The value of biofilm testing to guide antimicrobial stewardship in chronic respiratory diseases.

Introduction: Biofilm production is an important yet currently overlooked aspect of diagnostic microbiology that has implications for antimicrobial stewardship. In this study, we aimed to validate and identify additional applications of the BioFilm Ring Test® (BRT) for Pseudomonas aeruginosa (PA) isolates from patients with bronchiectasis (BE). Materials and methods: Sputa were collected from BE patients who had at least one PA positive culture in the previous year. We processed the sputa to isolate both mucoid and non-mucoid PA, and determined their susceptibility pattern, mucA gene status, and presence of ciprofloxacin mutations in QRDR genes. The Biofilm production index (BPI) was obtained at 5 and 24 hours. Biofilms were imaged using Gram staining. Results: We collected 69 PA isolates, including 33 mucoid and 36 non-mucoid. A BPI value below 14.75 at 5 hours predicted the mucoid PA phenotype with 64% sensitivity and 72% specificity. Conclusion: Overall, our findings suggest that the fitness-cost associated with the mucoid phenotype or ciprofloxacin resistance is shown through a time-dependent BPI profile. The BRT has the potential to reveal biofilm features with clinical implications.

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples.

16S rRNA gene profiling, which contains nine hypervariable regions (V1-V9), is the gold standard for identifying taxonomic units by high-throughput sequencing. Microbiome studies combine two or more region sequences (usually V3-V4) to increase the resolving power for identifying bacterial taxa. We compare the resolving powers of V1-V2, V3-V4, V5-V7, and V7-V9 to improve microbiome analyses in sputum samples from patients with chronic respiratory diseases. DNA were isolated from 33 human sputum samples, and libraries were created using a QIASeq screening panel intended for Illumina platforms (16S/ITS; Qiagen Hilden, Germany). The analysis included a mock community as a microbial standard control (ZymoBIOMICS). We used the Deblur algorithm to identify bacterial amplicon sequence variants (ASVs) at the genus level. Alpha diversity was significantly higher for V1-V2, V3-V4, and V5-V7 compared with V7-V9, and significant compositional dissimilarities in the V1-V2 and V7-V9 analyses versus the V3-V4 and V5-V7 analyses. A cladogram confirmed these compositional differences, with the latter two being very similar in composition. The combined hypervariable regions showed significant differences when discriminating between the relative abundances of bacterial genera. The area under the curve revealed that V1-V2 had the highest resolving power for accurately identifying respiratory bacterial taxa from sputum samples. Our study confirms that 16S rRNA hypervariable regions provide significant differences for taxonomic identification in sputum. Comparing the taxa of microbial community standard control with the taxa samples, V1-V2 combination exhibits the most sensitivity and specificity. Thus, while third generation full-length 16S rRNA sequencing platforms become more available, the V1-V2 hypervariable regions can be used for taxonomic identification in sputum.

Resistance mechanisms and molecular epidemiology of Pseudomonas aeruginosa strains from patients with bronchiectasis.

BACKGROUND: Non-cystic fibrosis bronchiectasis (BE) is a chronic structural lung condition that facilitates chronic colonization by different microorganisms and courses with recurrent respiratory infections and frequent exacerbations. One of the main pathogens involved in BE is Pseudomonas aeruginosa. OBJECTIVES: To determine the molecular mechanisms of resistance and the molecular epidemiology of P. aeruginosa strains isolated from patients with BE. METHODS: A total of 43 strains of P. aeruginosa were isolated from the sputum of BE patients. Susceptibility to the following antimicrobials was analysed: ciprofloxacin, meropenem, imipenem, amikacin, tobramycin, aztreonam, piperacillin/tazobactam, ceftazidime, ceftazidime/avibactam, ceftolozane/tazobactam, cefepime and colistin. The resistance mechanisms present in each strain were assessed by PCR, sequencing and quantitative RT-PCR. Molecular epidemiology was determined by MLST. Phylogenetic analysis was carried out using the eBURST algorithm. RESULTS: High levels of resistance to ciprofloxacin (44.19%) were found. Mutations in the gyrA, gyrB, parC and parE genes were detected in ciprofloxacin-resistant P. aeruginosa strains. The number of mutated QRDR genes was related to increased MIC. Different ß-lactamases were detected: blaOXA50, blaGES-2, blaIMI-2 and blaGIM-1. The aac(3)-Ia, aac(3)-Ic, aac(6″)-Ib and ant(2″)-Ia genes were associated with aminoglycoside-resistant strains. The gene expression analysis showed overproduction of the MexAB-OprM efflux system (46.5%) over the other efflux system. The most frequently detected clones were ST619, ST676, ST532 and ST109. CONCLUSIONS: Resistance to first-line antimicrobials recommended in BE guidelines could threaten the treatment of BE and the eradication of P. aeruginosa, contributing to chronic infection.

Exacerbations and Changes in Physical Activity and Sedentary Behaviour in Patients with Bronchiectasis after 1 Year.

