Bronchoalveolar Lavage Samples Research Articles

Polycyclic aromatic hydrocarbons and their metabolites in bronchoalveolar lavage and urine samples from patients with inhalation injury throughout their hospitalization: A prospective pilot study.

Specific toxic compounds, such as polycyclic aromatic hydrocarbons (PAHs) and their metabolites, may affect the inhalation injury (INHI) grade, patients' status, and prognosis for recovery. This pilot prospective study aimed to: i) evaluate the suitability of bronchoalveolar lavage (BAL) for determination of PAHs in the LRT and of urine for determination of hydroxylated metabolites (OH-PAHs) in patients with INHI, ii) describe the dynamic changes in the levels of these toxic compounds, and iii) correlate these findings with clinical variables of the patients with INHI. The BAL and urine samples from 10 patients with INHI were obtained on Days 1, 3, 5, 7, and 14 of hospitalization, if possible, and PAHs (BAL) and OH-PAHs (urine) were analyzed using chromatographic methods (GC-MS and HPLC). Concentrations of analyzed PAHs were in most cases and time points below the limit of quantification in BAL samples. Nine OH-PAHs were detected in the urine samples; however, their concentrations sharply decreased within the first three days of the hospitalization. On Day 14, the total amount of OH-PAHs in urine was higher in surviving patients with High-grade INHI (≥3) than in those with Low-grade INHI (<3, p = 0.032). Finally, a significant correlation between certain OH-PAHs and clinical variables (AST/ALT, TBSA, ABSI) from Day 1 of the hospitalization was observed (p<0.05). BAL samples are not suitable for the analysis of PAHs. However, the OH-PAHs levels in urine can be measured reliably and were correlated with several clinical variables. Moreover, High-grade INHI was associated with higher total concentrations of OH-PAHs in urine.

A case series on reactive atypia findings in cytology examination of bronchoalveolar lavage samples

ABSTRACT Reactive atypia in bronchoalveolar lavage (BAL) cells reflects cellular changes frequently observed in respiratory cytology, typically resulting from injury, inflammation, or irritation rather than malignancy. This review examines the nature, causes, and diagnostic implications of reactive atypia in BAL specimens. BAL is a diagnostic procedure used to collect cells from the lower respiratory tract. Identifying atypical cells in BAL samples poses a significant challenge, as their morphology can resemble that of neoplastic processes. Characteristics of reactive atypia include nuclear enlargement, hyperchromasia, irregular nuclear contours, and increased nucleocytoplasmic ratios. These changes are often attributable to inflammation, infections, toxic exposures (such as smoking), and chronic respiratory diseases, including asthma and chronic obstructive pulmonary disease. This case series discusses three instances of reactive atypia encountered in BAL sample analysis. Reactive atypia in BAL cells is a common, benign response to various stimuli. Accurate diagnosis necessitates a comprehensive approach that integrates cytological findings, clinical context, and adjunctive diagnostic tools. Ongoing research into the molecular characteristics of reactive atypia has the potential to enhance diagnostic precision and improve patient care.

Histoplasmosis in patients living with HIV in Europe: review of literature.

