Bronchoalveolar Lavage Specimens Research Articles

Multicentric evaluation of BioFire FilmArray Pneumonia Panel for rapid bacteriological documentation of pneumonia

ObjectivesTo evaluate performances of the rapid multiplex PCR assay BioFire FilmArray Pneumonia Panel (FA-PP) for detection of bacterial pathogens and antibiotic resistance genes in sputum, endotracheal aspirate (ETA) and bronchoalveolar lavage (BAL) specimens. MethodsThis prospective observational study was conducted in 11 French university hospitals (July to December 2018) and assessed performance of FA-PP by comparison with routine conventional methods. ResultsA total of 515 respiratory specimens were studied, including 58 sputa, 217 ETA and 240 BAL. The FA-PP detected at least one pathogen in 384 specimens, yielding an overall positivity rate of 74.6% (384/515). Of them, 353 (68.5%) specimens were positive for typical bacteria while eight atypical bacteria and 42 resistance genes were found. While identifying most bacterial pathogens isolated by culture (374/396, 94.4%), the FA-PP detected 294 additional species in 37.7% (194/515) of specimens. The FA-PP demonstrated positive percentage agreement and negative percentage agreement values of 94.4% (95% CI 91.7%–96.5%) and 96.0% (95% CI 95.5%–96.4%), respectively, when compared with culture. Of FA-PP false-negative results, 67.6% (46/68) corresponded to bacterial species not included in the panel. At the same semi-quantification level (in DNA copies/mL for FA-PP versus in CFU/mL for culture), the concordance rate was 43.4% (142/327) for culture-positive specimens with FA-PP reporting higher semi-quantification of ≥1 log10 in 48.6% (159/327) of cases. Interestingly, 90.1% of detected bacteria with ≥106 DNA copies/mL grew significantly in culture. ConclusionsFA-PP is a simple and rapid molecular test that could complement routine conventional methods for improvement of diagnosis accuracy of pneumonia.

Performance of a Semiquantitative Multiplex Bacterial and Viral PCR Panel Compared With Standard Microbiological Laboratory Results: 396 Patients Studied With the BioFire Pneumonia Panel.

BackgroundMicrobiologic results are critical to optimal management of patients with lower respiratory tract infection, but standard methods may take several days. The multiplex polymerase chain reaction BioFire Pneumonia (PN) panel detects 15 common bacterial species semiquantitatively as copy number/mL, 8 viral species, and 7 resistance genes in about an hour within the clinical laboratory.MethodsWe tested 396 unique endotracheal or bronchoalveolar lavage specimens with the BioFire Pneumonia panel and compared the bacterial detections to conventional gram stain and culture results.ResultsOf the 396 patients, 138 grew at least 1 bacterium that had a target on the PN panel, and 136/138 (98.6%) were detected by the panel. A total of 177 isolates were recovered in culture and the PN panel detected 174/177 (98.3%). A further 20% of patients had additional targets detected that were not found on standard culture (specificity 69%, positive predictive value 63%, and negative predictive value 98.9%). Copy number was strongly related to standard semiquantitative growth on plates reported by the laboratory (eg, 1+, 2+, 3+ growths) and was significantly higher in those specimens that grew a potential pathogen. Both higher copy number and bacterial detections found by the PN panel, but not found in culture, were strongly positively related to the level of white blood cells reported in the initial gram stain.ConclusionsHigher copy number and bacterial detections by the PN panel are related to the host respiratory tract inflammatory response. If laboratories can achieve a rapid turnaround time, the PN panel should have a significant impact both on patient management and on antibiotic stewardship.

Time to Result for Pathogen Identification and Antimicrobial Susceptibility Testing of Bronchoalveolar Lavage and Endotracheal Aspirate Specimens in U.S. Acute Care Hospitals.

Identification (ID) and antimicrobial susceptibility testing (AST) of respiratory pathogens are critical to the management of patients with pneumonia to facilitate optimal antibiotic therapy selection. Few studies have examined the time to results (TTR) for this critical specimen, and such data can be valuable for benchmarking the current paradigm of diagnostic approaches. TTR for bronchoalveolar lavage (BAL) and endotracheal aspirate (ETA) specimens from hospitalized patients was evaluated using the Premier Healthcare Database, a comprehensive database of 194 U.S. hospitals. Times from specimen collection to reporting of organism ID/AST were evaluated and compared by specimen types and characteristics. A total of 79,662 (43,129 BAL; 36,533 ETA) specimens were included, of which 19.3% harbored no growth, 47.1% contained normal respiratory flora alone (including yeast), and 0.6% contained mycobacteria/molds. Potential bacterial pathogens (PBP) were recovered from 33.0%. ETA specimens had a higher proportion of specimens with isolation of PBP (39.2% versus 27.7%) and with normal respiratory flora (52.0% versus 43.0%) and were less likely to be negative (8.2% versus 28.6%) than BAL specimens (all P < 0.0001). Staphylococcus aureus and Pseudomonas aeruginosa were isolated in 10.5 and 6.4% of the specimens, respectively, and were the most common organisms identified. Median (interquartile range) TTR were 37.0 h (21.8 to 51.7 h) and 60.5 h (46.6 to 72.4 h) for ID and AST, respectively. Median TTR for major respiratory pathogens by organism ranged from 29.2 to 43.9 h for ID and from 47.9 to 73.9 h for AST. Organism type, specimen collection time, and hospital teaching status influenced TTR. Mechanically vented patients and ETA specimens were more likely to recover PBP.

