Practices should be implemented in provincial abattoirs, stressing the importance of having a uniform national food safety standard.
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Enfermedades de los Bovinos/epidemiología , Infecciones por Escherichia coli/veterinaria , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Mataderos , Animales , Argentina/epidemiología , Bovinos , Enfermedades de los Bovinos/microbiología , Electroforesis en Gel de Campo Pulsado/veterinaria , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/microbiología , Escherichia coli O157/aislamiento & purificaciónRESUMEN
Influenza A virus (IAV) subtypes H1N1, H1N2, and H3N2 are endemic in swine herds in most pork producing countries; however, the viruses circulating in different geographic regions are antigenically and genetically distinct. In this sense, the availability of a rapid diagnostic assay to detect locally adapted IAVs and discriminate the virus subtype in clinical samples from swine is extremely important for monitoring and control of the disease. This study describes the development and validation of a multiplex RT-PCR assay for detection and subtyping of IAV from pigs. The analytical and diagnostic specificity of the assays was 100% (94.3-100.0, CI 95%), and the limit of detection was 10-3 TCID50/mL. A total of 100 samples (IAV isolates and clinical specimens) were tested, and the virus subtype was determined for 80 samples (80%; 71.1-86.7, CI 95%). From these, 50% were H1N1, 22.5% were H1N2, and 7.5% were H3N2. Partial subtyping was determined for 8.75% samples (H1pdmNx and HxN2). Additionally, mixed infections with two virus subtypes (H1N2 + H3N2 and H1N1pdm + H1pdmN2; 2.5%) and reassortant viruses (H1pdmN2, 6.25%; and H1N1hu, 2.5%) were detected by the assay. A rapid detection of the most prevalent IAV subtypes and lineages in swine is provided by the assays developed here, improving the IAV diagnosis in Brazilian laboratories, and contributing to the IAV monitoring.
Asunto(s)
Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Subtipo H1N2 del Virus de la Influenza A/aislamiento & purificación , Subtipo H3N2 del Virus de la Influenza A/aislamiento & purificación , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones por Orthomyxoviridae/veterinaria , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Enfermedades de los Porcinos/virología , Animales , Brasil/epidemiología , Subtipo H1N1 del Virus de la Influenza A/genética , Subtipo H1N2 del Virus de la Influenza A/genética , Subtipo H3N2 del Virus de la Influenza A/genética , Infecciones por Orthomyxoviridae/diagnóstico , Infecciones por Orthomyxoviridae/epidemiología , Infecciones por Orthomyxoviridae/virología , Filogenia , Porcinos , Enfermedades de los Porcinos/diagnóstico , Enfermedades de los Porcinos/epidemiologíaRESUMEN
Blastocystis spp. has become one of the protozoans arousing the greatest scientific interest because of the controversy surrounding its biology; it is currently considered one of the most prevalent organisms in humans and animals worldwide. Such prevalence increases, especially in tropical countries where infection rates are high, highlighting the need to conduct studies focused on understanding this protozoan's biology. Interestingly, molecular tools are emerging as the best option for diagnosing this infection. This study was thus aimed at conventional PCR molecular detection and characterisation of Blastocystis spp. in human faecal samples from Ibagué, Colombia, using primers targeting the small subunit ribosomal ribonucleic acid (rRNA) gene. One hundred human faecal samples with confirmed Blastocystis spp. were studied, revealing the following subtype genetic diversity: ST1 50%, ST2 33% and ST3 17%. The results contributed to the limited information available regarding Blastocystis spp. in Colombia and created a reference point for further studies in the region.