Histoplasma capsulatum (var. capsulatum Hcc and duboisii Hcd), is a dimorphic fungus that causes histoplasmosis. It usually affects people coming from endemic areas, causing a variety of clinical manifestations up to progressive disseminated histoplasmosis (PDH), especially among people living with HIV (PLWH). We conducted a systematic review to assess histoplasmosis burden of PLWH in Europe. The review follows PRISMA guidelines, with protocol registered in PROSPERO (CRD42023429779). Seventy-eight articles were selected, including 109 patients (32 women). On overall, median age was 37 years. Forty-six patients were Americans, 39 Africans, 17 Europeans, 5 Asians, in 2 cases nationality was not specified. Cases were mainly diagnosed in Italy (28.4%), France (17.3%) and Spain (17.4%), with a north-south gradient. Six cases lacked epidemiologic links with endemic areas. Concerning CDC HIV staging at diagnosis, the information was available for 60 PLWH (55%) and all subjects were at stage C3 except for two subjects at stage B3. PDH was the AIDS-presenting illness in 39 patients. Most patients had a PDH (80.7%); other common extrapulmonary forms were isolated cutaneous histoplasmosis (7.3%), or lymphatic localization (2.7%). In 30 cases, the diagnosis was made by analyzing only one sample. For the remaining 79 cases, multiple samples were collected from each patient. Regarding the biological sample more frequently used for the diagnosis of histoplasmosis, bronchoalveolar lavage sample was taken from 39 patients, and tested positive in 51.3% of cases; 36 patients underwent a skin biopsy which was positive in 86.1% of cases and 28 patients performed bone-marrow biopsy, which led to the diagnosis of histoplasmosis in 92.9% of cases. The identification of Histoplasma capsulatum was available in 97 PLWH through examination of different samples: Hcc and Hcd were identified in 89 and 8 PLWH, respectively. Concerning therapies, 67.9% were treated with liposomal amphotericin B, 18.3% with itraconazole, 10 died pre-treatment. The overall mortality rate was 23.6%. Non-survivors exhibited more frequently gastrointestinal symptoms (p = 0.017), while cutaneous signs correlated with better survival (p = 0.05). Untreated patients faced higher mortality (p < 0.001). Histoplasmosis should be considered amongst opportunistic infection in PLWH, even in Europe, especially if patients originate from or have travelled to endemic areas. Systematic review registration: The registration number is CRD42023429779.

The Double Trouble Monster – Unmasking Hidden Tuberculosis in Silicosis Patients: A Case Series

Abstract Tuberculosis occurs commonly in silicosis and is difficult to diagnose. We are presenting four cases of silicotuberculosis. The first three cases of silicotuberculosis have occupational risk factors such as borewell driller, construction sites, and quarry presented with silicotuberculosis clinic radiological features with negative sputum acid-fast bacilli and positive results for tuberculosis obtained from bronchoalveolar lavage samples. The last case developed silicosis due to inhalational burned sugarcane crops. Antituberculosis therapy started after microbiological confirmation for tuberculosis. Hence, a vigorous search of tuberculosis in silicosis patients is highly warranted.

Clonal spread of trimethoprim-sulfamethoxazole-resistant Stenotrophomonas maltophilia isolates in a tertiary hospital.

The aims of this study were to: (i) determine antibiotic susceptibility of clinical Stenotrophomonas maltophilia isolates, (ii) investigate the presence of different classes of integrons and sul genes responsible for sulphonamide resistance, (iii) assess the molecular epidemiology of the isolates by determining their clonal relatedness, and (iv) investigate the potential sources of infection by collecting environmental samples when necessary. 99 S. maltophilia isolates from clinical specimens of hospitalized patients were screened by PCR for sul1, sul2, sul3 genes, and integron-associated integrase genes: intI1, intI2, and intI3. PFGE was used to determine the clonal relatedness of the isolates. Susceptibility rates for trimethoprim-sulfamethoxazole, levofloxacin, and ceftazidime were 90.9%, 91.9%, and 53.5% respectively. All trimethoprim-sulfamethoxazole-resistant isolates were positive for intI1 and sul1. PFGE analysis revealed that 24 of the isolates were clonally related, clustering in seven different clones. Five of the nine trimethoprim-sulfamethoxazole-resistant isolates were clonally related. The first isolate in this clone was from a wound sample of a patient in the infectious diseases clinic, and the other four were isolated from the bronchoalveolar lavage samples of patients in the thoracic surgery unit. The patient with the first isolate neither underwent bronchoscopy nor stayed in the thoracic surgery unit. Although clustering was observed in bronchoalveolar lavage samples, no S. maltophilia growth was detected in environmental samples. The findings demonstrated that the sul1 gene carried by class 1 integrons plays an important role in trimethoprim-sulfamethoxazole resistance in S. maltophilia isolates. PFGE analysis revealed a high degree of genetic diversity. However, detection of clonally related isolates suggests the acquisition from a common source and/or cross-transmission of this microorganism between the patients.

Dynamic shifts in lung cytokine patterns in post-COVID-19 interstitial lung disease patients: a pilot study.