Frequency and Duration of SARS-CoV-2 Shedding in Oral Fluid Samples Assessed by a Modified Commercial Rapid Molecular Assay.

Background: RT-PCR on nasopharyngeal (NPS)/oropharyngeal swabs is the gold standard for diagnosis of SARS-CoV-2 infection and viral load monitoring. Oral fluid (OF) is an alternate clinical sample, easy and safer to collect and could be useful for COVID-19 diagnosis, monitoring viral load and shedding. Methods: Optimal assay conditions and analytical sensitivity were established for the commercial Simplexa™ COVID-19 Direct assay adapted to OF matrix. The assay was used to test 337 OF and NPS specimens collected in parallel from 164 hospitalized patients; 50 bronchoalveolar lavage (BAL) specimens from a subgroup of severe COVID-19 cases were also analysed. Results: Using Simplexa™ COVID-19 Direct on OF matrix, 100% analytical detection down to 1 TCID50/mL (corresponding to 4 × 103 copies (cp)/mL) was observed. No crossreaction with other viruses transmitted through the respiratory toute was observed. Parallel testing of 337 OF and NPS samples showed highly concordant results (κ = 0.831; 95 % CI = 0.771–0.891), and high correlation of Ct values (r = 0.921; p < 0.0001). High concordance and elevated correlation was observed also between OF and BAL. Prolonged viral RNA shedding was observed up to 100 days from symptoms onset (DSO), with 32% and 29% positivity observed in OF and NPS samples, respectively, collected between 60 and 100 DSO. Conclusions: Simplexa™ COVID-19 Direct assays on OF have high sensitivity and specificity to detect SARS-CoV-2 RNA and provide an alternative to NPS for diagnosis and monitoring SARS-CoV-2 shedding.

Rare infection diagnosed by cytology in a bronchoalveolar lavage specimen in a patient with massive pulmonary hemorrhage

Rare infection diagnosed by cytology in a bronchoalveolar lavage specimen in a patient with massive pulmonary hemorrhage

Bronchoalveolar lavage-based COVID-19 testing in patients with cancer

Objective/BackgroundA few case reports in the setting of coronavirus disease 2019 (COVID-19) and multiplex polymerase chain reaction (PCR)-based assays for common respiratory pathogens have shown a higher yield of bronchoalveolar lavage (BAL) samples than upper airway specimens in immunocompromised patients. MethodsA retrospective study was conducted reviewing patients diagnosed with COVID-19 at the Medical College of Wisconsin (Milwaukee, WI, USA) between March 13, 2020 and June 11, 2020. All patients tested positive for SARS-CoV-2 via real-time reverse transcriptase PCR (RT-PCR), through a nasopharyngeal or a bronchoscopy specimen. ResultsDuring the study period, 53 bronchoscopy procedures were performed at the institution, of which five patients tested positive for COVID-19. Of the five patients, three underwent BAL testing based on high clinical suspicion for COVID-19 after the nasopharyngeal (NP) swab(s) was negative. All three patients had underlying cancers and had lymphopenia for a considerable duration prior to being diagnosed with COVID-19. Two patients had better outcomes that could be attributed to earlier BAL specimen testing resulting in timely medical intervention. ConclusionThis study underscores the need for early lower respiratory tract sampling, whenever possible, in patients with cancer and prolonged lymphopenia. High clinical suspicion ought to supersede false-negative NP reverse transcriptase–PCR as early bronchoscopic evaluation in cancer patients, who are either receiving active treatment or are immunosuppressed, can allow timely institution of efficacious treatment, enrollment into clinical trials, as well as effective infection control. In the apt clinical setting in patients with cancer, presumptive treatment may also be considered to minimize exposure to healthcare providers and proceduralists.

CO-INFECTION WITH HISTOPLASMA CAPSULATUM AND PNEUMOCYSTIS JIROVECII IN A PATIENT WITH LIVER CIRRHOSIS: A DIAGNOSTIC DILEMMA