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El genoma del VIH contiene nueve genes, tres de estos genes (gag, pol y env) codifican proteínas estructurales. Existen dos variantes principales de este virus, VIH-1 y VIH-2. El primero es el causante de la mayoría de las infecciones a nivel mundial, actualmente se han identificado nueve subtipos de VIH-1 y 58 formas recombinantes circulantes (FRC). En Centroamérica, el subtipo B del VIH-1 es el causante de la mayoría de los casos de VIH positivo; en Guatemala se ha reportado la presencia de subtipo B, de formas recombinantes BF1 y del subtipo C; sin embargo, actualmente no existen análisis filogenéticos que indiquen las variantes de este subtipo. Debido a lo anterior, el objetivo del estudio fue llevar a cabo la subtipificación de 400 secuencias de la región pol del VIH-1 obtenidas de 400 pacientes VIH-1 positivos, en una clínica de atención integral de Guatemala del 2010 al 2015. Para determinar los distintos subtipos de VIH-1 presentes en Guatemala se realizó la subtipificación de las secuencias obtenidas por la prueba de genotipo en formato FASTA, con la herramienta REGA HIV-1 Subtyping Tool Version 3.0. Con el fin de determinar la relación entre las variantes de VIH-1, se realizó un alineamiento de secuencias y árboles filogenéticos utilizando el método Neighbor Joining y Máxima Verosimilitud con 100 réplicas bootstrap, con el programa MEGA 7.0.21. Se determinó que el subtipo con mayor frecuencia de las secuencias analizadas es el subtipo B con un 71.5 %, seguido de la forma recombinante BD (16.75 %) y el subtipo B-like (7.75 %)
The HIV genome contains nine genes, three of these genes (gag, pol, and env) encode structural proteins. There are two main variants of this virus, HIV-1 and HIV-2. The first one (HIV-1) is the cause of most infections worldwide, of which nine subtypes and 58 circulating recombinant forms (CRF) have been identified. In Central America, subtype B of HIV-1 is the cause of the majority of HIV positive cases. In Guatemala, it has been reported the presence of subtype B, recombinant forms BF1 and subtype C. However, no phylogenetic analysis has been performed to indicate the variants of this subtype. The aim of the study was to subtype 400 sequences of the pol region of HIV-1, of samples that were obtained from a care clinic during the period 2010 to 2015. To determine the different subtypes of HIV-1 present in Guatemala, the subtyping of the sequences obtained by the genotype test, in FASTA format, was performed with REGA HIV-1 Subtyping Tool - Version 3.0. In order to determine the relationship between HIV-1 variants, an alignment of sequences and phylogenetic trees was performed using the Neighbor Union and Maximum Likelihood method with 100 bootstrap replicas, with the MEGA 7.0.21 program. It was determined that the subtypes with the highest prevalence of the studied sequences are the subtype B (71.5 %), recombinant BD (16.75 %), and subtype B-like (7.75 %)
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Pandemic H1N1, human-like H1N2 and H3N2 influenza A (IAV) viruses are co-circulating in swine herds in Brazil. The genetic analysis of the Brazilian IAVs has shown that they are genetically distinct from viruses found in swine in other countries; therefore, an update of the diagnostic assays for IAV detection and subtyping is needed. This study describes the development and validation of a TaqMan based - one-step multiplex RT-qPCR to discriminate the hemagglutinin and neuraminidase genes of the three major IAV subtypes circulating in pigs in Brazil. The RT-qPCR assays presented 100% (95.7-100, CI 95%) of diagnostic sensitivity in the analysis of 85 IAVs, previously characterized by sequencing. The limits of detection ranged from 5.09 × 101 to 5.09 × 103 viral RNA copies/µL. For the analytical specificity, 73 pig samples collected during 2017 and 2018 were analyzed, resulting in the identification of the subtype in 74.0% (62.9-82.7, CI 95%) of samples. From these, 46.3% were H3N2, 33.3% were H1N1, 11.1% were H1N2 and 3.7% were HxN1. Mixed viral infections (3.7%) and reassortant viruses (1.9%) were also detected by the test. This multiplex RT-qPCR assay provides a fast and specific diagnostic tool for identification of different subtypes and lineages of IAV in pigs, contributing to the monitoring of influenza in swine.