The pathogenesis of post-COVID interstitial lung disease, marked by lung tissue scarring and functional decline, remains largely unknown. We aimed to elucidate the temporal cytokine/chemokine changes in bronchoalveolar lavage (BAL) from patients with post-COVID interstitial lung disease to uncover potential immune drivers of pulmonary complications. We evaluated 16 females diagnosed with post-COVID interstitial lung disease, originating from moderate to severe cases during the second epidemic wave in the Autumn of 2020, treated at the Pneumology Department of the Arad County Clinical Hospital, Romania. Their inflammatory response over time was compared to a control group. A total of 48 BAL samples were collected over three intervals (1, 3, and 6 months) and underwent cytology, gene, and protein expression analyses for pro/anti-inflammatory lung cytokines and chemokines using reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. One month after infection, there were significant increases in the levels of IL-6 and IL-8. These levels decreased gradually over the course of 6 months but were still higher than those seen in control. Interferon-gamma and tumor necrosis factor alpha exhibited similar patterns. Persistent elevations were found in IL-10, IL-13, and pro-fibrotic M2 macrophages' chemokines (CCL13 and CCL18) for 6 months. Furthermore, pronounced neutrophilia was observed at 1 month post-COVID, highlighting persistent inflammation and lung damage. Neutrophil efferocytosis, aiding inflammation resolution and tissue repair, was evident at the 1-month time interval. A notable time-dependent reduction in CD28 was also noticed. Our research provides insight into the immunological processes that may lead to the fibrotic changes noted in the lungs following COVID-19.

Development of a method for collecting bronchoalveolar lavage from calves for microbiological diagnosis of bronchopneumonia

A serious problem for the health of cattle, especially in highly productive animals, is infectious bronchopneumonia, which occurs when exposed to numerous adverse environmental factors and opportunistic microorganisms. Infectious bronchopneumonia is an important problem in the livestock industry and remains a major cause of significant economic losses in dairy herds and feedlots due to high morbidity and mortality rates, in addition to negatively affecting growth, reproductive performance and life expectancy. Therefore, the development of a new method for intravital minimally invasive diagnosis of calves with acute catarrhal bronchopneumonia using bronchoalveolar lavage sampling for subsequent microbiological studies is relevant. The invention relates to veterinary medicine and can be used in intravital diagnostics of bronchopneumonia in calves by isolating microorganisms that initiate the purulent-inflammatory process from samples of bronchoalveolar contents taken in the area of the tracheal bifurcation. A method for intravital diagnosis of bronchopneumonia in calves includes transnasal introduction to a sick animal of a sterile silicone medical tube with a diameter of 4 mm (the internal diameter of the hole is 3 mm), a wall thickness of 1.0 mm and a length of 150 cm, until slight resistance and a repeated cough reflex appear, upon reaching in the area of the tracheal bifurcation, the nasogastric tube is moved back 1 cm, a disposable syringe with a volume of 50 ml is attached to the free end, and with its help, 30-40 ml of sterile isotonic saline solution (0.9% NaCl solution, 37° C) is injected into the trachea, and then immediately aspirate up to 10 ml of bronchoalveolar contents.

Impact of lipopolysaccharide-induced acute lung injury in aged mice

Study Aim: As the geriatric population rapidly expands, there has been a concurrent increase in elderly admissions to intensive care units (ICUs). Acute lung injury (ALI) is a prevalent reason for these admissions and carries poorer survival rates for the aged population compared to younger counterparts. The aging lung is subject to physiological, cellular, and immunological changes. However, our understanding of how aging impacts the clinical progression of ALI is limited. This study explored the effect of aging using a murine model of ALI. Methods: Female C57BL/6J mice, aged 7–8 wk (young) and 18 months (aged), were divided into four groups: young controls, aged controls, young with ALI (YL), and aged with ALI (AL). ALI was induced via intratracheal administration of lipopolysaccharide (LPS, 0.5 mg/kg). The animals were euthanized 72 h after LPS exposure. Results: The AL group exhibited a significantly increased wet/dry ratio compared to the other three groups, including the YL group. The bronchoalveolar lavage (BAL) fluid in the AL group had more cells overall, including more neutrophils, than the other groups. Inflammatory cytokines in BAL fluid showed similar trends. Histological analyses demonstrated more severe lung injury and fibrosis in the AL group than in the other groups. Increased transcription of senescence-associated secretory phenotype markers, including PAI-1 and MUC5B, was more prominent in the AL group than in the other groups. This trend was also observed in BAL samples from humans with pneumonia. Conclusions: Aging may amplify lung damage and inflammatory responses in ALI. This suggests that physicians should exercise increased caution in the clinical management of aged patients with ALI.