SESSION TITLE: Medical Student/Resident Chest Infections Posters SESSION TYPE: Med Student/Res Case Rep Postr PRESENTED ON: October 18-21, 2020 INTRODUCTION: Histoplasma capsulatum and Pneumocystis jirovecii pulmonary coinfection are unusual in HIV negative populations. We present the case of a man in respiratory failure with H. capsulatum and P. jirovecii detected in bronchial washings. CASE PRESENTATION: A 64-year-old man with T2DM, moderate COPD, and NASH cirrhosis with pancytopenia presented with 2-month history of progressive hypoxic respiratory failure. CT chest revealed multifocal consolidations with mediastinal lymphadenopathy which progressed despite antimicrobial therapy (Fig. 1). Bronchoalveolar lavage (BAL) was remarkable for 2800 copies/mL of P. jirovecii PCR with beta-D-glucan of 286. BAL specimen also grew H. capsulatum on culture and the FNAC specimen taken from lymph node 7 during the transbronchial biopsy was indicative of fungal elements similar to Histoplasma (Fig. 2A-2C). The patient was started on itraconazole for Histoplasmosis and trimethoprim-sulfamethoxazole with steroids for P. jirovecii pneumonia (PJP). He was tested during the hospitalization and found to be negative for HIV but had CD4 and CD8 counts at 86 and 70 x10E9/L respectively. Due to progression of his disease the patient was transitioned to comfort measures and passed on hospital day 36. DISCUSSION: Histoplasmosis is an endemic mycosis in the Ohio and Mississippi river valleys often resulting in asymptomatic infection [1]. PJP has also been reported as an asymptomatic infection or colonization in immunocompetent hosts [2]. Co-infection with both H. capsulatum and PJP ranges from 0.5-13% in studies on HIV positive patient groups [3,4]. In the sample population studied by Carreto-Binaghi et al, a coinfection rate of 1.5% was noted in the HIV negative group [5]. Irrespective of host immune status, patients with coinfection have a higher mortality rate than with a single infection alone [5], thus warranting treatment for both pathogens. Our patient had a history of chronic lymphopenia which had been attributed to his cirrhosis, with tests showing extremely low CD4 counts. Patients with end stage liver disease are recognized as being relatively immunocompromised when compared to healthy individuals due to coexisting leucopenia, lymphopenia and CD4/CD8 ratio abnormalities [6]. This case raises the question if patients with cirrhosis and lymphopenia should be treated with prophylactic antimicrobial agents based on their CD4 counts. CONCLUSIONS: This case highlights the importance of recognizing and treating co-infection of PJP and Histoplasmosis in non-HIV infected individuals. Additionally, it reminds us that patients with liver disease have important deficiencies in their cellular and humoral immunity which make them more susceptible to unusual opportunistic infections. Reference #1: [1] Goodwin RA, Loyd JE, Des Prez RM. Histoplasmosis in Normal Hosts. Medicine. 1981; 60(4): 231-266. Reference #2: [2] Ponce CA, Gallo M, Bustamante R, et al. Pneumocystis colonization is highly prevalent in the autopsied lungs of the general population. Clin Infect Dis. 2010; 50(3):347-353. [3] Baughman RP, Dohn MN, Frame PT. The continuing utility of bronchoalveolar lavage to diagnose opportunistic infection in AIDS patients. Am J Med. 1994; 97(6): 515-522. Reference #3: [4] Wheat JL, Slama TG, Zeckel ML. Histoplasmosis in the acquired immune deficiency syndrome. Am J Med. 1985; 78(2): 203-210. [5] Carreto-Binaghi LE, Morales-Villarreal FR, García-de la Torre G, et al. Histoplasma capsulatum and Pneumocystis jirovecii coinfection in hospitalized HIV and non-HIV patients from a tertiary care hospital in Mexico. Int J of Inf Dis. 2019; 86: 65-72. [6] Tuchendler E, Tuchendler PK, Madej G. Immunodeficiency caused by cirrhosis. Clin Exp Hepatol. 2018;4(3):158-164. DISCLOSURES: No relevant relationships by James Dugan, source=Web Response No relevant relationships by Akisha Glasgow, source=Web Response No relevant relationships by Eduarda Grinsztejn, source=Web Response No relevant relationships by Amrita John, source=Web Response