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Virus de la Influenza A/clasificación , Virus de la Influenza A/aislamiento & purificación , Reacción en Cadena de la Polimerasa Multiplex/métodos , Reacción en Cadena de la Polimerasa Multiplex/veterinaria , Infecciones por Orthomyxoviridae/veterinaria , Enfermedades de los Porcinos/virología , Animales , Brasil , Hemaglutininas Virales/genética , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Subtipo H3N2 del Virus de la Influenza A/aislamiento & purificación , Límite de Detección , Neuraminidasa/genética , Infecciones por Orthomyxoviridae/diagnóstico , Infecciones por Orthomyxoviridae/virología , ARN Viral/genética , Sensibilidad y Especificidad , Porcinos , Enfermedades de los Porcinos/diagnósticoRESUMEN
Streptococcus pneumoniae expressing serotype 3 has a high virulence and a high case fatality ratio. Most studies of serotype 3 pneumococci have focused on a single lineage, the widespread sequence type 180 (ST180). To evaluate the serotype 3 lineages causing infections in Mexico, we characterized 196 isolates recovered from 1994 to 2017. The isolates were mostly susceptible to all antimicrobials tested. A single meningitis isolate was resistant to penicillin, and the resistance to erythromycin was 5.2%. The isolates represented the widely disseminated clonal complex 180 (CC180; n = 140), the unusual CC4909 (n = 42), CC260 (n = 11), and a few singletons (n = 3). CC260 was less frequent among pneumococcal invasive disease isolates than CC180 and CC4909 (P = 0.015). There was a decrease of CC4909 (P < 0.001) following PCV13 introduction (2012 to 2017). The CC4909 isolates were represented mostly by ST1119 (n = 40), seemingly having a restricted geographic origin, with isolates in the PubMLST database having been recovered only in Mexico, the United States, and Germany. A genomic analysis of publicly available genomes showed that ST1119 isolates have less than 32% similarity with ST180 isolates, indicating that these lineages are more separated than revealed by traditional multilocus sequence typing. Considering the suggestions of a lower efficacy of the 13-valent pneumococcal conjugate vaccine against serotype 3, the different dynamics of the two major serotype 3 lineages in Mexico following the introduction of PCV13 should be closely monitored.
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Infecciones Neumocócicas/epidemiología , Infecciones Neumocócicas/microbiología , Vacunas Neumococicas/administración & dosificación , Streptococcus pneumoniae/genética , Adolescente , Adulto , Anciano , Antibacterianos/farmacología , Niño , Preescolar , Farmacorresistencia Bacteriana , Monitoreo Epidemiológico , Femenino , Genoma Bacteriano/genética , Humanos , Lactante , Recién Nacido , Masculino , México/epidemiología , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Tipificación de Secuencias Multilocus , Infecciones Neumocócicas/prevención & control , Serogrupo , Serotipificación , Streptococcus pneumoniae/clasificación , Streptococcus pneumoniae/efectos de los fármacos , Adulto JovenRESUMEN
Shiga toxin-producing Escherichia coli (STEC) are important emerging foodborne human pathogens. Ruminants are the main animal reservoir of STEC currently known, and meat can become contaminated at different stages of the production chain. The aim of this work was to subtype and establish the epidemiological relatedness of non-O157 STEC strains isolated from ground beef and the environment in butcher shops before (evaluation stage, 2010-2011 period) and after (verification stage, 2013) implementing improvement actions. Sixty-eight non-O157 STEC strains were tested for eae, saa, ehxA, iha, efa1, toxB, subAB, cdt-V, astA, aggR, and aaiC genes, and stx1 and stx2 variants were determined. Pulsed-field gel electrophoresis (PFGE) was carried out with XbaI and XmaJI. From the 68 strains, 92.6%, 75.0%, 58.8%, 53.5%, 10.3%, 7.3%, and 4.4% were positive for iha, ehxA, subAB, saa, cdt-V, astA, and eae, respectively. All strains were aggR/aaiC-negative. PFGE showed that 19 strains grouped in 9 clusters and 41 showed unique XbaI patterns. During the evaluation stage (2010-2011), we identified clonal strains in different samples, circulating clones in different butcher shops, and more than one different strain in the same butcher shop. The bovine origin of meat and its manufacturing process could not ensure the total absence of all non-O157 STEC serotypes in this foodstuff. Most strains isolated during the evaluation (2010-2011) and verification (2013) stages did not exhibit a genotypic profile associated with human disease. It is necessary to conduct periodic reviews of the new epidemiological information and verify that the analyses of non-O157 STEC in food are appropriate to identify strains affecting the population.
