Whole-genome characterisation of Escherichia coli isolates from patients with bacteraemia presenting with sepsis or septic shock in Spain: a multicentre cross-sectional study.

BACKGROUND: Escherichia coli is the most frequent cause of bloodstream infections (BSIs). About one-third of patients with BSIs due to E coli develop sepsis or shock. The objective of this study is to characterise the microbiological features of E coli blood isolates causing sepsis or septic shock to provide exploratory information for future diagnostic, preventive, or therapeutic interventions. METHODS: E coli blood isolates from a multicentre cross-sectional study of patients older than 14 years presenting with sepsis or septic shock (according to the Third International Consensus Definitions for Sepsis and Septic Shock criteria) from hospitals in Spain between Oct 4, 2016, and Oct 15, 2017, were studied by whole-genome sequencing. Phylogroups, sequence types (STs), serotype, FimH types, antimicrobial resistance (AMR) genes, pathogenicity islands, and virulence factors were identified. Susceptibility testing was performed by broth microdilution. The main outcome of this study was the characterisation of the E coli blood isolates in terms of population structure by phylogroups, groups (group 1: phylogroups B2, F, and G; group 2: A, B1, and C; group 3: D), and STs and distribution by geographical location and bloodstream infection source. Other outcomes were virulence score and prevalence of virulence-associated genes, pathogenicity islands, AMR, and AMR-associated genes. Frequencies were compared using χ² or Fisher's exact tests, and continuous variables using the Mann-Whitney test, with Bonferroni correction for multiple comparisons. FINDINGS: We analysed 224 isolates: 140 isolates (63%) were included in phylogenetic group 1, 52 (23%) in group 2, and 32 (14%) in group 3. 85 STs were identified, with four comprising 44% (n=98) of the isolates: ST131 (38 [17%]), ST73 (25 [11%]), ST69 (23 [10%]), and ST95 (12 [5%]). No significant differences in phylogroup or ST distribution were found according to geographical areas or source of bloodstream infection, except for ST95, which was more frequent in urinary tract infections than in other sources (11 [9%] of 116 vs 1 [1%] of 108, p=0·0045). Median virulence score was higher in group 1 (median 25·0 [IQR 20·5-29·0) than in group 2 (median 14·5 [9·0-20·0]; p<0·0001) and group 3 (median 21 [16·5-23·0]; p<0·0001); prevalence of several pathogenicity islands was higher in group 1. No significant differences were found between phylogenetic groups in proportions of resistance to antibiotics. ST73 had higher median virulence score (32 [IQR 29-35]) than the other predominant clones (median range 21-28). Some virulence genes and pathogenicity islands were significantly associated with each ST. ST131 isolates had higher prevalence of AMR and a higher proportion of AMR genes, notably blaCTX-M-15 and blaOXA-1. INTERPRETATION: In this exploratory study, the population structure of E coli causing sepsis or shock was similar to previous studies that included all bacteraemic isolates. Virulence genes, pathogenicity islands, and AMR genes were not randomly distributed among phylogroups or STs. These results provide a comprehensive characterisation of invasive E coli isolates causing severe response syndrome. Future studies are required to determine the contribution of these microbiological factors to severe clinical presentation and worse outcomes in patients with E coli bloodstream infection. FUNDING: Instituto de Salud Carlos III.

Azole resistance survey on clinical Aspergillus fumigatus isolates in Spain.

OBJECTIVES: We aimed to assess the percentage of azole resistance in Aspergillus fumigatus in Spain. METHODS: Thirty participating Spanish hospitals stored all morphologically identified A. fumigatus sensu lato clinical isolates-regardless their clinical significance-from 15 February to 14 May 2019. Isolates showing azole resistance according to the EUCAST 9.3.2 methodology were molecularly identified and the cyp51A gene was studied in A. fumigatus sensu stricto isolates. RESULTS: Eight hundred and forty-seven isolates from 725 patients were collected in 29 hospitals (A. fumigatus sensu stricto (n = 828) and cryptic species (n = 19)). Isolates were mostly from the lower respiratory tract (94.0%; 797/847). Only cryptic species were amphotericin B resistant. Sixty-three (7.4%) out of the 847 isolates were resistant to ≥1 azole(s). Azole resistance was higher in cryptic species than in A. fumigatus sensu stricto (95%, 18/19 vs. 5.5%, 45/828); isavuconazole was associated to the lowest number of non-wild type isolates. The dominant mechanism of resistance was the presence of TR34-L98H substitutions (n = 24 out of 63). Out of the 725 patients, 48 (6.6%) carried either cryptic species (n = 14) or A. fumigatus sensu stricto (n = 34; 4.7%) resistant isolates. Aspergillus fumigatus sensu stricto harbouring either the TR34-L98H (n = 19) or TR46/Y121F/T289A (n = 1) mutations were detected in patients in hospitals located at 7/24 studied cities. DISCUSSION: Of the patients, 6.6% carry azole-resistant A. fumigatus sensu lato isolates in Spain. TR34-L98H is the dominant cyp51A gene substitutions, although its presence is not widespread.