PERSISTENT FUNGEMIA WITH CANDIDA AURIS IN A PATIENT WITH ENTEROCUTANEOUS FISTULA

SESSION TITLE: Medical Student/Resident Critical Care Posters SESSION TYPE: Med Student/Res Case Rep Postr PRESENTED ON: October 18-21, 2020 INTRODUCTION: Candida auris has been emerging as a fearsome adversary in the severely debilitated and ICU patients with complicated medical course. CASE PRESENTATION: A 61 year old Caucasian female with severe aortic stenosis, complicated diverticulitis, hemicolectomy and entero-cutaneous fistula (ECF), end stage renal disease on hemodialysis presented with several days of increased fistula leakage without any fevers or diarrhea. Initial vitals were stable, ECF with erythematous margins was noted. CBC was normal. CT was negative for peritonitis or perforation. Initial Blood cultures were negative, however urine grew insignificant Klebsiella pneumoniae and Streptococcus. Later, she deteriorated and was shifted to ICU, intubated, and started on vasopressors. Three more blood cultures were negative but the fourth grew Candida duobushaemulonii on VITEK. A bronchoalveolar lavage specimen and urine culture also grew Candida. She continued to have candidemia despite Micafungin. Central line exchange, line holiday and continuous renal replacement therapy were done. She transiently improved and was extubated but had to be promptly reintubated on deterioration. Persistent candidemia raised suspicion for C auris which was confirmed. A transesophageal echocardiogram revealed new mitral and aortic valve vegetations; however, she was a poor candidate for surgical procedures. She deteriorated despite aggressive measures. DISCUSSION: Misidentification of C auris with traditional phenotypic methods prompted CDC to publish guidelines to forward all C duobushaemulonii isolates on VITEK for accurate identification(1). Risk factors for persistent C auris candidemia include extensive surgery, cancers, underlying respiratory illness, diabetes mellitus, organ failure, prolonged ICU stay and previous antifungal exposure(2–4). After outbreaks in Asian(4) and European(5) hospitals, C. auris is emerging in American healthcare. Blood cultures and (1-3)-β-D-glucan assay are specific for diagnosis(3). It is notorious in causing native and prosthetic valve endocarditis(6). Transient candidemia and intestinal translocation result in persistent candidemia via biofilm(6). It’s generally resistant to azoles, susceptible to Echinocandins and Amphotericin B(5), but multidrug resistance is emerging(2,4). Work is ongoing on novel drugs like SCY-078 and VT-1598(2). Management includes early antifungals, removing foreign bodies(5) and may need surgery(6). Risk of biofilms and survivability on inanimate objects(5,6) need contact precautions and strict infection control. CONCLUSIONS: Prompt identification and institution of antifungals with ancillary measures including surgery remain key to successfully treating C auris. Reference #1: 1. Identification of Candida auris | Candida auris | Fungal Diseases | CDC. https://www.cdc.gov/fungal/candida-auris/recommendations.html. Published November 6, 2019. Accessed February 19, 2020. Reference #2: 2. Osei Sekyere J. Candida auris: A systematic review and meta-analysis of current updates on an emerging multidrug-resistant pathogen. MicrobiologyOpen. 2018;7(4):e00578. doi:10.1002/mbo3.578. Reference #3: 3. Xia R, Wang D. Risk factors of invasive candidiasis in critical cancer patients after various gastrointestinal surgeries: A 4-year retrospective study. Medicine (Baltimore). 2019;98(44):e17704. doi:10.1097/MD.0000000000017704. 4. Rudramurthy SM, Chakrabarti A, Paul RA, et al. Candida auris candidaemia in Indian ICUs: analysis of risk factors. J Antimicrob Chemother. 2017;72(6):1794-1801. doi:10.1093/jac/dkx034. 5. Ruiz-Gaitán A, Moret AM, Tasias-Pitarch M, et al. An outbreak due to Candida auris with prolonged colonisation and candidaemia in a tertiary care European hospital. Mycoses. 2018;61(7):498-505. doi:10.1111/myc.12781. 6. Giuliano S, Guastalegname M, Russo A, et al. Candida endocarditis: systematic literature review from 1997 to 2014 and analysis of 29 cases from the Italian Study of Endocarditis. Expert Rev Anti Infect Ther. 2017;15(9):807-818. doi:10.1080/14787210.2017.1372749. DISCLOSURES: No relevant relationships by Raisa Ghosh, source=Web Response No relevant relationships by Aveek Mukherjee, source=Web Response No relevant relationships by Haris Rana, source=Web Response

Local complement activation is associated with primary graft dysfunction after lung transplantation.

BACKGROUNDThe complement system plays a key role in host defense but is activated by ischemia/reperfusion injury (IRI). Primary graft dysfunction (PGD) is a form of acute lung injury occurring predominantly due to IRI, which worsens survival after lung transplantation (LTx). Local complement activation is associated with acute lung injury, but whether it is more reflective of allograft injury compared with systemic activation remains unclear. We proposed that local complement activation would help identify those who develop PGD after LTx. We also aimed to identify which complement activation pathways are associated with PGD.METHODSWe performed a multicenter cohort study at the University of Pennsylvania and Washington University School of Medicine. Bronchoalveolar lavage (BAL) and plasma specimens were obtained from recipients within 24 hours after LTx. PGD was scored based on the consensus definition. Complement activation products and components of each arm of the complement cascade were measured using ELISA.RESULTSIn both cohorts, sC4d and sC5b-9 levels were increased in BAL of subjects with PGD compared with those without PGD. Subjects with PGD also had higher C1q, C2, C4, and C4b, compared with subjects without PGD, suggesting classical and lectin pathway involvement. Ba levels were higher in subjects with PGD, suggesting alternative pathway activation. Among lectin pathway–specific components, MBL and FCN-3 had a moderate-to-strong correlation with the terminal complement complex in the BAL but not in the plasma.CONCLUSIONComplement activation fragments are detected in the BAL within 24 hours after LTx. Components of all 3 pathways are locally increased in subjects with PGD. Our findings create a precedent for investigating complement-targeted therapeutics to mitigate PGD.FUNDINGThis research was supported by the NIH, American Lung Association, Children’s Discovery Institute, Robert Wood Johnson Foundation, Cystic Fibrosis Foundation, Barnes-Jewish Hospital Foundation, Danish Heart Foundation, Danish Research Foundation of Independent Research, Svend Andersen Research Foundation, and Novo Nordisk Research Foundation.

Application of metagenomic next-generation sequencing technology for difficult lung lesions in patients with haematological diseases.

