RESUMEN
BACKGROUND: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. METHODS: We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. RESULTS: We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. CONCLUSIONS: COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.
Asunto(s)
COVID-19 , Hospitalización , SARS-CoV-2 , Humanos , COVID-19/epidemiología , COVID-19/virología , Hospitalización/estadística & datos numéricos , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/clasificación , Masculino , Femenino , Persona de Mediana Edad , Adulto , Anciano , Estonia/epidemiología , Genoma Viral , Adulto Joven , Filogenia , Pandemias , Adolescente , Niño , Lactante , Preescolar , Anciano de 80 o más AñosRESUMEN
BACKGROUND: Hospital-acquired strains (HASs) and multiresistant strains in neonatal intensive care unit often harbour virulence and resistance mechanisms, carrying the risk of invasive infections. We describe colonisation with Enterobacteriaceae in neonates receiving early directed versus routine family-integrated care (FIC) within the first month of life. METHODS: A prospective cohort study included neonates with a gestational age below 34 weeks. During the first period, neonates were admitted to an open bay unit with transfer to the single-family room if available; feeding with the mother's own breast milk (MOBM) was introduced within 24 hours, and skin-to-skin contact (SSC) within 5 days of life (the routine care group). During the second period, following a wash-in of 2 months, care in a single-family room within 48 hours, the introduction of MOBM within two and SSC in 48 hours were applied (the intervention group). Enterobacteriaceae isolated from neonatal stool, breast milk and parental skin swabs were genotyped, Simpson's Index of Diversity (SID) calculated, and extended-spectrum beta-lactamases (ESBL) detected. RESULTS: In 64 neonate-parents' groups, 176 Enterobacteriaceae, 87 in routine care and 89 in the intervention group were isolated; 26 vs 18 were HAS and one vs three ESBL positive, respectively. In the intervention group compared with the routine care group, SSC and MOBM feeding was started significantly earlier (p<0.001); during the first week of life, time spent in SSC was longer (median hours per day 4.8 (4-5.1) vs 1.9 (1.4-2.6), p<0.001) and the proportion of MOBM in enteral feeds was higher (median (IQR) 97.8% (95.1-100) vs 95.1% (87.2-97.4), p=0.011). Compared with the routine care group, the intervention group had higher SID and a reduction of HAS by 33.1% (95% CI 24.4% to 42.4%) in time series analysis. CONCLUSIONS: Early implementation of FIC measures may hold the potential to increase diversity and reduce colonisation with HAS Enterobacteriaceae.
Asunto(s)
Prestación Integrada de Atención de Salud , Infecciones por Enterobacteriaceae , Recién Nacido , Femenino , Humanos , Lactante , Enterobacteriaceae/genética , Unidades de Cuidado Intensivo Neonatal , Estudios Prospectivos , Infecciones por Enterobacteriaceae/terapiaRESUMEN
Protection against mucocutaneous candidiasis depends on the T helper (Th)17 pathway, as gene defects affecting its integrity result in inability to clear Candida albicans infection on body surfaces. Moreover, autoantibodies neutralizing Th17 cytokines have been related to chronic candidiasis in a rare inherited disorder called autoimmune polyendocriopathy candidiasis ectodermal dystrophy (APECED) caused by mutations in autoimmune regulator (AIRE) gene. However, the direct pathogenicity of these autoantibodies has not yet been addressed. Here we show that the level of anti-IL17A autoantibodies that develop in aged Aire-deficient mice is not sufficient for conferring susceptibility to oropharyngeal candidiasis. However, patient-derived monoclonal antibodies that cross-react with murine IL-22 increase the fungal burden on C. albicans infected mucosa. Nevertheless, the lack of macroscopically evident infectious pathology on the oral mucosa of infected mice suggests that additional susceptibility factors are needed to precipitate a clinical disease.