Tuberculosis por Mycobacterium bovis en la población de Castilla y León (España), 2006-2015 / Human Mycobacterium bovis infection in Castile and León (Spain), 2006-2015

Introducción: La incidencia anual de tuberculosis (TB) humana por Mycobacterium bovis ha disminuido considerablemente en los países industrializados desde inicios del sigloXX. El objetivo de este estudio fue conocer las características epidemiológicas, clínicas y microbiológicas de esta enfermedad en Castilla y León (CyL). Métodos: Estudio retrospectivo de los casos de TB por M. bovis de CyL en un periodo de 10 años, comparando la epidemiología, los factores de riesgo y la evolución entre las formas pulmonares (TBP) y extrapulmonares (TBEP). Resultados: Se recopilaron 75 casos de TB por M. bovis: 45 TBP y 31 TBEP. La incidencia acumulada de TB por M. bovis fue de 0,3 casos por 100.000 habitantes. Se mantuvo estable entre el primer y el segundo quinquenio (0,27 vs. 0,33, p = 0,656), a pesar del descenso de la incidencia global de la TB (13,58 vs. 10,71, p < 0,0001). La edad media fue de 66,2 + 21,3 años, principalmente varones (63%) y nacidos en España (92%). TBP fue significativamente más frecuente en varones, mayores de 66 años, con inmunosupresión o fumadores. La mortalidad fue del 9%, asociada a la edad, a la inmunosupresión o a un tratamiento diferente al recomendado por la OMS. Conclusiones: La incidencia de TB por M. bovis en CyL es superior a la de España y otros países europeos, y se mantuvo estable a pesar del descenso de la TB por MTC. Afectó mayoritariamente a población nacida en España que vivía en zonas rurales y con elevada media de edad

Introduction: The annual incidence of tuberculosis (TB) from Mycobacterium bovis in humans has considerably declined in industrialised countries since the early twentieth century. The objective of this study was to determine the epidemiological, clinical and microbiological characteristics of patients with this illness in Castile and León (CyL). Methods: Retrospective study of all M. bovis TB cases in CyL over a 10-year period, comparing the risk factors, the epidemiology and the clinical course between pulmonary (PTB) and extrapulmonary TB (EPTB). Results: 75 cases of TB were due to M. bovis: 45 PTB and 31 EPTB. The annual incidence of TB due to M. bovis was 0.3 cases per 100,000. It remained stable between the first and second five-year period (0.27 vs. 0.33, p = 0.656). However, the overall incidence of TB fell in both five-year periods (13.58 vs. 10.71, p < 0.0001). The mean age was 66.2 + 21.3 years, mainly men (63%) and Spanish patients (92%). PTB was significantly more frequent in men, aged over 66 years, with immunosuppressive conditions or who were smokers. Mortality was 9%, associated with higher age, immunosuppression or treatment different from that recommended by the WHO. Conclusions: The incidence of M. bovis TB in CyL was higher than that for Spain and for other European countries, and remained stable despite the decreased the TB due to MTC. It affected mostly Spanish-born patients who lived in rural areas and with a high mean age

Human Mycobacterium bovis infection in Castile and León (Spain), 2006-2015. / Tuberculosis por Mycobacterium bovis en la población de Castilla y León (España), 2006-2015.

