RESUMEN
OBJECTIVES: To determine how advanced genetic analysis methods may help in clinical diagnosis. STUDY DESIGN: We report a combined genetic diagnosis approach for patients with clinical suspicion of genetic liver diseases in a tertiary referral center, using tools either tier 1: Sanger sequencing on SLC2SA13, ATP8B1, ABCB11, ABCB4, and JAG1 genes, tier 2: panel-based next generation sequencing (NGS), or tier 3: whole-exome sequencing (WES) analysis. RESULTS: In a total of 374 patients undergoing genetic analysis, 175 patients received tier 1 Sanger sequencing based on phenotypic suspicion, and pathogenic variants were identified in 38 patients (21.7%). Tier 2 included 216 patients (39 of tier 1-negative patients) who received panel-based NGS, and pathogenic variants were identified in 60 (27.8%). In tier 3, 41 patients received WES analysis, and 20 (48.8%) obtained genetic diagnosis. Pathogenic variants were detected in 6 of 19 (31.6%) who tested negative in tier 2, and a greater detection rate in 14 of 22 (63.6%) patients with deteriorating/multiorgan disease receiving one-step WES (P = .041). The overall disease spectrum is comprised of 35 genetic defects; 90% of genes belong to the functional categories of small molecule metabolism, ciliopathy, bile duct development, and membrane transport. Only 13 (37%) genetic diseases were detected in more than 2 families. A hypothetical approach using a small panel-based NGS can serve as the first tier with diagnostic yield of 27.8% (98/352). CONCLUSIONS: NGS based genetic test using a combined panel-WES approach is efficient for the diagnosis of the highly diverse genetic liver diseases.
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Pruebas Genéticas , Hepatopatías , Humanos , Secuenciación del Exoma , Hepatopatías/diagnóstico , Hepatopatías/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , MutaciónRESUMEN
The Yanesha are a Peruvian population who inhabit an environment transitional between the Andes and Amazonia. They present cultural traits characteristic of both regions, including in the language they speak: Yanesha belongs to the Arawak language family (which very likely originated in the Amazon/Orinoco lowlands), but has been strongly influenced by Quechua, the most widespread language family of the Andes. Given their location and cultural make-up, the Yanesha make for an ideal case study for investigating language and population dynamics across the Andes-Amazonia divide. In this study, we analyze data from high and mid-altitude Yanesha villages, both Y chromosome (17 STRs and 16 SNPs diagnostic for assigning haplogroups) and mtDNA data (control region sequences and 3 SNPs and one INDEL diagnostic for assigning haplogroups). We uncover sex-biased genetic trends that probably arose in different stages: first, a male-biased gene flow from Andean regions, genetically consistent with highland Quechua-speakers and probably dating back to Inca expansion; and second, traces of European contact consistent with Y chromosome lineages from Italy and Tyrol, in line with historically documented migrations. Most research in the history, archaeology and linguistics of South America has long been characterized by perceptions of a sharp divide between the Andes and Amazonia; our results serve as a clear case-study confirming demographic flows across that 'divide'.
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Cromosomas Humanos Y/genética , ADN Mitocondrial/genética , Etnicidad/genética , Indígenas Sudamericanos/genética , Etnicidad/etnología , Genotipo , Haplotipos , Humanos , Indígenas Sudamericanos/etnología , Lenguaje , Masculino , Repeticiones de Microsatélite/genética , Polimorfismo de Nucleótido Simple/genética , América del SurRESUMEN
BACKGROUND: Allergic asthma is a globally respiratory inflammatory disease. Influenza virus is a respiratory pathogen that causes yearly epidemics and results in high rates of morbidity and mortality. Patients with allergic asthma had a more severe symptom and a higher mortality when they were infected with influenza virus. Hence, influenza vaccination is recommended for patients with asthma. OBJECTIVES: We evaluated the efficacy and effects of influenza vaccination on allergic asthma in a mouse model. METHODS: Ovalbumin-immunized mice were inoculated with inactivated influenza virus A/Puerto Rico/8/34 (PR8) as vaccines and morbidity or mortality and allergic asthma features of these mice were analyzed. RESULTS: Mice inoculated with inactivated PR8 induced high levels of anti-PR8 IgG2a and upregulation of Toll-like receptor (TLR) 7. Vaccinated allergic mice were healthy when they were challenged with live influenza virus while none of non-vaccinated allergic mice survived. Furthermore, inactivated influenza virus vaccine induced neither extra airway inflammation nor asthma features such as IgE, airway hyper-reactivity, and eosinophilia in allergic mice. Particularly, decreased frequency of immune cell infiltrated airways and Th2 cytokines IL-4 and IL-6 production in the bronchoalveolar lavage fluid were noted in vaccinated allergic mice. These results suggested that inactivated influenza virus vaccine is efficient to protect allergic mice from further influenza infection, and it does not exacerbate but reduces IL-4 and IL-6 of allergic asthma. CONCLUSION: Influenza vaccination is essential and efficient for allergic subjects to protect influenza virus infection.
