Is it in their eyes? Correlation between microorganisms isolated from bronchial aspirates and conjunctival swabs in a Pediatric Intensive Care Unit / ¿Está en sus ojos? Correlación entre microorganismos aislados de aspirados bronquiales e hisopos conjuntivales en una Unidad de Cuidados Intensivos Pediátricos

Objectives. Our observational, retrospective study aimed to determine the correlation between bacteria isolated from bronchial aspirates of pediatric ICU patients (PICU) with respiratory infections and those obtained from conjunctival swabs of the same patients exhibiting clinical conjunctivitis. Material and methods. Throughout the period from 2015 to 2022, we reviewed all clinically significant bronchial aspirates (≥105 CFU/mL) and positive conjunctival swabs obtained from PICU patients. These records were retrieved from the microbiology database, cross-referencing the data to identify patients who tested positive for both during the same clinical episode. Results. The median age of the patients was 5 months (interquartile range: 1-7). Among the cohort, twenty-one patients exhibited positivity in both bronchial aspirate and conjunctival swab samples, showcasing a microbial match in 85.71% of cases (18 out of 21). The most frequently isolated microorganisms were Haemophilus influenzae (55.6%), followed by Pseudomonas aeruginosa (14.3%), Klebsiella aerogenes (9.5%), and Escherichia coli, Stenotrophomonas maltophilia, and Enterobacter cloacae, each accounting for 4.8% of the isolates. Conclusions. Our study demonstrates a strong concordance between the isolated microorganisms from both samples in patients presenting clear symptoms of clinical conjunctivitis. These findings provide a basis for future prospective studies that may leverage conjunctival swabs as a predictive tool for identifying microorganisms involved in respiratory infections. (AU)

Objetivos. Nuestro estudio observacional y retrospectivo tuvo como objetivo determinar la correlación entre las bacterias aisladas de aspirados bronquiales de pacientes de UCI pediátrica (UCIP) con infecciones respiratorias y las obtenidas de hisopos conjuntivales de los mismos pacientes que presentaban conjuntivitis clínica. Material y métodos. A lo largo del periodo comprendido entre 2015 y 2022, se revisaron todos los aspirados bronquiales clínicamente significativos (≥105 UFC/mL) y los hisopos conjuntivalespositivos obtenidos de pacientes de UCIP. Estos registros se recuperaron de la base de datos de microbiología, cruzando los datos para identificar a los pacientes que dieron positivo en ambos durante el mismo episodio clínico. Resultados. La mediana de edad de los pacientes fue de 5 meses (rango intercuartílico: 1-7). Entre la cohorte, veintiún pacientes presentaron positividad tanto en las muestras de aspirado bronquial como en las de hisopo conjuntival, mostrando una coincidencia microbiana en el 85,71% de los casos (18 de 21). Los microorganismos más frecuentemente aislados fueron Haemophilus influenzae (55,6%), seguido de Pseudomonas aeruginosa (14,3%), Klebsiella aerogenes (9,5%) y Escherichia coli, Stenotrophomonas maltophiliay Enterobacter cloacae, cada uno de los cuales representó el 4,8% de los aislamientos. Conclusiones. Nuestro estudio demuestra una fuerte concordancia entre los microorganismos aislados de ambas muestras en pacientes que presentan síntomas claros de conjuntivitis clínica. Estos hallazgos proporcionan una base para futuros estudios prospectivos que podrían aprovechar los hisopos conjuntivales como herramienta predictiva para identificar microorganismos implicados en infecciones respiratorias. (AU)

Diagnostic value of systematic bronchial aspirate on postoperative pneumonia after pulmonary resection surgery for lung cancer: a monocentre retrospective study.