Asunto(s)
Anticuerpos Neutralizantes/inmunología , Autoanticuerpos/inmunología , Candidiasis Bucal/inmunología , Candidiasis Bucal/microbiología , Interleucinas/inmunología , Animales , Candida albicans/inmunología , Candidiasis Mucocutánea Crónica/inmunología , Candidiasis Mucocutánea Crónica/microbiología , Recuento de Colonia Microbiana , Reacciones Cruzadas , Modelos Animales de Enfermedad , Susceptibilidad a Enfermedades , Femenino , Humanos , Interleucina-17/inmunología , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Ratones Noqueados , Poliendocrinopatías Autoinmunes/inmunología , Células Th17/inmunología , Factores de Transcripción/deficiencia , Factores de Transcripción/genética , Factores de Transcripción/inmunología , Proteína AIRE , Interleucina-22RESUMEN
Clostridium difficile is the primary cause of nosocomial antibiotic-associated diarrhea in the Western world. The major virulence factors of C. difficile are two exotoxins, toxin A (TcdA) and toxin B (TcdB), which cause extensive colonic inflammation and epithelial damage manifested by episodes of diarrhea. In this study, we explored the basis for an oral antitoxin strategy based on engineered Lactobacillus strains expressing TcdB-neutralizing antibody fragments in the gastrointestinal tract. Variable domain of heavy chain-only (VHH) antibodies were raised in llamas by immunization with the complete TcdB toxin. Four unique VHH fragments neutralizing TcdB in vitro were isolated. When these VHH fragments were expressed in either secreted or cell wall-anchored form in Lactobacillus paracasei BL23, they were able to neutralize the cytotoxic effect of the toxin in an in vitro cell-based assay. Prophylactic treatment with a combination of two strains of engineered L. paracasei BL23 expressing two neutralizing anti-TcdB VHH fragments (VHH-B2 and VHH-G3) delayed killing in a hamster protection model where the animals were challenged with spores of a TcdA(-) TcdB(+) strain of C. difficile (P < 0.05). Half of the hamsters in the treated group survived until the termination of the experiment at day 5 and showed either no damage or limited inflammation of the colonic mucosa despite having been colonized with C. difficile for up to 4 days. The protective effect in the hamster model suggests that the strategy could be explored as a supplement to existing therapies for patients.
Asunto(s)
Anticuerpos Neutralizantes/inmunología , Antitoxinas/inmunología , Proteínas Bacterianas/inmunología , Toxinas Bacterianas/inmunología , Clostridioides difficile/inmunología , Enterocolitis Seudomembranosa/prevención & control , Lactobacillus/genética , Anticuerpos de Dominio Único/inmunología , Administración Oral , Animales , Anticuerpos Neutralizantes/genética , Antitoxinas/administración & dosificación , Camélidos del Nuevo Mundo , Clostridioides difficile/patogenicidad , Cricetinae , Modelos Animales de Enfermedad , Enterocolitis Seudomembranosa/microbiología , Escherichia coli/genética , Tracto Gastrointestinal/inmunología , Tracto Gastrointestinal/microbiología , Inmunización , Inmunización Pasiva , Cadenas Pesadas de Inmunoglobulina/genética , Cadenas Pesadas de Inmunoglobulina/inmunología , Cadenas Pesadas de Inmunoglobulina/aislamiento & purificación , Lactobacillus/inmunología , Proteínas Recombinantes/inmunología , Proteínas Recombinantes/aislamiento & purificación , Anticuerpos de Dominio Único/genéticaRESUMEN
The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprim-sulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups.
Asunto(s)
Infecciones por Escherichia coli/epidemiología , Escherichia coli/genética , Infecciones Urinarias/epidemiología , Antibacterianos/farmacología , Técnicas de Tipificación Bacteriana , Cefotaxima/farmacología , Cefuroxima/farmacología , Niño , Preescolar , Farmacorresistencia Bacteriana Múltiple/genética , Electroforesis en Gel de Campo Pulsado , Escherichia coli/clasificación , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/microbiología , Femenino , Gentamicinas/farmacología , Humanos , Integrones/genética , Masculino , Pruebas de Sensibilidad Microbiana , Filogenia , Recurrencia , Combinación Trimetoprim y Sulfametoxazol/farmacología , Infecciones Urinarias/tratamiento farmacológico , Infecciones Urinarias/microbiologíaRESUMEN
Comparing culture- and non-culture-based methods for quantifying Clostridium difficile in antibiotic-associated-diarrhea patients, we found that the real-time PCR method correlated well with quantitative culture and was more sensitive. A positive association between the population levels of C. difficile and the presence of its toxins was found.