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Asma/inmunología , Vacunas contra la Influenza/administración & dosificación , Vacunas contra la Influenza/inmunología , Interleucina-4/metabolismo , Interleucina-6/metabolismo , Animales , Modelos Animales de Enfermedad , Femenino , Humanos , Ratones , Ratones Endogámicos BALB C , Infecciones por Orthomyxoviridae/prevención & control , Ovalbúmina/inmunología , Puerto Rico , Vacunas de Productos Inactivados/administración & dosificación , Vacunas de Productos Inactivados/inmunologíaRESUMEN
BACKGROUND/PURPOSE: An increase in group D Salmonella isolates with high antimicrobial resistant rates is being seen in Taiwan. This study aimed to determine the multidrug-resistant (MDR, more than three antibiotics) phenotype, genotype, and the correlation between the presence of class 1 integrons and its invasiveness of Salmonella panama and Salmonella enteritidis isolated from children. METHODS: Twenty S. panama and 59 S. enteritidis isolates were examined for minimal inhibitory concentrations of ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline by agar dilution method. The presence of blaPSE-1, floR, aadA2, sul1, and tet(G) resistance genes, class 1 integrons, and Salmonella genomic island 1 (SGI1) was identified by polymerase chain reaction. The adhesion and invasion assays of S. panama to Caco-2 cells were determined using the pour plate method. RESULTS: All S. panama and 15 (25.4%) of the S. enteritidis isolates displayed MDR phenotype. Furthermore, MDR genotype was present in 70.0% of S. panama and 6.8% of S. enteritidis. Class 1 integrons were present in 40.0% of S. panama and 11.9% of S. enteritidis. None contained SGI1 or SGI1 variants. Strains carrying class 1 integrons were more frequently isolated from bacteria with MDR (73.3% vs. 37.5%; odds ratio, 4.6; 95% confidence interval, 1.3-16.0; p=0.01) and isolated from blood and cerebrospinal fluid (46.7% vs. 21.9%; odds ratio, 3.1; 95% confidence interval, 1.0-10.1; p=0.05) than noncarriers. S. panama carrying class 1 integrons were more invasive to Caco-2 cells than those without (p=0.01). CONCLUSION: S. panama and S. enteritidis with class 1 integrons are significantly related to the presence of MDR phenotype. Moreover, S. panama with class 1 integrons may present more invasiveness than those without.
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Farmacorresistencia Bacteriana Múltiple , Integrones , Salmonella enterica/efectos de los fármacos , Células CACO-2 , Niño , Farmacorresistencia Bacteriana/genética , Humanos , Salmonella enterica/clasificación , Salmonella enterica/genética , Salmonella enterica/patogenicidad , Serotipificación , Taiwán , VirulenciaRESUMEN
BACKGROUND AND PURPOSE: Previous studies have indicated that Salmonella enterica serotype Panama causes systemic infections in humans. The present study was undertaken to gain more understanding of the molecular epidemiology and antimicrobial resistance of Salmonella Panama. METHODS: Antimicrobial susceptibility testing and molecular typing were performed on 9 clinical isolates by pulsed-field gel electrophoresis (PFGE). The presence of resistance genes, Salmonella genomic island 1 (SGI1), and integrons was examined by polymerase chain reaction. Plasmid profiles of these isolates were also determined. RESULTS: Molecular typing showed 3 predominant PFGE types with 6 subtypes among these isolates. High rates of antimicrobial resistance to trimethoprim-sulfamethoxazole (66.7%), tetracycline (66.7%), chloramphenicol (66.7%), ampicillin (55.6%), streptomycin (55.6%), kanamycin (55.6%), and gentamicin (44.4%) were found. All 9 isolates were susceptible to ceftriaxone, cefixime, imipenem, amikacin, and ciprofloxacin. Isolates with PFGE type P1 and subtype P1-1 contained a class 1 integron and resistance genes sulI and str (p=0.048). Plasmids of 3 to 20 kb were found in all isolates belonging to PFGE type P1, subtypes P1-1 and P1-2, which were associated with multidrug resistance (p=0.012) and the resistant gene bla(TEM) (p=0.048). There was no SGI1 found in these 9 isolates. CONCLUSIONS: In view of the high rates of drug resistance to the antimicrobial agents tested, extended-spectrum cephalosporins and fluoroquinolones seem to be a better choice for treatment of systemic infection caused by Salmonella Panama. There is a major clone (P1 and its subtypes) among the Salmonella Panama isolates. Multidrug resistance was conferred by integrons or plasmids, rather than SGI1.