BackgroundThe purpose of this study was to evaluate the diagnostic value of combined virtual bronchoscopic navigation (Direct Path), radial endobronchial ultrasound with guide-sheath (EBUS), ultrathin bronchoscopy, rapid on-site evaluation of cytology (ROSE), and metagenomic next-generation sequencing (mNGS) for difficult lung lesions in patients with haematological diseases.MethodsIn this study, lung specimens were obtained from patients with haematological diseases by transbronchial lung biopsy (TBLB) and bronchoalveolar lavage (BAL). The specimens were subjected to mNGS for sequencing of pathogenic microorganisms and sent to the laboratory for examination and pathological analysis. Additionally, the clinical data and pathogenic characteristics of the patients were analysed. The sensitivity and specificity of mNGS for sequencing pathogenic microorganisms were compared between TBLB and BAL specimens.ResultsIn this study, the diagnosis of infectious pneumonia mainly included cytomegalovirus pneumonia, Pneumocystis jirovecii pneumonia (PCP), pulmonary aspergillosis, and tuberculosis. Some patients had non-infectious pulmonary complications, and the clinical and therapeutic outcomes were diagnosed as graft-versus-host disease (GVHD), idiopathic pneumonia syndrome (IPS), and delayed pulmonary toxicity syndrome (DPTS). The sensitivity of mNGS for pathogenic microbes in lung tissue is better than that of alveolar lavage fluid, whereas compared with alveolar lavage fluid, its specificity is reduced.ConclusionsThe results of this study indicate that combined virtual bronchoscopic navigation (Direct Path), radial EBUS, ultrathin bronchoscopy, and ROSE of target control specimens reduce the risk of bleeding, and their combination with mNGS has high diagnostic value for difficult lung lesions in patients with haematological diseases, especially in the field of infection diagnosis. TBLB and BAL specimens have respective advantages in specificity and sensitivity for mNGS analysis.

Diagnostic Performance of Xpert MTB/RIF in Bronchoalveolar Lavage of Sputum-Scarce Recurrent Pulmonary Tuberculosis Cases

Abstract Introduction Xpert MTB/RIF has greater sensitivity and specificity than smear microscopy. Bronchoalveolar lavage (BAL) is safe and valuable tool in sputum-scarce and sputum-negative tuberculosis (TB) patients. Our study evaluated the performance of Xpert in BAL specimen of sputum-scarce recurrent TB cases exclusively. Materials and Methods Sputum-scarce recurrent TB patients who underwent BAL between July 2018 and July 2019 were included. The diagnostic performance of Xpert and acid-fast bacilli (AFB) smear examination in BAL specimen was compared with liquid culture Mycobacterium TB (MTB) and composite reference standard. Results A total of 126 patients were included in the study. MTB culture was positive in 70 cases and nontuberculous mycobacteria were seen in five cases. Xpert was positive was in 63 patients. Sensitivity of Xpert and AFB smear was 84.29% (95% confidence interval [CI]: 73.62–91.89) and 18.57% (95% CI: 10.28–29.66), respectively, with p &lt; 0.001 proving the superiority of Xpert. Xpert had a specificity of 97.96 (89.15–99.95), positive predictive value of 93.65% (95% CI 85.19–97.42), and negative predictive value of 80.36% (95% CI: 70.26–87.63). Smear had a specificity of 91.84% (95% CI: 80.21–97.58) against 97.96 (89.15–99.95) of Xpert, and smear was positive in nontuberculous mycobacterium cases as well. Xpert showed no cross-reactivity between mycobacterial species. Rifampicin resistance was seen in 8 (12.69%) cases, and 21 patients had other diagnoses. Conclusion Xpert has greater sensitivity in comparison to AFB smear in BAL specimen. Sputum-scarce recurrent TB cases have a similar chance of rifampicin resistance as sputum smear-positive cases should undergo BAL for Xpert analysis routinely.

Epidemiology, laboratory diagnosis and clinical aspects of fungal pulmonary infections in 384 patients hospitalized in pulmonary units in Guilan province, Iran.

Background and Objectives:The respiratory tract is the most common site for developing fungal infections. People who have a weakened immune system are more susceptible to respiratory system involvement with fungi. Fungal infections of the respiratory tract are largely unrecognized and their true burden is elusive. Therefore, the aim of the current study was to evaluate the clinical spectrum, demographic characteristics, risk factors, and etiology of fungal respiratory infections in 384 patients hospitalized in pulmonary units of Razi hospital, Guilan province, Iran.Materials and Methods:A total of 384 lung specimens (192 Bronchoalveolar lavages (BAL) and 192 sputa) were obtained from patients who met the inclusion criteria. All samples were analyzed by direct microscopy and culture. Fungal identification was accomplished by internal transcribed spacer (ITS) and beta-tubulin sequencing. Also, in patients suspected to invasive pulmonary aspergillosis BAL specimens were tested for galactomannan (GM) antigen. According to the host factors (clinical symptoms, radiology findings and predisposing factors which were defined as inclusion criteria), and the positive results in direct examination, culture and serology (GM for aspergillosis) the infection was confirmed.Results:Fungal respiratory infection was confirmed in 137 cases (35.67%) including 86 (62.77%) males and 51 (37.23%) females and the highest prevalence of infection was found in the age group of 46–72 years (n=75, 54.74%). Cough (n=129, 94.16%), dyspnea (n=111, 81.02%), purulent sputum (n=85, 62.04%) and weight loss (n=77, 56.2%) were the predominant symptoms. Tuberculosis (n=34, 24.81%), taking chemotherapy regimen (n=30, 21.89%) and diabetes mellitus (n=27, 19.70%) were the predominant underlying conditions. Candida albicans (37.22%) and Candida tropicalis (21.89%) represent the two most commonly isolated species in the current study. Furthermore, according to revised EORTC/MSG (2008) definitions for invasive fungal infections, from 5 cases of pulmonary aspergillosis, 2 (40%) cases of probable invasive pulmonary aspergillosis (IPA) and 3 (60%) cases of possible IPA were diagnosed.Conclusion:According to the results of this study, infected infants with congenital CMV infection could identify at early stage by testing Guthrie cards (within 21 days of life). Furthermore, since there is a lack of CMV knowledge in our population, educating and effective counseling by obstetricians/gynecologists to the pregnant women are recommended.

