RESUMO
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.
RESUMO
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.
Assuntos
Matadouros , Salmonella enterica , Bovinos , Animais , Análise de Perigos e Pontos Críticos de Controle , Argentina , Salmonella/genética , Salmonella enterica/genética , Eletroforese em Gel de Campo Pulsado/métodosRESUMO
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.
Assuntos
Biomarcadores Tumorais , Neoplasias , Biomarcadores Tumorais/genética , Humanos , Neoplasias/diagnóstico , Neoplasias/genética , Neoplasias/terapia , Prognóstico , Modelos de Riscos ProporcionaisRESUMO
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.
Assuntos
Doenças dos Bovinos/epidemiologia , Infecções por Escherichia coli/veterinária , Escherichia coli Shiga Toxigênica/isolamento & purificação , Matadouros , Animais , Argentina/epidemiologia , Bovinos , Doenças dos Bovinos/microbiologia , Eletroforese em Gel de Campo Pulsado/veterinária , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/microbiologia , Escherichia coli O157/isolamento & purificaçãoRESUMO
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.
Assuntos
Infecções Pneumocócicas/epidemiologia , Infecções Pneumocócicas/microbiologia , Vacinas Pneumocócicas/administração & dosagem , Streptococcus pneumoniae/genética , Adolescente , Adulto , Idoso , Antibacterianos/farmacologia , Criança , Pré-Escolar , Farmacorresistência Bacteriana , Monitoramento Epidemiológico , Feminino , Genoma Bacteriano/genética , Humanos , Lactente , Recém-Nascido , Masculino , México/epidemiologia , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Infecções Pneumocócicas/prevenção & controle , Sorogrupo , Sorotipagem , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/efeitos dos fármacos , Adulto JovemRESUMO
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.
Assuntos
Técnicas de Tipagem Bacteriana , Contaminação de Alimentos/análise , Microbiologia de Alimentos , Escherichia coli Shiga Toxigênica/isolamento & purificação , Animais , Argentina , Toxinas Bacterianas/isolamento & purificação , Bovinos , Eletroforese em Gel de Campo Pulsado , Doenças Transmitidas por Alimentos/microbiologia , Humanos , Projetos Piloto , Carne Vermelha/análise , Carne Vermelha/microbiologia , Escherichia coli Shiga Toxigênica/genéticaRESUMO
El objetivo de este trabajo fue confirmar por Electroforesis de Campo Electrico Pulsado (PFGE) que la Salmonella aislada del alimento implicado en el brote (queso blanco) fue la responsable del evento.La muestra de queso blanco presento elevado recuento de coliformes, E. coli y S. aureus,ademas, presencia de Salmo nella spp., lo que indico condiciones sanitarias inadecuadas y posible contaminacion de origen fecal. Para la confirmacion de las cepas sospechosas de Sal monella spp, aisladas de los pacientes y del alimento, se utilizaron tecnicas bioquimicas convencionales, la serotipificacion se realizo siguiendo el esquema de White-kauffmann-LeMinor y la sensibilidad a los antimicrobianos (Ampicilina, Trimetroprim-Sulfametoxazole, Ciprofloxacina, Amoxicilina, Ac.Clavulanico, Cloranfenicol, Ceftriaxone y Tetraciclina) por la tecnica kirby-Bauer. Las cepas bacterianas de Salmonella spp aisladas fueron identificadas como Salmonella Javiana [1,9,12:l, z28:1,5] y resultaron sensibles a todos los antibioticos probados.La Tipificacion Molecular de las cepas, se realizo por PFGE, se gun protocolo estandarizado de PulseNet para Salmonella y el analisis de los patrones se estudio utilizando el programa BioNumerics, version 4.0, lo cual mostro que los aisla dos de Salmonella Javiana procedentes tanto de pacientes como del alimento tenian identico patron de restriccion, en tamano y numero de fragmentos. La ocurrencia de un patron unico de PFGE (Coeficiente de similitud 100%) entre los aislados permitio demostrar que el queso contaminado con Salmonella Javiana fue el responsable del brote familiar.
The aim of this work was confirmation through Pulse Field Gel Electrophoresis (PFGE) that Salmonella isolated from the food implicated in the outbreak (white cheese) was responsible for the event. The white cheese sample showed a high count of Coli orms,f E. coli and S. aureus. Moreover, Salmonella was pre ent,s which indicated inadequate sanitary conditions and possible fecal contamination. The suspected Salmonella strains isolated from patients and the food sample, were confirmed using conventional biochemical techniques, serotyping according to the White-kauffmann-Le Minor scheme and antibiotics sensibility (Am picillin, Trimetroprim-Sulfametoxazole, Ciprofloxacin, Amoxicillin, Clavulanic Acid, Cloranfenicol, Ceftriaxone and tetraciclin) following kirby-Bauers technique. The Salmonella strains were identified as Salmonella Javiana [1,9,12:I, z28:1,5]and were sensitive to all the antibiotics tested. The molecular typing of the strains was performed using PFGE, according to the PulseNet standardized protocol for Salmonella. The pattern analysis was studied using Bionunella merics program, version 4.0, which showed that the Sal monella Javiana isolates from patients as the food sample had an identical restriction pattern in size and fragments number. The incidence of a unique pattern of PFGE (similarity coefficient 100%) between isolates demonstrated that the cheese contaminated with Salmonella Javiana was responsible for the family outbreak.