Clinical Implementation of β-Tubulin Gene-Based Aspergillus Polymerase Chain Reaction for Enhanced Aspergillus Diagnosis in Patients with Hematologic Diseases: A Prospective Observational Study.

The β-tubulin (benA) gene is a promising target for the identification of Aspergillus species. Assessment of the clinical implementation and performance of benA gene-based Aspergillus polymerase chain reaction (PCR) remains warranted. In this study, we assessed the analytical performance of the BenA probe PCR in comparison with the Aspergenius kit. We prospectively collected bronchoalveolar lavage (BAL) fluid via diagnostic bronchoscopy from adult patients with hematologic diseases. BenA gene-based multiplex real-time PCR and sequential melting temperature analysis were performed to detect the azole resistance of Aspergillus fumigatus. In total, 76 BAL fluids in 75 patients suspicious of invasive pulmonary aspergillosis (IPA) were collected. Before the application of PCR, the prevalence of proven and probable IPA was 32.9%. However, after implementing the benA gene-based PCR, 15.8% (12 out of 76) of potential IPA cases were reclassified as probable IPA. The analytical performance of the BenA probe PCR in BAL samples was comparable to that of the Aspergenius kit. The diagnostic performance was as follows: sensitivity, 52.0%; specificity, 64.7%; positive predictive value, 41.9%; negative predictive value, 73.3%; positive likelihood ratio, 1.473; and negative likelihood ratio, 0.741. Moreover, benA gene-based Aspergillus PCR discriminated all major sections of Aspergillus, including cryptic species such as Aspergillus tubingensis. Sequential melting temperature analysis successfully detected 2 isolates (15.4%) of A. fumigatus carrying resistant mutations. BenA gene-based Aspergillus PCR with melting temperature analysis enhances diagnostic accuracy and detects not only cryptic species but also resistant mutations of A. fumigatus. It shows promise for clinical applications in the diagnosis of IPA.

Mucosal and systemic antigen-specific antibody responses correlate with protection against active tuberculosis in nonhuman primates

Increasing evidence supports that antibodies can protect against active tuberculosis (TB) but knowledge of potentially protective antigens, especially in the airways, is limited. The main objective of this study was to identify antigen-specific airway and systemic immunoglobulin isotype responses associated with the outcome of controlled latent Mycobacterium tuberculosis (Mtb) infection (LTBI) versus uncontrolled infection (TB) in nonhuman primates. In a case-control design, using non-parametric group comparisons with false discovery rate adjustments, we assessed antibodies in 57 cynomolgus macaques which, following low-dose airway Mtb infection, developed either LTBI or TB. We investigated airway and systemic IgG, IgA, and IgM responses in paired bronchoalveolar lavage and plasma samples prior to, two-, and 5-6-months post Mtb infection using an antigen-unbiased approach with Mtb glycan and proteome-wide microarrays. Macaques that developed LTBI (n=36) had significantly increased airway and plasma IgA reactivities to specific arabinomannan (AM) motifs prior to Mtb infection compared to those that developed TB (n=21; p<0.01, q<0.05). Furthermore, LTBI macaques had higher plasma IgG reactivity to protein MTB32A (Rv0125) early post Mtb infection (p<0.05) and increasing airway IgG responses to some proteins over time. Our results support a protective role of pre-existing mucosal (lung) and systemic IgA to specific Mtb glycan motifs, suggesting that prior exposure to nontuberculous mycobacteria could be protective against TB. They further suggest that IgG to Mtb proteins early post infection could provide an additional protective mechanism. These findings could inform TB vaccine development strategies. NIH/NIAID AI117927, AI146329, and AI127173 to JMA.

Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis

BackgroundLower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species. MethodsThis review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies. ResultsThis work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82–93%) while their specificity was 90% (66–98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4. ConclusionThe AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.

Feasibility and acceptability of undertaking postmortem studies for tuberculosis medical research in a low income country.