INTRODUCTION: The annual incidence of tuberculosis (TB) from Mycobacterium bovis in humans has considerably declined in industrialised countries since the early twentieth century. The objective of this study was to determine the epidemiological, clinical and microbiological characteristics of patients with this illness in Castile and León (CyL). METHODS: Retrospective study of all M. bovis TB cases in CyL over a 10-year period, comparing the risk factors, the epidemiology and the clinical course between pulmonary (PTB) and extrapulmonary TB (EPTB). RESULTS: 75 cases of TB were due to M. bovis: 45 PTB and 31 EPTB. The annual incidence of TB due to M. bovis was 0.3 cases per 100,000. It remained stable between the first and second five-year period (0.27 vs. 0.33, p=0.656). However, the overall incidence of TB fell in both five-year periods (13.58 vs. 10.71, p<0.0001). The mean age was 66.2+21.3 years, mainly men (63%) and Spanish patients (92%). PTB was significantly more frequent in men, aged over 66 years, with immunosuppressive conditions or who were smokers. Mortality was 9%, associated with higher age, immunosuppression or treatment different from that recommended by the WHO. CONCLUSIONS: The incidence of M. bovis TB in CyL was higher than that for Spain and for other European countries, and remained stable despite the decreased the TB due to MTC. It affected mostly Spanish-born patients who lived in rural areas and with a high mean age.

Contribución de la microbiología al diagnóstico de la tuberculosis en Castilla y León: conclusiones del estudio GRUMICALE 2013 / Contribution of microbiology in the diagnosis of tuberculosis in Castile and León (Spain): Findings of the GRUMICALE 2013 study

Introducción y objetivos: Estudio retrospectivo que recoge datos microbiológicos de tuberculosis (TB) en Castilla y León durante el año 2013 para conocer los datos microbiológicos de incidencia y distribución de TB, resistencias a los fármacos antituberculosos y compararlos con los datos epidemiológicos ofrecidos por los servicios de vigilancia epidemiológica (SIVE). Material y métodos: Microbiólogos de los 14 hospitales de la red sanitaria pública de Castilla y León (GRUMICALE) han recogido datos epidemiológicos, microbiológicos y de funcionamiento de los laboratorios de microbiología de la comunidad durante el año 2013. Se consideró un solo aislamiento de Mycobacterium tuberculosis complex (MTC) por paciente. Resultados: Se obtuvieron 270 aislamientos de MTC (tasa de incidencia de 11,63 casos/100.000 hab./año). Según datos epidemiológicos, se recogieron un total de 288 casos de TB (11,43 casos/100.000 hab./año), 243 confirmados, 29 sospechosos y 16 probables. Predomina la localización pulmonar, seguida de lejos por la pleural y por el resto. Se procesaron un total de 27.620 muestras para micobacterias. En un 3,46% de los medios de cultivos líquidos se obtuvo crecimiento de micobacterias, y en un 50,37% la tinción directa (baciloscopia) fue positiva. Dieciséis aislamientos de Mycobacterium tuberculosis (MT) presentaron resistencia a algún fármaco antituberculoso, predominando la resistencia a isoniazida (5,92%). La provincia con mayor incidencia y número de aislamientos fue León (24,23 casos/100.000 hab./año), siendo la máxima en el área sanitaria de El Bierzo (30,46 casos/100.000 hab./año). Conclusiones: Una adecuada recogida de la información microbiológica es fundamental para el conocimiento de la epidemiologia de la TB en nuestra comunidad (AU)

Introduction and objectives: A retrospective study was conducted by collecting microbiological tuberculosis (TB) data in Castile and León during the year 2013 in order to determine the incidence and distribution of TB, and resistance to the tuberculostatic drug, and compare them with the epidemiological data provided by the Department of Epidemiological Surveillance (SIVE). Material and methods: Microbiologists of the 14 hospitals of the Castile and León public health network (GRUMICALE) collected epidemiological, microbiological, and management data from the Microbiology laboratories in the community during the year 2013. A single isolate of Mycobacterium tuberculosis complex (MTC) per patient was considered. Results: The study included a total of 270 MTC isolates (an incidence rate of 11.63 cases/100,000 inhab./year). A total of 288 cases of TB (11.43 cases/100,000 inhab. year) were recovered using epidemiological data, which included 243 confirmed, 29 suspected, and 16 as probable cases. Pulmonary TB was predominant, followed a long way off by the pleural TB and the remaining locations. A total of 27,620 samples were processed for mycobacterial detection. Mycobacterial growth was observed in 3.46% of automated fluid cultures, and 50.37% were positive by direct staining of the smear. Resistance to one tuberculostatic drug, mostly to isoniazid, was observed in 16 (5.92%) isolates of Mycobacterium tuberculosis (MT). The province with greater incidence and number of isolates was León (24.23 cases/100,000 inhab./year), with the highest being observed in El Bierzo health area (30.46 cases/100,000 inhab./year). Conclusions: An adequate collection of microbiological information is essential to determine the epidemiology of TB in our region (AU)