BACKGROUND: Low physical activity and high sedentary behaviour in patients with bronchiectasis are associated with hospitalisation over one year. However, the factors associated with longitudinal changes in physical activity and sedentary behaviour have not been explored. We aimed to identify clinical and sociodemographic characteristics related to a change in physical activity and sedentary behaviour in patients with bronchiectasis after one year. METHODS: This was a prospective observational study during which physical activity measurements were recorded using a SenseWear Armband for one week at baseline and at one year. At each assessment point, patients were classified as active or inactive (measured as steps per day) and as sedentary or not sedentary (measured as sedentary time). RESULTS: 53 patients with bronchiectasis were analysed, and after one year, 18 (34%) had worse activity and sedentary levels. Specifically, 10 patients became inactive and sedentary. Multivariable analysis showed that the number of exacerbations during the follow-up period was the only outcome independently associated with change to higher inactivity and sedentary behaviour (odds ratio (OR), 2.19; 95% CI, 1.12 to 4.28). CONCLUSIONS: The number of exacerbations in patients with bronchiectasis was associated with changes in physical activity and sedentary behaviour. Exacerbation prevention may appear as a key factor in relation to physical activity and sedentary behaviour in patients with bronchiectasis.

Aetiological diagnosis in new adult outpatients with bronchiectasis:role of predictors derived from real life experience.

BACKGROUND: In adult patients with bronchiectasis (BE) the identification of the underlying aetiology may be difficult. In a new patient with BE the performance of a panel of tests is recommended, even though this practice may be expensive and the level of evidence supporting is low. We aimed to identify a panel of variables able to predict the aetiological diagnosis of BE. METHODS: Our prospective study derived from our real-life experience on the management of adult stable BE outpatients. We recorded variables concerning clinical, radiological, microbiological and laboratory features. We identified five groups of aetiological diagnosis of BE (idiopathic, post-infective, COPD, asthma and non-common diseases [immunodeficiency or other rare conditions]). Multivariate models were used to identify predictors of each aetiological diagnosis. The suitability of performing a specific test for the diagnosis was also considered. RESULTS: We enrolled 354 patients with a new diagnosis of BE. Patients with different aetiological causes differed significantly with regard to age, sex, smoking habit, comorbidities, dyspnoea perception, airflow obstruction and severity scores. Various predictors were assessed, including sex, previous respiratory infections, diffuse localization of BE, risk scores, and laboratory variables (sodium and eosinophils). The levels of autoantibodies or immunoglobulins were reserved for the diagnosis of non-common disease. CONCLUSION: Our research confirms that some predictors are specific for the aetiological diagnosis of BE. The possibility of integrating this information may represent a useful tool for the diagnosis. The execution of certain specific tests should be reserved for patients with a non-common disease.

Clinical Factors Associated with a Shorter or Longer Course of Antibiotic Treatment in Patients with Exacerbations of Bronchiectasis: A Prospective Cohort Study.

BACKGROUND: Bronchiectasis exacerbations are often treated with prolonged antibiotic use, even though there is limited evidence for this approach. We therefore aimed to investigate the baseline clinical and microbiological findings associated with long courses of antibiotic treatment in exacerbated bronchiectasis patients. METHODS: This was a bi-centric prospective observational study of bronchiectasis exacerbated adults. We compared groups receiving short (≤14 days) and long (15-21 days) courses of antibiotic treatment. RESULTS: We enrolled 191 patients (mean age 72 (63, 79) years; 108 (56.5%) females), of whom 132 (69%) and 59 (31%) received short and long courses of antibiotics, respectively. Multivariable logistic regression of the baseline variables showed that long-term oxygen therapy (LTOT), moderate-severe exacerbations, and microbiological isolation of Pseudomonas aeruginosa were associated with long courses of antibiotic therapy. When we excluded patients with a diagnosis of community-acquired pneumonia (n = 49), in the model we found that an etiology of P. aeruginosa remained as factor associated with longer antibiotic treatment, with a moderate and a severe FACED score and the presence of arrhythmia as comorbidity at baseline. CONCLUSIONS: Decisions about the duration of antibiotic therapy should be guided by clinical and microbiological assessments of patients with infective exacerbations.

Características clínicas y evolución de los pacientes con intoxicación por metanol atendidos en un hospital general / Clinical characteristics and outcome of patients with methanol poisoning treated in a general hospital

Objetivo: Describir las características clínicas y la evolución de los pacientes con intoxicación por metanol. Material y métodos: Estudio descriptivo, transversal, retrospectivo, tipo serie de casos en pacientes con diagnóstico de intoxicación por metanol, atendidos en el Hospital Nacional Cayetano Heredia entre el 2004 y 2008. Resultados: Se encontraron 8 pacientes (6 varones y 2 mujeres) atendidos por intoxicación por metanol, 6 sobrevivieron. En todos los casos la vía de ingreso fue oral, 7 en forma accidental; 4 de los pacientes tenía antecedentes de dependencia alcohólica y 3 de depresión. Al ingreso, 7 presentaron alteración del nivel de conciencia, 7 visión borrosa y 4 vómitos y los niveles de metanol sérico estuvieron entre 67 a 93 mg/dL. Todos los pacientes presentaron acidosis metabólica con anión gap elevado. Los pacientes fallecidos tuvieron pH menor de 7,0. La principal complicación fue neumonía aspirativa. Conclusiones: Debido al escaso número de casos no podemos llegar a conclusiones; sin embargo, podemos decir que la intoxicación por metanol generalmente se produce por ingesta accidental, debido al consumo de licores adulterados en varones adultos de limitados recursos económicos, los síntomas más frecuentes de presentación son la alteración de la conciencia y la visión borrosa, y aparentemente el riesgo de muerte está relacionado con la severidad de la acidosis metabólica.