If we are to break new ground in difficult-to-treat or difficult-to-vaccinate diseases (such as HIV, malaria, or tuberculosis), we must have a better understanding of the immune system at the site of infection in humans. For tuberculosis (TB), the initial site of infection is the lungs, but obtaining lung tissues from subjects suffering from TB has been limited to bronchoalveolar lavage (BAL) or sputum sampling, or surgical resection of diseased lung tissue. We examined the feasibility of undertaking a postmortem study for human tuberculosis research at Mulago National Referral Hospital in Kampala, Uganda. Postmortem studies give us an opportunity to compare TB-involved and -uninvolved sites, for both diseased and non-diseased individuals. We report good acceptability of the next-of-kin to consent for their relative's tissue to be used for medical research; that postmortem and tissue processing can be undertaken within 8 hours following death; and that immune cells remain viable and functional up to 14 hours after death. Postmortem procedures remain a valuable and essential tool both to establish cause of death, and to advance our medical and scientific understanding of infectious diseases.

Evaluation of the BioFire® FilmArray® Pneumonia plus Panel for Detecting Bacterial Etiological Agents of Lower Respiratory Tract Infections in an Oncologic Hospital. Comparison with Conventional Culture Method.

Conventional methods used to determine pneumonia pathogens are characterized by low sensitivity and long turnaround times. Introducing new tests with better parameters in patients at higher risk of infections is highly anticipated. The results of the conventional quantitative culture method (CM) in determining the bacterial etiology of pneumonia were compared with the results of the Pneumonia plus Panel test (PNP; BioFire® Diagnostics, USA) in 79 samples of bronchoalveolar lavage (BAL). Materials were collected from 79 patients with suspected pneumonia treated in an oncologic hospital due to solid tumors. Only 16/79 BAL samples (20.3%) were true positive (TP) for bacterial etiology in CM vs. 27/79 samples (34.2%) true positive in the PNP test. The total agreement between methods of interpreting the result (positive or negative) was 84.8%. The most prevalent pathogens in both methods were Staphylococcus aureus, followed by Escherichia coli, Pseudomonas aeruginosa, and Haemophilus influenzae. The PNP test identified several respiratory pathogens that were not grown in culture. The semiquantitative value reported by the PNP test was higher than that reported by culture. The PNP test vs. combined test (PNP test and CM methods) demonstrated positive predictive value (PPV) and negative predictive value (NPV) values of 100.0% and 98.1%, and the sensitivity and specificity were 96.4% and 100.0%. The PNP test is a good tool for determining the etiology of bacterial pneumonia and may support the care of an oncologic patient. However, further large-sample studies are needed to research in strictly defined groups of oncologic patients.

Molecular Detection of Pneumocystis jirovecii in the Bronchoalveolar Lavage Samples in Patients with Various Pulmonary Disorders(Original Article)

Molecular Detection of Pneumocystis jirovecii in the Bronchoalveolar Lavage Samples in Patients with Various Pulmonary Disorders(Original Article)

1678. Non-Invasive and invasive Pediatric Group A Streptococcus Infections (iGAS) Admissions During 2021 and 2022 at a Tertiary Health Care Center: Resurgence and Concomitant Viral Infections