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Técnicas de Tipificación Bacteriana , Contaminación de Alimentos/análisis , Microbiología de Alimentos , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Animales , Argentina , Toxinas Bacterianas/aislamiento & purificación , Bovinos , Electroforesis en Gel de Campo Pulsado , Enfermedades Transmitidas por los Alimentos/microbiología , Humanos , Proyectos Piloto , Carne Roja/análisis , Carne Roja/microbiología , Escherichia coli Shiga-Toxigénica/genéticaRESUMEN
Verotoxin-producing E. coli (VTEC) O157:H7 is the dominant serotype isolated from patients with HUS and, Argentina has the highest rate of HUS in the world. Molecular typing had allowed to identify subpopulations related to the origin and virulence of O157:H7 strains. Our aim was to perform a genetic characterization of 43 O157:H7 strains isolated in Argentine mostly from cattle and humans in order to establish the potential public health risk. For it, we used a combination of molecular subtyping methods in order to identify clade 8_rhsA (C3468G), LSPA-6 and virulence profiles and, a cytotoxicity assay on Vero cell. All isolates carried the clade 8 SNP variant and 98% of them belonged to lineage I/II (2% lineage II). Isolates were grouped into eleven nle profiles, 46% were positive for all nle genes, while the remaining isolates, except two, showed incomplete OI-71, particularly lacked nleF. All isolates showed the plasmid profile ehxA-espP-katP-stcE and harbored ehaA, elfA, iha and lpfA variants lpfA1-3 and lpfA2-2 and, ECSP_0242. The frequencies of the remaining ECSP genes were 95% ECSP_2687, 88% ECSP_3286, 86% ECSP_3620, 53% ECSP_2870/2872 and 44% ECSP_1733. All O157:H7 strains, except the isolate identified as lineage II, were cytotoxic on Vero cells. Among Argentinean strains, most genetic markers occur at equal relative frequencies among clinical and bovine isolates, showing diversity mostly in nle genes profiles. The belonging of the isolates to hypervirulent clade 8 and lineage I/II, the high prevalence of nle and putative virulence factors genes, would allow assigning most O157:H7 strains of this region a high risk to public health.
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Enfermedades de los Bovinos/microbiología , Escherichia coli O157/fisiología , Proteínas de Escherichia coli/genética , Síndrome Hemolítico-Urémico/microbiología , Toxinas Shiga/biosíntesis , Animales , Argentina/epidemiología , Adhesión Bacteriana/genética , Bovinos , Enfermedades de los Bovinos/epidemiología , Análisis por Conglomerados , Escherichia coli O157/clasificación , Genotipo , Síndrome Hemolítico-Urémico/epidemiología , Humanos , Fenotipo , Plásmidos/genética , Virulencia/genética , Factores de Virulencia/genéticaRESUMEN
Introducción: en infecciones por Streptococcus beta hemolíticos los del grupo A de Lancefield son el principal causante de faringitis en niños, y entre los no A los del Grupo C ocupan un lugar importante.Objetivo: tipificar molecularmente las cepas que participaron en un brote de faringitis en niños y demostrar la utilidad de la técnica de electroforesis de campos pulsantes en la identificación de las cepas circulantes.Métodos: se caracterizaron mediante electroforesis de campos pulsantes 12 aislados de Streptococcusbeta hemolíticos pertenecientes a niños atendidos en el Hospital Juan Manuel Márquez durante un brote de faringitis aguda en los meses de enero a marzo de 2008.Resultados: mediante el test de seroagrupamiento se encontró que 6 de los aislados, correspondiente al primer periodo del brote, eran Streptococcus del grupo C y los otros 6 aislados clasificaron como Streptococcuspyogenes, con una mayor presencia en la segunda etapa del brote. La subtipificación mediante la macrorrestriccion con SmaI y electroforesis de campos pulsantes mostró la existencia de dos poblaciones clonales consecutivas durante el brote.Conclusiones: los resultados obtenidos demuestran la utilidad que pudiera tener la subtipificación de aislados mediante electroforesis de campos pulsantes durante un brote o una reemergencia facilitando el control epidemiológico, la localización de la fuente y la toma de decisiones cuando esta fuera necesaria(AU)
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Humanos , Electroforesis en Gel de Campo Pulsado/métodos , Faringitis/terapia , Streptococcus agalactiae , Streptococcus/fisiología , Técnicas de Tipificación Bacteriana/métodos , Bacterias/clasificaciónRESUMEN