Asunto(s)
Antibacterianos/efectos adversos , Carga Bacteriana/métodos , Clostridioides difficile/aislamiento & purificación , Infecciones por Clostridium/microbiología , Diarrea/microbiología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Toxinas Bacterianas/análisis , Niño , Preescolar , Femenino , Humanos , Masculino , Persona de Mediana Edad , Sensibilidad y Especificidad , Estadística como Asunto , Adulto JovenRESUMEN
We aimed to elucidate the immunological (cytokines), biochemical (antioxidative), and patho-morphological responses in the gut and liver evoked by the addition of Lactobacillus fermentum ME-3 to ofloxacin (OFX) treatment in an experimental infection model of Salmonella enterica serovar Typhimurium. After challenge with S. Typhimurium and treatment according to different schemes, either with OFX and/or addition of L. fermentum ME-3, the mice were killed. Blood, liver, spleen, and small intestine samples were plated to detect S. Typhimurium and lactobacilli. Histological slides were prepared from the liver and ileum. The cytokines (IL-10, IFN-γ, and TNF-α), the glutathione peroxidase and reductase, the glutathione ratio, and the lipid peroxides (LPO) in mucosa of the small intestine and liver were estimated. The addition of L. fermentum ME-3 to OFX increased the eradication of S. Typhimurium from tested sites because of antagonistic and antioxidative properties, reduced the presence of typhoid nodules in the liver, and decreased the values of LPO. The immunological response included the reduction of pro-inflammatory cytokines interferon-γ and tumour necrosis factor-α and the increase in anti-inflammatory cytokine interleukin-10 in the livers of mice without typhoid nodules.
Asunto(s)
Antibacterianos/farmacología , Limosilactobacillus fermentum/fisiología , Ofloxacino/farmacología , Fiebre Paratifoidea/terapia , Probióticos/farmacología , Salmonella typhimurium/crecimiento & desarrollo , Animales , Citocinas/análisis , Modelos Animales de Enfermedad , Glutatión Peroxidasa/análisis , Glutatión Reductasa/análisis , Inmunohistoquímica , Intestino Delgado/enzimología , Intestino Delgado/inmunología , Intestino Delgado/microbiología , Peróxidos Lipídicos/análisis , Hígado/enzimología , Hígado/inmunología , Hígado/microbiología , Modelos Logísticos , Masculino , Ratones , Fiebre Paratifoidea/tratamiento farmacológico , Fiebre Paratifoidea/inmunología , Fiebre Paratifoidea/microbiología , Salmonella typhimurium/metabolismo , Bazo/inmunología , Bazo/microbiologíaRESUMEN
The aim of this study was to screen intestinal lactobacilli strains for their advantageous properties to select those that could be used for the development of novel gastrointestinal probiotics. Ninety-three isolates were subjected to screening procedures. Fifty-nine percent of the examined lactobacilli showed the ability to auto-aggregate, 97% tolerated a high concentration of bile (2% w/v), 50% survived for 4 h at pH 3.0, and all strains were unaffected by a high concentration of pancreatin (0.5% w/v). One Lactobacillus buchneri strain was resistant to tetracycline. None of the tested strains caused lysis of human erythrocytes. Six potential probiotic strains were selected for safety evaluation in a mouse model. Five of 6 strains caused no translocation, and were considered safe. In conclusion, several strains belonging to different species and fermentation groups were found that have properties required for a potential probiotic strain. This study was the first phase of a multi-phase study aimed to develop a novel, safe and efficient prophylactic and therapeutic treatment system against gastrointestinal infections using genetically modified probiotic lactobacilli.
Asunto(s)
Lactobacillus/fisiología , Probióticos , Ácidos/toxicidad , Animales , Antibacterianos/toxicidad , Traslocación Bacteriana , Bilis/metabolismo , ADN Bacteriano/química , ADN Bacteriano/genética , Eritrocitos/microbiología , Hemólisis , Humanos , Concentración de Iones de Hidrógeno , Lactobacillus/clasificación , Lactobacillus/efectos de los fármacos , Lactobacillus/crecimiento & desarrollo , Ratones , Ratones Endogámicos BALB C , Viabilidad Microbiana/efectos de los fármacos , Datos de Secuencia Molecular , Pancreatina/toxicidad , Análisis de Secuencia de ADNRESUMEN
BACKGROUND: The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals. METHODS: One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR. RESULTS: Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical interventions, we found a higher resistance and frequency of integrons in strains from hospitalized elderly persons compared with non-hospitalized ones. Children treated with antibiotics had strains with higher MIC values (when compared with antibiotic-naive ones), but the integron-bearing in strains was similar. In most cases, the differences in resistance between the groups (integron-positive and negative strains separately) were higher than the differences between integron-positive and negative strains within the groups. CONCLUSION: The prevalence of integrons in commensal E. coli strains in persons without previous medical intervention depended on age. The resistance of integron-carrying and non-carrying strains is more dependent on influencing factors (hospitalization and antibiotic administration) in particular groups than merely the presence or absence of integrons.