Abstract Background A resurgence of invasive Group A Streptococcus (iGAS) infection in children was observed in Colorado and Minnesota by the Centers For Disease Control and Prevention (CDC) during the fall of 2022. Cases were accompanied by hospitalizations for respiratory syncytial virus (RSV) and influenza. We describe hospital admissions with iGAS and non iGAS infections at a tertiary health care center in Augusta, GA during 2021 and 2022; the only children’s Hospital with 150 licensed beds and a population of 201.196 as of 2021. Methods We used the iGAS definition by the CDC as a Group A Streptococcus (GAS) isolated by culture in specimens obtained from a sterile body site, or GAS isolated from wound culture and necrotizing fasciitis or streptococcal toxic shock syndrome. We conducted a retrospective chart review of iGAS and non iGAS cases admitted to the Children’s Hospital of Georgia during January to December 2021 and January to December 2022. We collected demographics, site of infection, concomitant viral infections diagnosed by nasopharyngeal (NP) PCR, intensive care unit (ICU) admission and mortality. Results During 2021, only 1 patient was admitted with non iGAS, a 7-year-old with a wound infection. In 2022, 15 patients were diagnosed with GAS infection, 7 of them had iGAS and 8 had noninvasive disease. We included positive peritoneal and pleural fluid, joint/bone aspirates, bronchoalveolar lavage samples, and blood cultures for iGAS. The age range for iGAS was 6-17 years and for noninvasive, 16 mo to 11 years. In 2022, 25% of noninvasive cases had concomitant influenza compared to 43% of iGAS cases. Only one patient with non iGAS tested positive for RSV. 2 patients had rhinovirus, one had adenovirus. One patient with iGAS was positive for metapneumovirus (HMPV). 57% of iGAS cases were admitted to the ICU (n=4). 50% of noninvasive cases (n=4) were admitted to the ICU. One iGAs case died. All noninvasive cases survived. Conclusion There was increase in iGAS and noninvasive GAS infections during 2022 compared to 2021 in our institution. iGAS was more common in older children. Of iGAS cases, the only coexisting viruses were influenza and HMPV. Most cases were seen during Fall of 2022. The cause of reappearance of iGAS and non iGAS is still unknown but believed to be related to end of mask mandates for COVID 19 infections. Disclosures All Authors: No reported disclosures

621. Evaluation of a Multiplex Endpoint PCR for the Detection of 21 Fungi Commonly Causing Fungal Pneumonia Using Barcoded Magnetic Bead Technology

Abstract Background Fungal pneumonia caused by Aspergillus, Mucorales, and other fungi are potentially life-threatening and often are difficult to diagnose due to similar clinical presentations and poor sensitivity by culture. The BioCode MDx-3000 from Applied BioCode uses Barcoded Magnetic Bead (BMB) technology to digitally detect 21 fungi in a multiplex PCR. We evaluated the BioCode assay using clinically simulated samples and retrospective frozen bronchoalveolar lavage samples. Methods For limit of detection (LOD), 10-20 replicates of each organism were run at 1E4-10 spores/mL. Reproducibility was performed by running three replicates of each target (1E3 spores/mL) within one run, three separate times. Specificity was determined by testing for 37 fungal analytes not targeted by the panel. Matrix specific inhibition was also tested by spiking each organism in the following matrices: whole blood, plasma, serum and BAL. 90 retrospective BAL samples from patients with fungal culture results were run to assess clinical performance. Results LOD of 21 fungal organisms ranging from 19.83 – 271.76 spores/ml. Detection rate was 100% (36/36) in all samples mixed with two fungi; 95% (20/21) in all samples mixed with three fungi. No detection or cross-reactivity was observed in samples containing any of the 37 non-targeted fungi. All replicates were detected in Inter- and intra- reproducibility experiments. No difference or inhibition was observed in detection of targeted fungi spiked in different matrices. Testing retrospective BAL samples showed an overall positive concordance of 61.4% and negative concordance of 98.1%. In 23 BALs positive by both calcofluor white stain (hypha elements) and culture, the BioCode assay correctly detected fungal targets in 78% (18/23) of the samples. Additionally, the assay produced positive detection in 25% of BALs that were culture negative. Limit of Detection and Concordance Limit of detection for the 21 fungal targets. Concordance for each target in retrospective BALs compared to culture. N/A indicates not tested. Conclusion The BioCode assay showed an overall good analytical sensitivity and specificity. Analysis of retrospective BAL samples demonstrated the assay showing good concordance with the culture results. Further studies are warranted to determine the assay’s clinical sensitivity and specificity in aid in diagnosis of fungal pneumonia. Disclosures Kristen Haag, BS, Applied BioCode, Inc.: I am an employee of Applied BioCode|Applied BioCode, Inc.: Stocks/Bonds Michael Aye, PhD, Applied BioCode: Stocks/Bonds Martín Cardona, BS, Applied BioCode, Inc.: I am an employee of Applied BioCode. Sean Zhang, PhD, Applied BioCode: Grant/Research Support|IMMY Diagnostics: Grant/Research Support|KARIUS: Advisor/Consultant|Pearl Diagnostics: Grant/Research Support|Scanogen: Grant/Research Support|T2 Biosystems: Advisor/Consultant|Vela Diagnostics: Grant/Research Support