Introducción: en infecciones por Streptococcus beta hemolíticos los del grupo A de Lancefield son el principal causante de faringitis en niños, y entre los no A los del Grupo C ocupan un lugar importante. Objetivo: tipificar molecularmente las cepas que participaron en un brote de faringitis en niños y demostrar la utilidad de la técnica de electroforesis de campos pulsantes en la identificación de las cepas circulantes. Métodos: se caracterizaron mediante electroforesis de campos pulsantes 12 aislados de Streptococcusbeta hemolíticos pertenecientes a niños atendidos en el Hospital Juan Manuel Márquez durante un brote de faringitis aguda en los meses de enero a marzo de 2008. Resultados: mediante el test de seroagrupamiento se encontró que 6 de los aislados, correspondiente al primer periodo del brote, eran Streptococcus del grupo C y los otros 6 aislados clasificaron como Streptococcuspyogenes, con una mayor presencia en la segunda etapa del brote. La subtipificación mediante la macrorrestriccion con SmaI y electroforesis de campos pulsantes mostró la existencia de dos poblaciones clonales consecutivas durante el brote. Conclusiones: los resultados obtenidos demuestran la utilidad que pudiera tener la subtipificación de aislados mediante electroforesis de campos pulsantes durante un brote o una reemergencia facilitando el control epidemiológico, la localización de la fuente y la toma de decisiones cuando esta fuera necesaria(AU)
Introduction: in the context of infection by beta hemolytic Streptococci, Lancefield group A is the main cause of pharyngitis in children, whereas Streptococci C play an important role in the non group A. Aims: the purpose of the study was to molecularly typify the strains involved in a pharyngitis outbreak in children, and show the usefulness of pulsed field gel electrophoresis technique for identification of circulating strains. Methods: twelve beta hemolytic Streptococcus isolates from children cared for at Juan Manual Márquez hospital were characterized by pulsed field gel electrophoresis during an acute pharyngitis outbreak from January to March 2008. Results: the serogrouping test found that six of the isolates, corresponding to the first stage of the outbreak, were group C Streptococci, whereas the other six classified as Streptococcus pyogenes, with a greater presence in the second stage. Subtyping by Sma I macrorestriction and pulsed field gel electrophoresis revealed the presence of two consecutive clonal populations during the outbreak. Conclusions: results show the potential usefulness of subtyping isolates with pulsed field gel electrophoresis during an outbreak or an instance of re-emergence, thus facilitating epidemiological control, location of the source, and decision making when required(AU)
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Humanos , Streptococcus/fisiología , Faringitis/epidemiología , Técnicas de Tipificación Bacteriana/métodos , Electroforesis en Gel de Campo Pulsado/métodos , Bacterias/clasificaciónRESUMEN
BACKGROUND: The hepatitis E virus (HEV) is an emergent causative agent of acute hepatitis worldwide, transmitted by fecal-oral route. In Argentina it is considered rare, so differential laboratory testing is not routinely performed. Besides, in Argentina's central area epidemiological and molecular characteristics of HEV are still unknown. OBJECTIVES: Provide evidence of local circulation of HEV by molecular detection on environmental samples and by serological survey in healthy adult population of Córdoba city, Argentina. STUDY DESIGN: Environmental surveillance was conducted in river and sewage samples collected between 2007 and 2009-2011. Viral detection was performed by RT-Nested PCR of ORF-1 and ORF-2 partial regions. Anti-HEV IgG was determined by EIA in 433 serum samples collected between 2009 and 2010. RESULTS: HEV was detected in 6.3% of raw sewage samples and in 3.2% of riverine samples. Nucleotide sequencing analyses revealed that all isolates belonged to genotype 3, subtypes a, b and c. The prevalence of IgG anti-HEV was 4.4%. Seroprevalence increased with the age of the individuals (OR: 3.50; 95% CI 1.39-8.87; p=0.0065) and, although the prevalence was higher in low income population, no statistical relation was found between anti-HEV and socioeconomic level. CONCLUSIONS: The environmental findings added to serological results, demonstrate that HEV circulates in central Argentina. Contamination of water with HEV could represent a route of transmission for local populations, which have a high number of susceptible individuals. This fact alerts local health care systems in order to include detection of HEV in the diagnostic algorithm of viral hepatitis.