OBJECTIVES: Intraoperative bacterial airway colonization seems to be associated with an increased risk of postoperative pneumonia (POP). It can be easily assessed by performing a bronchial aspirate (BA). The objective of this study is to assess the diagnostic performance of the BA to predict POP. METHODS: We conducted a single-centre retrospective observational study over a period of 10 years, from 1 January 2011 to 30 December 2020. The population study included patients admitted for a scheduled pulmonary resection surgery for lung cancer. Patients were classified into 2 populations depending on whether or not they developed a POP. Uni- and multivariable analyses were performed to identify risk factors for developing POP. The diagnostic performance of BA was represented by its sensitivity, specificity and positive and negative predictive values. RESULTS: A total of 1006 patients were included in the study. Uni- and multivariable analyses found that a positive BA was independently associated with a greater risk of developing POP with an odds ratio of 6.57 [4.165-10.865]; P < 0.001. Its specificity was 95%, sensitivity was 31%, positive predictive value was 66% and negative predictive value was 81%. CONCLUSIONS: A positive intraoperative BA is an independent risk factor for POP after lung cancer surgery. Further trials are required to validate the systematic implementation of BA as an early diagnostic tool for POP.

Is it in their eyes? Correlation between microorganisms isolated from bronchial aspirates and conjunctival swabs in a Pediatric Intensive Care Unit.

OBJECTIVE: Our observational, retrospective study aimed to determine the correlation between bacteria isolated from bronchial aspirates of pediatric ICU patients (PICU) with respiratory infections and those obtained from conjunctival swabs of the same patients exhibiting clinical conjunctivitis. METHODS: Throughout the period from 2015 to 2022, we reviewed all clinically significant bronchial aspirates (≥105 CFU/mL) and positive conjunctival swabs obtained from PICU patients. These records were retrieved from the microbiology database, cross-referencing the data to identify patients who tested positive for both during the same clinical episode. RESULTS: The median age of the patients was 5 months (interquartile range: 1-7). Among the cohort, twenty-one patients exhibited positivity in both bronchial aspirate and conjunctival swab samples, showcasing a microbial match in 85.71% of cases (18 out of 21). The most frequently isolated microorganisms were Haemophilus influenzae (55.6%), followed by Pseudomonas aeruginosa (14.3%), Klebsiella aerogenes (9.5%), and Escherichia coli, Stenotrophomonas maltophilia, and Enterobacter cloacae, each accounting for 4.8% of the isolates. CONCLUSIONS: Our study demonstrates a strong concordance between the isolated microorganisms from both samples in patients presenting clear symptoms of clinical conjunctivitis. These findings provide a basis for future prospective studies that may leverage conjunctival swabs as a predictive tool for identifying microorganisms involved in respiratory infections.

Usefulness of Routine Bronchial Aspirate of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration

Introduction: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is commonly used for the study of intrathoracic lymphadenopathy and centrally tumours but no report has discussed the contribution of routine cytological and microbiological BA during the procedure. The aim of the study was to analyse the diagnostic yield of BA during EBUS, and to determine the potential cost reduction. Methods: A prospective study of cytological and microbiological BA collected during EBUS-TBNA was conducted between January 2021 and June 2022. Demographic data, indication, previous BA bronchoscopy or EBUS diagnosis were recorded. The main variable tested was the number of patients in which the result of the BA obtained through EBUS-TBNA determined a change in the diagnosis. Results: A total of 450 (70.9% male) patients were included. BA cytology showed abnormal cells in 33 (7.3%) of patients, and only 1 case (0.2%) provided a previously unknown diagnosis. All these cases were patients with suspected malignancy. BA microbiological samples found germens in 30 (6.7%) patients but only in 5 cases (1.1%) found microbiological specimens not detected in previous bronchoscopy. None of them received antibiotics and evolved correctly. The potential total cost reduction during the study period at our centre if routine BA was deleted would be 21,937.50€ for routinely combined study. Conclusions: The low diagnostic yield of cytological and microbiological bronchial aspirate in EBUS-TBNA supports the idea of not performing routine BA. Although the potential for cost savings in caring for an individual patient is modest, many centres routinely perform BA, so the potential savings could be significant. (AU)

Usefulness of Routine Bronchial Aspirate of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration.