Utility of Bronchoalveolar Lavage for the Diagnosis and Management of COVID-19 in Patients With Cancer.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) on nasopharyngeal swab (NPS), remains the most reliable and practical test to diagnose coronavirus disease 2019 (COVID-19). Current literature is sparse regarding the rates of discordance between NPS and bronchoalveolar lavage (BAL) in patients with cancer. We conducted a retrospective cohort study of adult patients with cancer who had BAL samples tested for SARS-CoV-2 at a comprehensive cancer center. Patients without NPS PCR for SARS-CoV-2 before BAL were excluded. In a cohort of 345 patients, 12% and 17% tested positive for SARS-CoV-2 on NPS and BAL, respectively. There was a 6.3% NPS-/BAL+ discordance rate and a 9.5% NPS+/BAL- discordance rate. Patients with lymphoma (adjusted odds ratio [aOR] = 4.06; P = .007) and Hispanic patients (aOR = 3.76; P = .009) were more likely to have NPS-/BAL+ discordance on multivariate analysis. Among patients with NPS- /BAL- for SARS-CoV-2, an alternate infectious (23%) and a noninfectious etiology (16%) were identified in BAL. Our discordance rates between NPS and BAL were sufficient to recommend BAL in certain patients with cancer with a high clinical suspicion of COVID-19. BAL has value in identifying alternative etiologies of illness in patients with suspected or confirmed COVID-19.

Molecular identification of multiple drug resistance (MDR) strain of Mycobacterium tuberculosis.

Isoniazid and rifampin are the first -line drugs against Mycobacterium tuberculosis. Resistance to these important drugs is a serious threat to human public health. Therefore, this study aimed at molecular detection of resistance to these valuable drugs. In this descriptive cross-sectional study, 111 non - duplicated clinical samples including sputum and Bronchoalveolar lavage (BAL) samples were collected from patients referred to the Ardabil Health Center between 2017 and 2020. The samples were first examined by microscopic method, then their DNA was extracted using the boiling method. Specific primers and MAS-PCR method were employed for the detection resistance to isoniazid and rifampin drugs and identification of MDR strain. of 111 specimens, 15.3% belonged to NTM. In total, the resistance rate to isoniazid and rifampin was 17% and 27% respectively while the resistance rate to isoniazid and rifampin among NTM was 61.54% and 38.46%. In our study, the prevalence of resistance to isoniazid and rifampin among Mycobacterium tuberculosis complex(MTC) and non-tuberculous mycobacteria(NTM) was investigated using the MAS-PCR method. This work highlighted the high anti- tuberculosis resistance rate among NTM compared to MTC strains.

Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study

BackgroundHospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise.MethodsThis proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients.ResultsA total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test.ConclusionsThis study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.

Performance evaluation of the automated body fluid analysis of the new Sysmex XR haematology analyser

Abstract Objectives The cellular composition of body fluids (BF) provides insight into disease pathology and is an important diagnostic parameter. The well-established Sysmex XN haematology analyser (XN) offers automated BF analysis and is in routine use in many laboratories. In this study the performance of the new Sysmex XR analyser (XR) in testing BF is compared to the XN. Methods Cerebrospinal, pleural, peritoneal, and synovial fluids, as well as bronchoalveolar lavage (BAL) samples, were processed in BF mode on both analysers. Standard statistical methods were used to evaluate the performance of XR compared to the reference XN. Results Cell counts were generated from a total of 356 measurements from 307 patient BF samples. After application of exclusion criteria, 86 cerebrospinal, 77 peritoneal, 78 pleural, and 89 synovial fluid sample pairs were compared. An excellent correlation coefficient (r) between the two analysers was observed for all diagnostic parameters; WBC-BF: 0.996, RBC-BF: 0.974, TC-BF: 0.995, MN#: 0.994, MN%: 0.830, PMN#: 0.985 and PMN%: 0.835. The research parameters also performed equally well (r values of 0.900–0.994). The performance of diluted and undiluted samples was equally good. Similar results for diagnostic and research parameters were obtained from 62 BAL samples (r values of 0.899–0.992). Conclusions This study demonstrates that the automated BF counts on the new Sysmex XR analyser are equivalent to that of the XN for all BF types analysed.