Asunto(s)
Farmacorresistencia Bacteriana Múltiple , Infecciones por Escherichia coli/microbiología , Escherichia coli/genética , Escherichia coli/aislamiento & purificación , Heces/microbiología , Integrones , Anciano , Anciano de 80 o más Años , Antibacterianos/farmacología , Estudios de Casos y Controles , Escherichia coli/efectos de los fármacos , Infecciones por Escherichia coli/tratamiento farmacológico , Femenino , Hospitalización , Humanos , Lactante , Recién Nacido , Masculino , Pruebas de Sensibilidad MicrobianaRESUMEN
We assessed the clonality of consecutive Escherichia coli isolates during the course of recurrent urinary tract infections (RUTI) in childhood in order to compare clonality with phenotypic antibiotic resistance patterns, the presence of integrons, and the presence of the sul1, sul2, and sul3 genes. Altogether, 78 urinary E. coli isolates from 27 children, who experienced recurrences during a 1-year follow-up after the first attack of acute pyelonephritis, were investigated. The MICs of sulfamethoxazole, trimethoprim-sulfamethoxazole (SXT), ampicillin, cefuroxime, cefotaxime, and gentamicin and the presence or absence of the intI gene for class 1 integrons and the sulfamethoxazole resistance-encoding genes sul1, sul2, and sul3 were determined. All E. coli strains were genotyped by pulsed-field gel electrophoresis. There were no significant differences in the prevalences of resistance to beta-lactams and SXT between initial and consecutive E. coli isolates (41 versus 45% and 41 versus 29%, respectively). However, the E. coli strains obtained after SXT administration more frequently carried two or more sul genes than the nonexposed strains (9/21 [43%] versus 11/57 [19%], respectively; P = 0.044). In 78% of the patients, the recurrence of unique clonal E. coli strains alone or combined with individual strains was detected. Phenotypic resistance and the occurrence of sul genes were more stable in clonal strains than in individual strains (odds ratios, 8.7 [95% confidence interval {95% CI}, 1.8 to 40.8] and 4.4 [95% CI, 1.1 to 17.7], respectively). Thus, in children with RUTIs, the majority of E. coli strains from consecutive episodes are unique persisting clones, with rare increases in the initially high antimicrobial resistance, the presence of sul genes, and the presence of integrons.
Asunto(s)
Técnicas de Tipificación Bacteriana , Farmacorresistencia Bacteriana , Infecciones por Escherichia coli/microbiología , Escherichia coli/clasificación , Escherichia coli/efectos de los fármacos , Infecciones Urinarias/microbiología , Adolescente , Niño , Preescolar , Análisis por Conglomerados , ADN Bacteriano/genética , Electroforesis en Gel de Campo Pulsado , Escherichia coli/aislamiento & purificación , Femenino , Genes Bacterianos , Genotipo , Humanos , Lactante , Integrones , Masculino , Pruebas de Sensibilidad Microbiana , Fenotipo , RecurrenciaRESUMEN
BACKGROUND: The aim of the study was to detect whether in experimental Salmonella enterica Typhimurium infection the probiotic Lactobacillus fermentum ME-3 in combination with fluoroquinolone therapy would eradicate S. Typhimurium, prevent the development of liver and spleen granulomas and improve the indices of oxidative stress in the ileum mucosa. The selected bacteriological, histological and biochemical methods were applied. RESULTS: Combined treatment with L. fermentum ME-3 and ofloxacin eradicated Salmonella Typhimurium from blood, ileum and liver, decreased the number of animals with liver and spleen granulomas and reduced the value of lipid peroxides in the ileum mucosa. Higher total counts of intestinal lactobacilli in all experimental groups were associated with the absence of liver granulomas. CONCLUSION: The antimicrobial and antioxidative probiotic L. fermentum ME-3 combined with ofloxacin enhances the eradication of experimental S. Typhimurium infection. These observations on probiotic and antimicrobial co-action may serve as basis to develop new strategies for treatment of invasive bacterial infections of the gut.