Lady Windermere syndrome in Castile and León. / Síndrome de Lady Windermere en Castilla y León.

INTRODUCTION: Lady Windermere syndrome (LWS) is a pulmonary disease caused by Mycobacterium avium complex (MAC). The objective of this study is to ascertain its frequency and characteristics in the northern area of the autonomous community of Castile and León. METHODS: A retrospective study of patients with MAC isolates in respiratory samples from five public hospitals in the autonomous community over a six-year period, following the ATS/IDSA criteria. The MAC strains were identified by GenoType Mycobacterium reverse hybridisation probes or PCR-RFLP analysis of the hsp65 gene. RESULTS: Of 183 cases of MAC identified, only five women (2.7%) aged 68.8±10.7years met LWS criteria. In three cases, MAC was isolated jointly and intermittently with other pathogens. Only one patient was treated according to ATS/IDSA criteria. DISCUSSION: LWS remains underestimated, with affected patients representing a significant burden on healthcare resources over long periods of time. As a result, greater microbiological and therapeutic knowledge of the syndrome is needed.

Contribution of microbiology in the diagnosis of tuberculosis in Castile and León (Spain): Findings of the GRUMICALE 2013 study. / Contribución de la microbiología al diagnóstico de la tuberculosis en Castilla y León: conclusiones del estudio GRUMICALE 2013.

INTRODUCTION AND OBJECTIVES: A retrospective study was conducted by collecting microbiological tuberculosis (TB) data in Castile and León during the year 2013 in order to determine the incidence and distribution of TB, and resistance to the tuberculostatic drug, and compare them with the epidemiological data provided by the Department of Epidemiological Surveillance (SIVE). MATERIAL AND METHODS: Microbiologists of the 14 hospitals of the Castile and León public health network (GRUMICALE) collected epidemiological, microbiological, and management data from the Microbiology laboratories in the community during the year 2013. A single isolate of Mycobacterium tuberculosis complex (MTC) per patient was considered. RESULTS: The study included a total of 270 MTC isolates (an incidence rate of 11.63 cases/100,000 inhab./year). A total of 288 cases of TB (11.43 cases/100,000 inhab. year) were recovered using epidemiological data, which included 243 confirmed, 29 suspected, and 16 as probable cases. Pulmonary TB was predominant, followed a long way off by the pleural TB and the remaining locations. A total of 27,620 samples were processed for mycobacterial detection. Mycobacterial growth was observed in 3.46% of automated fluid cultures, and 50.37% were positive by direct staining of the smear. Resistance to one tuberculostatic drug, mostly to isoniazid, was observed in 16 (5.92%) isolates of Mycobacterium tuberculosis (MT). The province with greater incidence and number of isolates was León (24.23 cases/100,000 inhab./year), with the highest being observed in El Bierzo health area (30.46 cases/100,000 inhab./year). CONCLUSIONS: An adequate collection of microbiological information is essential to determine the epidemiology of TB in our region.

Aspergílosis maxilar invasiva: presentación de un caso clínico y revisión de la literatura / Invasive maxillary aspergillosis: report of a case and review of the literature

Se presenta un caso clínico de aspergilosis maxilar en un paciente inmunodeprimido. La aspergilosis de senos paranasales es una entidad poco común, sin embargo su frecuencia ha aumentado en los últimos años. Se puede manifestar de cuatro formas: alérgica, no-invasiva, invasiva y fulminante. La spergilosis invasiva fulminante es un proceso muy grave que afecta generalmente a pacientes inmunodeprimidos. Para evitar el elevado índice de mortalidad y morbilidad asociado con este proceso, es fundamental el realizar un diagnóstico y tratamiento precoz (AU)