key: cord-0794455-kch7j4aj authors: Bansal, S.; Kalpakam, H.; Kumar, A.; Varshaa, A.; Thorbole, A.; Mehta, R. M. title: Lower respiratory tract sampling via bronchoscopy in COVID-19 ARDS - A focus on microbiology, cellular morphology, cytology and management impact date: 2021-02-23 journal: nan DOI: 10.1101/2021.02.22.21252201 sha: 7130b7bfa62df11953708d9142f272675cdac91d doc_id: 794455 cord_uid: kch7j4aj Background: Lower respiratory tract (LRT) sampling via bronchoscopy has been done sparingly in COVID 19 ARDS due to the high aerosol risk for the health care workers (HCW). Valuable information can be gained by detailed evaluation of bronchoscopic LRT samples. Methods: LRT samples were obtained by bedside bronchoscopy performed in suspected or confirmed severe COVID -19 ARDS patients on mechanical ventilation. Only positive cases were included in the study. Microbiological, cellular and cytological studies including LRT COVID-19 RT-PCR were performed and analyzed. Results: 100 samples were collected from 63 patients, 53 were males (84%). 43 patients (68%) had at least 1 comorbidity. 55% cases had secondary bacterial infection as demonstrated by positive culture. Most of these infections were due to multi-drug resistant organisms (94.5%). The most common organisms were Klebsiella pneumoniae and Acinetobacter baumanii in 56.3% and 14.5% cases respectively. Fungal superinfection was observed in 9 patients (14.3%). Bronchoscopy helped confirm COVID-19 diagnosis in 1 patient and helped rule out COVID-19 in 3 patients who were eventually excluded from the study. The median BAL fluid (BALF) WBC count was 953 (IQR; 400-2717), with mean neutrophil count 85.2% (SD 13.9), and mean lymphocyte count 14.8% (SD 13.9). Repeat sampling done in some patients showed a progressive increase in the total WBC count in BALF, an increase in neutrophil percentage, and a higher chance of isolating an organism on the culture (81% repeat procedures were culture positive). The rate of super-infection increased with longer duration of illness. Patients with superinfection also had an increased WBC count (1001 vs 400), and lower lymphocyte percentage (19% vs 12% OR 6.8 [95%CI 14.3 to 0.7]). Bronchoscopic LRT sampling contributed significantly to modifying antibiotic coverage and discontinuing steroids in 37% cases. Conclusion: This study describes a detailed analysis of bronchoscopic LRT sampling in critically ill COVID-19 patients. This provided important basic and applied information augmenting disease understanding and contributing to clinical management when there was scant information available in the pandemic. Retrospective study of 100 LRT samples collected by bronchoscopy performed for clinical indications at a tertiary committed COVID care center between August 25, 2020 and January 5, 2021, for MV C-ARDS patients with initially proven or later confirmed COVID-19. Microbiological, cellular and cytological evaluation of these samples were done, and their management impact was analysed. Other relevant information recorded included demographic and clinical parameters including age, gender, duration of symptoms prior to hospitalization, presence of common co-morbidities and duration of ventilatory support prior to sampling. Data was tabulated and analysed using SPSS (ver. 25.0, SPSS Inc). Results were analysed in a descriptive fashion as number and percentages, mean and standard deviation, median and inter quartile range (IQR). Difference between mean and medians was expressed using chisquare test and Mann-Whitney U-test respectively. Correlation analysis was done using linear . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted February 23, 2021. ; https://doi.org/10.1101/2021.02.22.21252201 doi: medRxiv preprint correlation and results expressed using Pearson's correlation coefficient. Statistical significance was taken at P <0.5. 100 bronchoscopic LRT samplings were done in 63 MV C-ARDS patients. 43 Gram stain could detect an organism in 36 cases (36%) -Gram negative bacilli (GNB) in 34 cases and Gram-positive cocci (GPC) in 2 cases, with culture positivity in 55 cases (55%). (ii) Culture reports: Of the 100 cases, bacterial culture was positive in 55 cases (55%) with colony counts >10 5 CFU/ml and sterile in 45 cases (45%). All these patients were on prior antibiotics. Klebsiella pneumoniae & Acinetobacter baumannii were most commonly isolated organisms in 31 cases (56.3%) and in 8 cases (14.5%) respectively. Other organisms isolated were Burkholderia cepacia in 4 cases (7.2%), Enterobacter cloacae in 3 cases (5.4%), and Acinetobacter iwoffii, Providencia stuartii and Serratia marcescens in 2 cases each. MRSA, Citrobacter freundii were other sporadically isolated organisms. 3 patients grew more than 1 organism in the BAL fluid. In 2 cases, these were Klebsiella pneumoniae with Enterobacter cloacae, while in 1 case it was Acinetobacter baumannii with . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) Fungal culture was positive in only 2 patients, but majority of these patients were on empirical anti-fungal medications. One patient grew Aspergillus niger, and the other patient grew Aspergillus fumigatus. 4 of these patients with a positive KOH mount also had bacterial co-infection with MDR organisms, while 3 were bacterial culture sterile. BAL galactomannan was sent for 6 patients and was elevated in all the cases. Galactomannan values were 1.65, 2.88, 1.72, 2.03, 1.52 and 2.14 in these 6 patients respectively (done by immune-enzymatic sandwich microplate assay; > 0.5 ODI considered positive). While 3 of these cases had a positive KOH mount, 3 did not stain with KOH. All 6 were culture negative. Appropriate anti-fungal agents were added in all the cases. Simultaneous blood cultures (±1 day) sent in these patients grew fungi in 3/9 patients -1 patient grew Candida auris, and 2 Candida albicans. Sampling was done with prior broad-spectrum antibiotics on board, as per our clinical protocol for MV patients. Since majority of patients grew MDR organisms sensitive only to the polymyxin group of antibiotics, we changed our policy mid-way to empiric polymyxins for any patients suspected of new onset infection on MV. A new strategy also was the additional use of nebulized colistin via a closed, in-line nebulization circuit in patients who had copious purulent secretions in the airways. Subsequent culture reports confirmed MDR organisms in all these cases. After nebulized antibiotics, we found a reduction in the quantity and purulence of secretions in the majority of these patients. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted February 23, 2021. ; https://doi.org/10.1101/2021.02.22.21252201 doi: medRxiv preprint The median WBC count was 953 (IQR; 400-2717), with mean neutrophils 85.2% (±13.9), and mean lymphocytes 14.8% (±13.9). 51% of patients showed ≥ 10% lymphocytes, 25.5% had ≥ 20%, 14.3% had ≥ 30%, while 6% patients had ≥ 40% lymphocytes in the fluid analysis. Mean neutrophil to lymphocyte ratio (NLR) in BAL was 13.3. The following findings were noted correlating duration of illness with BAL cytology: . As the duration of illness progressed, the mean lymphocyte count in BAL reduced, while the neutrophil count increased. Pearson's correlation coefficient between duration of illness and BAL lymphocyte 28/63 (44.5%) patients had a documented superinfection -bacterial, fungal or both. A comparative analysis of patients with and without superinfection is presented in A subgroup of 20 patients had repeat bronchoscopy procedures with LRT sampling, majority for recurrent thick secretions in the endotracheal tube causing ventilation issues. The following aspects were noted. There was a greater chance of isolating an organism on culture when procedures were repeated (81% repeat procedures were culture positive). Serial changes noted on baseline broad-spectrum antibiotics included the following: 1. 14 patients had reduced secretion amount and purulence over serial procedures. WBC count also reduced sequentially in these patients. 4 patients turned culture negative on . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In our study, cultures were positive for various bacteria in 55% cases. The various . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted February 23, 2021. mentioned that BAL impacted decision making in 71% cases: introduction, continuation, switch, or withdrawal of antimicrobial therapy in 50% cases, and decision to start (21%) or not start (21%) corticosteroid therapy. (5) This is one of the few studies with comprehensive LRT sampling via bronchoscopy at the height of the COVID-19 pandemic, and correlates clinical, microbiological, cellular and RT-PCR findings. This is one of the few studies to report all these aspects with uniform steroid use. This data improves C-ARDS disease understanding, as well as help in clinical decision making in this critically ill population. Course corrections, such as altering the antibiotic strategy were implemented, and adding nebulized antibiotics was done as an additional strategy. The information gained from repeat procedures in some patients adds to the . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted February 23, 2021. ; https://doi.org/10.1101/2021.02.22.21252201 doi: medRxiv preprint understanding of disease course. Our study did have certain limitations. We were restricted to only intubated critically ill COVID-19 ARDS patients, and not able to do galactomannan and molecular microbiological testing on all the samples. A fundamental limitation in MV COVID-19 patients was restricted suctioning due to aerosol risk, limiting many aspects of diagnosis and information to guide therapy. This study describes the detailed analysis and impact of bronchoscopic LRT sampling in critically ill C-ARDS patients at a stage when there was scant information available in the pandemic. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted February 23, 2021. 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