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Background In the diagnosis of SARS-COV-2, upper respiratory tract specimens are primarily used for PCR testing. This study aims to evaluate the clinical and diagnostic role of bronchoalveolar lavage (BAL) in diagnosing and managing COVID-19. Methods Patients admitted to Keck Medical Center (Los Angeles, CA) during March 2020-May 2021 who had SARS-CoV-2 PCR tested on both nasopharyngeal swab (NPS) and BAL specimens (QIAGEN QIAstat-Dx RP) were included. Four patient groups were designated by PCR results: (A) NPS+/BAL+ (n=34), (B) NPS+/BAL- (n=26), (C) NPS-/BAL+ (n=5), (D) NPS-/BAL- (n=89). Clinical and laboratory data were retrospectively reviewed. Statistical analysis included the use of one-way ANOVA with Tukey HSD and Fisher’s exact test. Results 154 inpatients had NPS and BAL tested for SARS-CoV-2 RNA (mean age 55.1 y, 59.6% male). BAL was performed mainly to further assess abnormal respiratory function (n=43) or chest imaging findings (n=27), or for COVID-19 work-up (n=17). Mean turnaround time for BAL PCR was 4 h 5 min. Ct values, available on 28 BAL+ samples, did not significantly differ between patients who died (mean Ct 29.9, n=18) vs. survived (mean Ct 28.7, n=10). Time from symptom onset to BAL was significantly longer in Group B (34.2 d) vs. D (13.7 d, p< 0.01) or C (12.8 d, p< 0.05) but not vs. A (23.9 d). Groups did not differ significantly in patient comorbidities, mortality, length of hospital stay, or immunosuppressive status. SARS-CoV-2 NPS+/BAL+ patients were more likely to have diffuse or bilateral chest radiographic opacities (p< 0.01), respiratory culture with Aspergillus spp. (p< 0.05), and ARDS diagnosis than those who were NPS+/BAL- (p< 0.01). Conclusion BALs were an important specimen source for the detection of SARS-CoV-2 in the lower respiratory tract particularly when NPS at admission was PCR-negative and for ruling out COVID-19 pneumonia as a cause of abnormal pulmonary findings or declining respiratory status. BAL positivity for SARS-CoV-2 RNA was associated with higher frequency of diffuse or bilateral opacities on CXR, culture recovery of Aspergillus spp., and ARDS. Ct values of BAL+ samples did not predict mortality though sample size was limited. Further studies on the role of viral detection in BALs in patient management and prognosis are warranted. Disclosures All Authors: No reported disclosures.

Background Antimicrobial resistance (AMR) is a pressing global challenge detected by antimicrobial susceptibility testing (AST) performed by clinical laboratories. AST results are interpreted using clinical breakpoints, which are updated to enable accurate detection of new and emerging AMR. Laboratories that do not apply up-to-date breakpoints impede global efforts to address the AMR crisis, but the extent of this practice is poorly understood. Methods A total of 1490 clinical laboratories participating in a College of American Pathologists proficiency testing survey for bacterial cultures were queried to determine use of obsolete breakpoints. Results Between 37.9% and 70.5% of US laboratories reported using obsolete breakpoints for the antimicrobials that were queried. In contrast, only 17.7%–43.7% of international laboratories reported using obsolete breakpoints (P Conclusions These data demonstrate a significant gap in the ability to detect AMR in the US, and to a lesser extent internationally. Improved application of current breakpoints by clinical laboratories will require combined action from regulatory agencies, laboratory accreditation groups, and device manufacturers.

Background Syndromic PCR testing for lower respiratory pathogens may give rapid, actionable results to aid in management decisions for suspected pneumonia cases. We sought to evaluate the performance of a multiplexed PCR pneumonia panel compared to routine microbiologic work-up in a tertiary care patient population. Methods Sputum and bronchoalveolar lavage (BAL) samples from Keck Medical Center (Los Angeles, CA) inpatients submitted for clinical microbiology work-up Dec 2019-Jun 2020 were tested by a multiplexed PCR panel (FilmArray Pneumonia Panel, BioFire Diagnostics). We compared panel results for typical bacterial pathogens to those of quantitative culture and susceptibility testing. We retrospectively determined the incidence of non-panel respiratory pathogens as detected by standard of care tests in this patient cohort. Results 68 of 180 samples yielded 80 positive bacterial PCR results: 34 were detected by both PCR panel and culture and 46 by PCR panel only, yielding a sensitivity of 100% (34/34) for pathogens detected and specificity of 73.1% (114/156) among negative cultures (normal flora or no growth). Concordant results had PCR Bin values ≥10^5 copies/mL whereas all 18 targets detected at 10^4 copies/mL were culture-negative. Among resistance gene targets, the panel detected 12 MRSA specimens, of which MRSA grew in only 4 cultures; E. coli and CTX-M in 1 specimen from which grew normal flora; and multiple gram-negative organisms and KPC in 1 specimen from which culture isolated carbapenem-resistant P. aeruginosa. Quantitation from positive BAL cultures (n=25) correlated weakly with PCR Bin values (R-squared=0.17). Non-PCR panel pathogens were detected in 22 of 180 (12.2%) specimens through routine methods (16 molds, 3 AFB, and 3 non-fermenter gram-negative bacteria). Conclusion The pneumonia panel had excellent sensitivity for its target bacterial pathogens, but results were often positive in negative cultures. This could be due to antecedent antibiotic therapy, differences in reporting threshold versus culture, or inability of PCR to discern results from normal flora. Non-panel pathogens were detected in a significant proportion in our population. The pneumonia panel should be implemented and interpreted carefully with consideration of antimicrobial stewardship. Disclosures All Authors: No reported disclosures