Correlation between the Expression of Melanoma-Associated Antigen-A3 and Cytology Results on Bronchoalveolar Lavage on Nsclc

Background: Lung cancer is still considered an alarming health problem, causing a major cause of death in malignant disease. The incidence rate is likely to increase and most of it comes with an advanced stage of diagnosis. To improve the healing rate and life expectancy, the detection of lung cancer should be done early, when it is still small and localized. Bronchoalveolar lavage (BAL) cytology is a method of examination that can be used in lung cancer. The expression of Melanoma-Associated Antigen (MAGE) becomes the marker that is sensitive to certain types of cancer, including lung cancer. Objective:To analyze the correlation between expression MAGE-A3 and cytology of BAL specimen on NSCLC. Method: Bronchoscopy was performed on patients with NSCLC lung tumor at pulmonology unit of Dr. Soetomo Teaching Hospital Surabaya Indonesia to collect the BAL. Histologic examination for BAL and MAGE-A3 examination were conducted on patients. Statistical analysis used to determine the correlation between the expression of MAGE A3 and cytology of BAL specimens on NSCLC was fisher’s exact test. Result: We found that there were 7.14% of subjects with BAL cytology had cancer cells (adenocarcinoma). MAGE-A3 expression was positive only in 28.60% of subjects diagnosed with NSCLC. The result of MAGE A3 expression analysis with cytology of BAL specimen showed p = 0.286. Conclusion: There was no significant correlation between MAGE-A3 expression and histopathology type. The results of MAGE A3 RT PCR fluid expression examination showed that most of them were in the negative category.

Evaluation of Real-Time Polymerase Chain Reaction in Pneumocystis jirovecii Laboratory Diagnosis

Pneumocystis jirovecii is a human-specific species and causes fatal infections like P.jirovecii pneumonia (PCP) in immunocompromised persons. Although direct microscopy is the gold standard in the diagnosis of the microorganism, molecular methods such as polymerase chain reaction (PCR) are needed in non-human immune deficiency virus (HIV) immunosuppresive patients with low P.jirovecii burden. In this study, we aimed to evaluate the value of real-time PCR (Rt-PCR) in the laboratory diagnosis of P.jirovecii. Bronchoalveolar lavage (BAL) specimens of 658 patients sent to Dokuz Eylul University Hospital Central Medical Parasitology Laboratory on suspicion of PCP were included in the study. BAL fluids were evaluated for identification of P.jirovecii mitochondrial gene coding ribosomal large subunit (mtLSUrRNA) using Rt-PCR. In addition, Giemsa and Gomori's methenamine silver (GMG) staining assays were applied to all samples and nested PCR (n-PCR) assay was applied to positive samples detected by real time PCR. Ninety-two (14.3%) of these samples were positive by Rt-PCR. Of these 92 patients, 85 (92.4%) were positive with n-PCR. Only seven of the specimens had P.jirovecii cysts and trophozoites with microscopic examination. The mean cycle threshold (CT ) value of Rt-PCR positive patients was 29.7 (18.17 ≤ CT ≤ 37.96). P.jirovecii load in these patients was calculated as 2.6 x 101-6.15 x 107 copies/ml. The difference between the mean CT values of n-PCR positive and negative results was statistically significant (p< 0.01). The CT values of Rt-PCR of the samples with positive microscopy were; 18.2, 20.9, 22.2, 24.3, 24.7, 26.5, 29.7. The difference between the CT means of the samples with positive and negative microscopy was statistically significant (p< 0.05). When positive patients were grouped according to their diagnosis; the lowest mean CT value (CTmean= 24.8) was found in HIV-positive patients. On the other hand, CT values were found to be significantly lower in the organ transplantation patients (CTmean= 26.15) and in the collagen-vascular-inflammatory patient group (CTmean= 27.8). This study demonstrated that Rt-PCR was the effective method in the diagnosis of P.jirovecii in the laboratory. Conventional n-PCR method was found to be more unsuccessful than Rt-PCR in the presence of very low density organism; direct microscopy is generally found to be positive in samples with a higher burden of P.jirovecii.