Objective: To describe clinical characteristics and evolution of patients with methanol poisoning. Methods: A descriptive, transversal, retrospective study, case series report of patients with methanol poisoning at the Hospital Nacional Cayetano Heredia between 2004 and 2008. Results: We found 8 patients (6 men and 2 women) with methanol poisoning, 6 survived. In all cases pathway entrance was oral, 7 were accidental; 4 patients were alcoholics and 3 had depression. At admission, 7 had consciousness disorder, 7 blurred vision, 4 vomits and serum methanol levels were between 67-93 mg/dl. All patients had metabolic acidosis with elevated anion gap. The main complication was aspiration pneumonia. Conclusions: Due to the small number of cases we can reach conclusions, but we can say methanol poisoning is usually caused by accidental ingestion, mainly from adulterated liquor consumption by adult men with limited economic resources, most common symptoms are consciousness disorder and blurred vision, and apparently risk of death is related to severity of metabolic acidosis.

Manifestaciones oftalmológicas en los pacientes seropositivos para el VIH atendidos en un hospital general / Ophtalmologic complications in the attended HIV seropositive patients in a general hospital

OBJETIVO: Describir las características de las manifestaciones oculares de los pacientes diagnosticados con el virus de la inmunodeficiencia humana (VIH) antes y después de implementar el tratamiento antirretroviral de gran actividad (Tárga). MATERIAL Y MÉTODOS: Se realizó un estudio descriptivo, retrospectivo y observacional en los pacientes seropositivos para el VIH en el Servicio de Oftalmología del Hospital Nacional Arzobispo Loayza de Lima, entre 1995 y 2008. RESULTADOS: Se evaluaron 584 historias clínicas: 421 pacientes del período 1995-2003 (pre Targa, pre- T) y 163 del período 2004-2008 (Targa, T). La edad promedio en pre-T fue de 24 años y en T fue de 29 años. En pre- T, 271 pacientes fueron varones y 150 mujeres. En T, 107 fueron varones y 56 mujeres. En cuanto a Los factores de riesgo, en pre-T: 82 homosexuales, 42 trabajadoras sexuales, 80 bisexuales y 217 no determinados. En T: 93 homosexuales, 2 heterosexuales y 68 no determinados. En pre-T: 342, (81 por ciento) hicieron compromiso ocular y en T: 145 (89 por ciento). El compromiso ocular más frecuente en ambos períodos fue la retinitis por citomegalovirus (CMV), 39 por ciento en pre T y 32 por ciento en T. La microangiopatía retinal no infecciosa 29 por ciento, en pre T y 3 por cienot en T. En este grupo se encontró microangiopatía conjuntival 15 por ciento, blefaritis 6 por ciento y chalazion 0,6 por ciento. Con menor frecuencia para ambos grupos se presentaron la criptococosis y la toxoplasmosis ocular. En T se observó disminución progresiva de la frecuencia de retinitis por CMV: 16 casos en 2004 hasta 3 en 2008. CONCLUSIONES: La frecuencia de manifestaciones oculares en pacientes, VIH positivos ha disminuido en la era Targa. Los agentes causales siguen siendo los mismos.

OBJECTIVE: To describe the ocular characteristics of the HIN patients pre and post highly active antiretroviral treatment (HAART). MATERIAL AND METHODS: It was carried out a descriptive, retrospective and observational study of the HN patients that attended to the Ophthalmology Service of the Hospital Nacional Arzobispo Loayza of Lima, between 1995 and 2008. RESULTS: A total of 584 clínical records were included: 421 patients of the period 1995-2003 (pre-HAART period) and 163 of the period 2004-2008 (HAART period). Mean age were 24 and 29 year old age, respectively. In the former group, 271 male and 150 women, and in the latter group, 107 male and 56 women. And, for risk factors, in the pre-HAART- homosexual 82, prostitutes 42, bisexual, 80 and not determined 217; and, in the HAART group: homosexual 93, heterosexual 2, not determined 68. Ocular involvement was present in 81 per cent and 89 per cent, respectively. CMV retinitis was the most frequent involvement in both groups, 39 per cent and 32 per cent, respectively. Non infectious retinal microangiopathy 29 per cent in pre HAART group and 3 per cent in the other. In the latter, it was found conjunctival microangiopathy 15 per cent, blepharitis, 6 per cent and chalazion 0,6 per cent. Ocular cryptococosis and toxoplasmosis were found with less frequency. In the HAART group a diminished frequency of CMV retinitis was observed: 16 cases in 2004 and only 3 in 2008. Conclusions: The frequency of ocular involvement in the HN patients has diminished during the HAART periodo The causative agents are stíll being the same as the pre HAART period.