INTRODUCTION: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is commonly used for the study of intrathoracic lymphadenopathy and centrally tumours but no report has discussed the contribution of routine cytological and microbiological BA during the procedure. The aim of the study was to analyse the diagnostic yield of BA during EBUS, and to determine the potential cost reduction. METHODS: A prospective study of cytological and microbiological BA collected during EBUS-TBNA was conducted between January 2021 and June 2022. Demographic data, indication, previous BA bronchoscopy or EBUS diagnosis were recorded. The main variable tested was the number of patients in which the result of the BA obtained through EBUS-TBNA determined a change in the diagnosis. RESULTS: A total of 450 (70.9% male) patients were included. BA cytology showed abnormal cells in 33 (7.3%) of patients, and only 1 case (0.2%) provided a previously unknown diagnosis. All these cases were patients with suspected malignancy. BA microbiological samples found germens in 30 (6.7%) patients but only in 5 cases (1.1%) found microbiological specimens not detected in previous bronchoscopy. None of them received antibiotics and evolved correctly. The potential total cost reduction during the study period at our centre if routine BA was deleted would be 21,937.50€ for routinely combined study. CONCLUSIONS: The low diagnostic yield of cytological and microbiological bronchial aspirate in EBUS-TBNA supports the idea of not performing routine BA. Although the potential for cost savings in caring for an individual patient is modest, many centres routinely perform BA, so the potential savings could be significant.

Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study.

Background: The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests. Methods: We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient. Results: The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001). Conclusions: PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.

Multiplex protein profiling of bronchial aspirates reveals disease-, mortality- and respiratory sequelae-associated signatures in critically ill patients with ARDS secondary to SARS-CoV-2 infection.

Introduction: Bronchial aspirates (BAS) obtained during invasive mechanical ventilation (IMV) constitutes a useful tool for molecular phenotyping and decision making. Aim: To identify the proteomic determinants associated with disease pathogenesis, all-cause mortality and respiratory sequelae in BAS samples from critically ill patients with SARS-CoV-2-induced ARDS. Methods: Multicenter study including 74 critically ill patients with COVID-19 and non-COVID-19 ARDS. BAS were obtained by bronchoaspiration after IMV initiation. Three hundred sixty-four proteins were quantified using proximity extension assay (PEA) technology. Random forest models were used to assess predictor importance. Results: After adjusting for confounding factors, CST5, NADK, SRPK2 and TGF-α were differentially detected in COVID-19 and non-COVID-19 patients. In random forest models for COVID-19, CST5, DPP7, NADK, KYAT1 and TYMP showed the highest variable importance. In COVID-19 patients, reduced levels of ENTPD2 and PTN were observed in nonsurvivors of ICU stay, even after adjustment. AGR2, NQO2, IL-1α, OSM and TRAIL showed the strongest associations with in-ICU mortality and were used to construct a protein-based prediction model. Kaplan-Meier curves revealed a clear separation in mortality risk between subgroups of PTN, ENTPD2 and the prediction model. Cox regression models supported these findings. In survivors, the levels of FCRL1, NTF4 and THOP1 in BAS samples obtained during the ICU stay correlated with lung function (i.e., DLCO levels) 3 months after hospital discharge. Similarly, Flt3L and THOP1 levels were correlated with radiological features (i.e., TSS). These proteins are expressed in immune and nonimmune lung cells. Poor host response to viral infectivity and an inappropriate reparative mechanism seem to be linked with the pathogenesis of the disease and fatal outcomes, respectively. Conclusion: BAS proteomics identified novel factors associated with the pathology of SARS-CoV-2-induced ARDS and its adverse outcomes. BAS-based protein testing emerges as a novel tool for risk assessment in the ICU.

Very High Negative Concordance Rate of RT-PCR for SARS-CoV-2 in Nasopharyngeal Swab and Tracheo-Bronchial Aspirate in Children.