Study on invasive aspergillosis using galactomannan enzyme immunoassay and determining antifungal drug susceptibility among hospitalized patients with hematologic malignancies or candidates for organ transplantation

The incidence of invasive aspergillosis (IA) has dramatically increased during the last decade. This infection is associated with high morbidity and mortality, ranging from 30% to 70%, especially in immunocompromised patients. Delay in diagnosis and treatment is usually associated with high mortality rates. This study was aimed to assess the diagnostic value of Galactomannan EIA (GM) for early diagnosis of aspergillosis in hospitalized patients with underlying conditions. Also, the antifungal drug susceptibility profiles of causative agents were investigated. In this descriptive cross-sectional study, during the period of 18 months starting from September 2017 until February 2019, 22 bronchoalveolar lavage (BAL) and 13 biopsies from infected sinuses were obtained from a total of 150 patients suffering from different types of hematologic malignancies. All the samples were subjected to microscopic examination and fungal culture. Also, serum specimens were obtained from all patients (n = 135). 22 serum and 17 BAL specimens were tested for the GM level. Fungal identified were confirmed through the PCR-sequencing of the β-tubulin gene. The susceptibility to amphotericin B, itraconazole, voriconazole, posaconazole, ravuconazole, and caspofungin was evaluated according to the Clinical and Laboratory Standards Institute document M38-A2 (CLSI M38-A2) broth microdilution protocol. The results showed that the incident rate of IA was 23.33% and 35 patients with IA (12 proven cases and 23 probable cases) were diagnosed according to the European Organization for Research and Treatment of Cancer and Mycoses Study Group criteria. The 35 patients with IA in the current study comprised 19 men (54.29%) and 16 women (45.71%) with the median age of 42 years. AML (31.5%) was documented as the most prevalent risk factor among our subjects with IA and Aspergillus flavus (65.7%) was the most prevailing causal agent in this study. Among patients with IA, ague (71%) and cough (60%) were the most common symptoms. In the present study, a sensitivity of 94% and a specificity of 98% was reported for GM ELISA in BAL specimens. Also, a sensitivity of 58% and a specificity of 98% was reported for GM ELISA in serum samples. Among 6 tested antifungal drugs, the lowest minimum inhibitory concentration (MIC) values were observed for posaconazole and ravuconazole which showed the range of 0.008–0.0062 μgml and 0.031–0.125 μgml, respectively. The current study has demonstrated that determining the value of GM investigation in BAL and serum specimens can be promising in early diagnosis of IA, also molecular identification of the agents causing IA and their antifungal susceptibility patterns are essential issues for the targeted antifungal therapy and outcome improvement of patients with this life-threatening disease.

Proteomic Analysis of the Air-Way Fluid in Lung Cancer. Detection of Periostin in Bronchoalveolar Lavage (BAL).

Background: Bronchoalveolar lavage (BAL) is a specific type of air-way fluid. It is a commonly used clinical specimen for the diagnosis of benign diseases and cancers of the lung. Although previous studies have identified several disease-associated proteins in the BAL, the potential utility of BAL in lung cancer is still not well-studied. Based upon the fact that the majority of secreted proteins are glycoproteins, we have profiled N-glycoproteins in BAL collected from lung cancers, and investigated the expression of glycoproteins such as the matrix N-glycoprotein, periostin, in lung cancers.Methods: BAL specimens (n = 16) were collected from lung cancer patients, and analyzed using mass spectrometry-based quantitative N-glycoproteomic technique. Additional BAL specimens (n = 39) were independently collected to further evaluate the expression of periostin by using an enzyme-linked immunosorbent assay (ELISA).Results: A total of 462 glycoproteins were identified in BAL samples using N-glycoproteomic technique, including 290 in lung adenocarcinoma (ADC, n = 5), 376 in squamous cell carcinoma (SQCC, n = 4), 309 in small cell lung carcinoma (SCLC, n = 4), and 316 in benign lung disease (n = 3). The expressions of several glycoproteins were elevated, including 8 in ADC, 12 in SQCC, and 17 in SCLC, compared to benign BALs. The expression of periostin was detected in all subtypes of lung cancers. To further investigate the expression of periostin, an ELISA assay was performed using additional independently collected BALs (n = 39) The normalized levels of periostin in benign disease, ADC, SQCC, and SCLC were 255 ± 104 (mean ± SE) and 4,002 ± 2,181, 3,496 ± 1,765, and 1,772 ± 1,119 ng/mg of total BAL proteins.Conclusion: Our findings demonstrate that proteomic analysis of BAL can be used for the study of cancer-associated extracellular proteins in air-way fluid from lung cancer patients.

Utility of Bronchoalveolar Lavage in the Diagnosis of Sputum Negative Pulmonary Tuberculosis

INTRODUCTION: Sputum smear examination for acid fast bacilli (AFB) by Ziehl-Neelsen stain (ZN stain) is the initial approach to the diagnosis of pulmonary tuberculosis (PTB). But 50% of the cases are reported to be sputum smear negative. This study was aimed to investigate the diagnostic yield of fibreoptic bronchoscopy (FOB) guided bronchoalveolar lavage (BAL) in patients suspected to have tuberculosis. The sample was tested for Mycobacterium tuberculosis using the XpertMTB/RIF assay, which is a new test that detects Mycobacterium tuberculosis complex and resistance to rifampin in less than two hours.&#x0D; MATERIAL AND METHODS: This is a prospective cross sectional study carried out on 58 sputum smear negative patients who were clinically suspected to have pulmonary tuberculosis from April 2017 to January 2019. All patients are subjected to FOB, BAL and BAL specimens were stained for AFB and also sent for Xpert (MTB)/RIF.&#x0D; RESULTS: Among 58 patients enrolled for the study 26 patients were positive for acid fast bacilli (AFB) through BAL stain and Xpert (MTB)/RIF combined.&#x0D; CONCLUSION: FOB guided BAL is a reliable, alternative and rapid method for diagnosing smear negative pulmonary tuberculosis with minimal complications.

Fungal Isolates of the Respiratory Tract in Symptomatic Patients Hospitalized in Pulmonary Units: A Mycological and Molecular Epidemiologic Study.

IntroductionFungal respiratory infections are being recognized with increasing frequency in parallel with an expanding population of immunocompromised patients. In most cases, colonization is the first step in the progression to pulmonary fungal infection. This study was designed to evaluate the distribution of fungal elements in the respiratory tract of symptomatic patients hospitalized in pulmonary units.MethodsThis descriptive cross-sectional study was carried out over a period of two years, from October 2017 to October 2019 in Guilan province, located in Iran’s northern region. In the current study, bronchoalveolar lavage or sputum specimens were collected. All samples were analyzed by direct microscopy using KOH 10% and culture. Fungal identification was accomplished by internal transcribed spacer (ITS) and beta-tubulin sequencing. Also, in patients suspected of invasive pulmonary aspergillosis, BAL specimens were tested for galactomannan (GM) antigen.ResultsA total of 384 lung specimens (192 bronchoalveolar lavage (BAL) and 192 sputum samples) were obtained from symptomatic patients hospitalized in pulmonary units. Of these, 137 (35.67%) were positive in direct examination and culture. Among the 137 positive cases, most isolates were from male patients 86 (62.77%) and most of them were between 46 and 72 years. Candida albicans (37.22%) and Candida tropicalis (21.89%) represent the two most commonly isolated species in the current study. Cough (94.16%), dyspnea (81.02%), purulent sputum (62.04%) and weight loss (56.2%) were the predominant symptoms and tuberculosis (24.81%), chemotherapy (21.89%) and diabetes mellitus (19.70%) were the predominant underlying conditions. Also, 5 cases of invasive pulmonary aspergillosis and 1 case of mucormycosis were diagnosed.ConclusionCandida albicans was the most common fungal species isolated from symptomatic patients hospitalized in pulmonary units. Tuberculosis, chemotherapy and diabetes mellitus were important underlying conditions for pulmonary fungal colonization and/or infection.

Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections.

Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents. The potential severity of these infections combined with a failure to clearly identify the causative pathogen results in administration of empirical antibiotic agents based on clinical presentation and other risk factors. We examined the impact of the multiplexed, semiquantitative BioFire FilmArray Pneumonia panel (PN panel) test on laboratory reporting for 259 adult inpatients submitting bronchoalveolar lavage (BAL) specimens for laboratory analysis. The PN panel demonstrated a combined 96.2% positive percent agreement (PPA) and 98.1% negative percent agreement (NPA) for the qualitative identification of 15 bacterial targets compared to routine bacterial culture. Semiquantitative values reported by the PN panel were frequently higher than values reported by culture, resulting in semiquantitative agreement (within the same log10 value) of 43.6% between the PN panel and culture; however, all bacterial targets reported as >105 CFU/ml in culture were reported as ≥105 genomic copies/ml by the PN panel. Viral targets were identified by the PN panel in 17.7% of specimens tested, of which 39.1% were detected in conjunction with a bacterial target. A review of patient medical records, including clinically prescribed antibiotics, revealed the potential for antibiotic adjustment in 70.7% of patients based on the PN panel result, including discontinuation or de-escalation in 48.2% of patients, resulting in an average savings of 6.2 antibiotic days/patient.

Role of cartridge based nucleic acid amplification test in bronchoscopy guided bronchial wash specimens in sputum smear negative PTB patients attending government general hospital, Kakinada

Tuberculosis is a global health burden still causing large mortality and morbidity. According to WHO’s 2018 Global TB Report two main routes for reducing TB incidence and death are- diagnosis and treatment. The main challenging issue with TB is to obtain a rapid and accurate diagnosis for initiating early treatment. Sometimes patient with active pulmonary tuberculosis fail to produce adequate sputum resulting in increase of false-negatives. Sputum-smear negative pulmonary tuberculosis is highly infectious and remains a diagnostic challenge. Fiber-optic bronchoscopy is an important tool for early detection and confirmation of sputum smear-negative and sputum-scarce PTB as it provides high-quality biological samples like bronchoalveolar lavage (BAL) fluid. The aim of the present study was to evaluate role of in Gene Xpert MTB/RIF on bronchoscopic specimens in sputum smear negative patients with suspicion of PTB. A prospective observational study was done on 100 patients with clinical suspicion of PTB who either have a negative sputum smear microscopy or unable to produce qualitative sputum attending outpatient and admitted in Pulmonology department, Government General Hospital, Kakinada.Out of 100 patients, 47 were diagnosed and confirmed as pulmonary tuberculosis of which bronchial specimens smear positive were 5(10.6%),bronchial specimens smear negative but CBNAAT positive were 42(89.3%). At last as CBNAAT has dual diagnostic advantage of detecting rifampicin resistance, about 5 cases were detected as rifampicin resistance. CBNAAT/RIF assay on BAL specimen provides an accurate diagnosis of PTB in patients with sputum smear negative results or those who cannot expectorate sputum and superior to sputum smears in detecting rifampicin resistance.