Reliable testing methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children are essential to allow normal activities. Diagnosis of SARS-CoV-2 infection is currently based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR) performed on nasopharyngeal (NP) swabs; concerns have been raised regarding NP swab accuracy in children to detect the virus because of potential lack of cooperation of the patients or due to general uncertainties about concordance between high and low respiratory tract specimens in children. The aim of the study (IRB approval: ST/2020/405) is to prospectively compare RT-PCR results on NP and tracheo-bronchial aspirate (TA) in children admitted to the hospital for surgery or admitted to the Pediatric Intensive Care Unit (PICU) of a tertiary children hospital in Milano, Italy, during a peak of COVID-19 infections in the city. A total of 385 patients were enrolled in the study: 364 from surgical theater and 21 from PICU. Two patients (0.5%) tested positive on TA and were negative on NP; both cases occurred in November 2020, during a peak of infection in the city. Specificity of NP swab was.995 (95% CI: 0.980-0.999). Two patients with positive NP swabs tested negative on TA. Conclusion: Our study shows that the specificity of SARS-CoV-2 RT-PCR on TA swab, compared to results of SARS-CoV-2 RT-PCR on NP, was very high for negative cases in our pediatric cohort during a period of high epidemiological pressure.

Dynamics of SARS-CoV2 Infection and Multi-Drug Resistant Bacteria Superinfection in Patients With Assisted Mechanical Ventilation.

Objective: To investigate the presence of bacteria and fungi in bronchial aspirate (BA) samples from 43 mechanically ventilated patients with severe COVID-19 disease. Methods: Detection of SARS-CoV-2 was performed using Allplex 2019-nCoV assay kits. Isolation and characterisation of bacteria and fungi were carried out in BA specimens treated with 1X dithiothreitol 1% for 30 min at room temperature, using standard culture procedures. Results: Bacterial and/or fungal superinfection was detected in 25 out of 43 mechanically ventilated patients, generally after 7 days of hospitalisation in an intensive care unit (ICU). Microbial colonisation (colony forming units (CFU) <1000 colonies/ml) in BA samples was observed in 11 out of 43 patients, whereas only 7 patients did not show any signs of bacterial or fungal growth. Pseudomonas aeruginosa was identified in 17 patients. Interestingly, 11 out of these 17 isolates also showed carbapenem resistance. The molecular analysis demonstrated that resistance to carbapenems was primarily related to OprD mutation or deletion. Klebsiella pneumoniae was the second most isolated pathogen found in 13 samples, of which 8 were carbapenemase-producer strains. Conclusion: These data demonstrate the detection of bacterial superinfection and antimicrobial resistance in severe SARS-CoV-2-infected patients and suggest that bacteria may play an important role in COVID-19 evolution. A prospective study is needed to verify the incidence of bacterial and fungal infections and their influence on the health outcomes of COVID-19 patients.

Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples.

OBJECTIVES: In order to cope with the rapid spread of the COVID-19 pandemic, we introduced on our in-house high-throughput molecular diagnostic platform (MDx Platform) a real-time reverse transcriptase PCR (RT-PCR) to detect the SARS-CoV-2 from any clinical specimens. The aim of this study was to compare the RT-PCR results obtain with the MDx Platform and the commercial assay cobas SARS-CoV-2 (Roche) on nasopharyngeal swab and other clinical specimens including sputum, bronchial aspirate, bronchoalveolar lavage and anal swabs. METHODS: Samples received in our laboratory from patients suspected of COVID-19 (n = 262) were tested in parallel with our MDx platform SARS-CoV-2 PCR and with the cobas SARS-CoV-2 test. RESULTS: The overall agreement between the two tests for all samples tested was 99.24% (260/262), which corresponded to agreements of 100% (178/178) on nasopharyngeal swabs, 95.45% (42/44) on lower respiratory tract specimen with discordant resultS obtained for very high cycle threshold (Ct) value and 100% (40/40) on anorectal swabs. The Ct values for nasopharyngeal swabs displayed an excellent correlation (R2 > 96%) between both tests. CONCLUSIONS: The high agreements between the cobas SARS-CoV-2 test and the MDx platform supports the use of both methods for the diagnostic of COVID-19 on various clinical samples. Very few discrepant results may occur at very low viral load.

Diagnostic performance of the bronchial aspirate collected before and after the bronchial biopsy in patients with pulmonary neoplasia with endobronchial lesion. / Rendimiento diagnóstico del broncoaspirado recogido antes y después de la biopsia bronquial en pacientes con neoplasia pulmonar y lesión endobronquial.

BACKGROUND AND OBJECTIVES: In patients with lung cancer (LC) and endobronchial lesion, the optimal sequence for collecting bronchial aspirate, before (BASpre) or after the biopsy (BASpost) is not yet established. The aim of this study was to compare the diagnostic performance of BASpre with BASpost. MATERIALS AND METHODS: Retrospective study of patients with LC and endobronchial lesion undergoing bronchoscopy with bronchial biopsy and BASpre and BASpost samples. The diagnostic performance of both techniques was calculated. RESULTS: A total of 144 patients were included. BASpre was diagnostic in 24 (16.7%) cases and BASpost in 33 (22.9%) (Chi-squared P<0.009). The number of cases in which it was the only diagnostic method was identical: Two for BASpre and two cases for BASpost. CONCLUSIONS: In patients with LC and endobronchial lesion, BASpost is diagnosed in a higher percentage of cases than BASpre. This difference does not affect the overall diagnostic performance of bronchoscopy as the number of times in which either is the only diagnostic procedure is identical.

Protracted bacterial bronchitis: bronchial aspirate versus bronchoalveolar lavage findings: a single-centre retrospective study.

Retrospective chart review of 133 children who underwent bronchoscopy because of possible protracted bacterial bronchitis to compare the results of bronchial aspirates with those of bronchoalveolar lavage (BAL). When comparing BAL and bronchial aspirate in 70 patients where both samples were available, the result was comparable in 46 cases (65%). If only bronchial aspirates would have been available, seven patients (10%) would have been overtreated, four children (6%) undertreated and three (4%) would have received a different treatment. Although, BAL and bronchial aspirate are comparable in the majority of cases, differences exist with an impact on treatment decision, underlying the uncertainties in the pathophysiology of protracted bacterial bronchitis.

The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients.

BACKGROUND: The bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was obtained by 16S rRNA gene amplification and sequencing, and functional capabilities through PICRUSt. RESULTS: Thirteen patients with severe asthma were included and provided 11 bronchial biopsies (BB) and 12 bronchial aspirates (BA) suitable for sequence analyses. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria showed relative abundances (RAs) over 5% in BB, a cutoff that was reached by Streptococcus and Prevotella at genus level. Legionella genus attained a median RA of 2.7 (interquartile range 1.1-4.7) in BB samples. In BA a higher RA of Fusobacteria was found, when compared with BB [8.7 (5.9-11.4) vs 4.2 (0.8-7.5), p = 0.037], while the RA of Proteobacteria was lower in BA [4.3 (3.7-6.5) vs 17.1 (11.2-33.4), p = 0.005]. RA of the Legionella genus was also significantly lower in BA [0.004 (0.001-0.02) vs. 2.7 (1.1-4.7), p = 0.005]. Beta-diversity analysis confirmed the differences between the microbial communities in BA and BB (R2 = 0.20, p = 0.001, Adonis test), and functional analysis revealed also statistically significant differences between both types of sample on Metabolism, Cellular processes, Human diseases, Organismal systems and Genetic information processing pathways. CONCLUSIONS: The microbiota in the bronchial mucosa of severe asthma has a specific pattern that is not accurately represented in bronchial secretions, which must be considered a different niche of bacteria growth.