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Hematopoietic stem cell transplant (HSCT) recipients are at increased risk for a wide spectrum of infections, including opportunistic infections with atypical presentations. Diagnosis can be challenging and often requires extensive testing and invasive procedures. Sequencing of plasma microbial cell-free DNA (mcfDNA) allows non-invasive untargeted detections of human pathogens, making this modality appealing for this patient population.The purpose of this study was to perform a meta-analysis to evaluate the diagnostic value of sequencing of plasma mcfDNA for infections in HSCT recipients. We searched for relevant articles in BASE, PubMed, andClinicalTrials.govfrom January 1996 to November 2022. Studies were eligible for inclusion if they assessed the diagnostic performance of sequencing of plasma mcfDNA and included HSCT recipients with sufficient data to assign plasma mcfDNA test results as true positive, true negative, false positive, or false negative, which were used to calculate diagnostic test accuracy.A total of 6 studies and 69 patients were included. All included studies were published in 2019 or later and were conducted in the United States. Three studies were exclusively pediatric, two exclusively adult, and one a mixture of both adult and pediatric patients. The pooled sensitivity was 0.90 (95% CI 0.71-0.97) and the pooled specificity was 0.75 (0.49-0.90).The high pooled diagnostic odds ratio suggests that sequencing of plasma mcfDNA may have a unique diagnostic role in HSCT recipients. Its high sensitivity and capability to detect a broad array of pathogens makes it a promising adjunct to traditional diagnostic testing.

Background The diagnosis of infective endocarditis (IE) can be difficult, particularly if blood cultures fail to yield a pathogen. This study evaluates the potential utility of microbial cell-free DNA (mcfDNA) as a tool to identify the microbial etiology of IE. Methods Blood samples from patients with suspected IE were serially collected. mcfDNA was extracted from plasma and underwent next-generation sequencing. Reads were aligned against a library containing DNA sequences belonging to >1400 different pathogens. mcfDNA from organisms present above a statistical threshold were reported and quantified in molecules per milliliter (MPM). Additional mcfDNA was collected on each subject every 2–3 days for a total of 7 collections or until discharge. Results Of 30 enrolled patients with suspected IE, 23 had definite IE, 2 had possible IE, and IE was rejected in 5 patients by modified Duke Criteria. Only the 23 patients with definite IE were included for analysis. Both mcfDNA and blood cultures achieved a sensitivity of 87%. The median duration of positivity from antibiotic treatment initiation was estimated to be approximately 38.1 days for mcfDNA versus 3.7 days for blood culture (proportional odds, 2.952; P = .02771), using a semiparametric survival analysis. mcfDNA (log10) levels significantly declined (−0.3 MPM log10 units, 95% credible interval −0.45 to −0.14) after surgical source control was performed (pre- vs postprocedure, posterior probability >0.99). Conclusion mcfDNA accurately identifies the microbial etiology of IE. Sequential mcfDNA levels may ultimately help to individualize therapy by estimating a patient’s burden of infection and response to treatment.

We developed a simple, noninvasive mask sampling method to quantify and sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from exhaled breath. We found substantial variation between individuals in SARS-CoV-2 copies exhaled over a 15-minute period, which moderately correlated with nasal swab viral load. Talking was associated with a median of 2 log10 greater exhaled viral copies. Exposure varies substantially between individuals but may be risk stratified by nasal swab viral load and whether the exposure involved conversation.

Using face mask bioaerosol sampling, we found substantial variation between individuals in SARS-CoV-2 copies exhaled over a 15-minute period, which moderately correlated with nasal swab viral load. Talking was associated with a median of 2 log10 greater exhaled viral copies. Exposure varies substantially between individuals but may be risk stratified by nasal swab viral load and whether the exposure involved conversation.

Given the rapidly progressing coronavirus disease 2019 (COVID-19) pandemic, this report on a US cohort of 54 COVID-19 patients from Stanford Hospital and data regarding risk factors for severe disease obtained at initial clinical presentation is highly important and immediately clinically relevant. We identified low presenting oxygen saturation as predictive of severe disease outcomes, such as diagnosis of pneumonia, acute respiratory distress syndrome, and admission to the intensive care unit, and also replicated data from China suggesting an association between hypertension and disease severity. Clinicians will benefit by tools to rapidly risk stratify patients at presentation by likelihood of progression to severe disease.

Introduction: There is significant interest in the use of angiotensin converting enzyme inhibitors (ACE-I) and angiotensin II receptor blockers (ARB) in coronavirus disease 2019 (COVID-19) and concern over potential adverse effects since these medications upregulate the severe acute respiratory syndrome coronavirus 2 host cell entry receptor ACE2. Recent studies on ACE-I and ARB in COVID-19 were limited by excluding outpatients, excluding patients by age, analyzing ACE-I and ARB together, imputing missing data, and/or diagnosing COVID-19 by chest computed tomography without definitive reverse transcription polymerase chain reaction (RT-PCR), all of which are addressed here. Methods: We performed a retrospective cohort study of 1023 COVID-19 patients diagnosed by RT-PCR at Stanford Hospital through April 8, 2020 with a minimum follow-up time of 14 days to investigate the association between ACE-I or ARB use with outcomes. Results: Use of ACE-I or ARB medications was not associated with increased risk of hospitalization, intensive care unit admission, or death. Compared to patients with charted past medical history, there was a lower risk of hospitalization for patients on ACE-I (odds ratio (OR) 0.43; 95% confidence interval (CI) 0.19–0.97; P = 0.0426) and ARB (OR 0.39; 95% CI 0.17–0.90; P = 0.0270). Compared to patients with hypertension not on ACE-I or ARB, patients on ARB medications had a lower risk of hospitalization (OR 0.09; 95% CI 0.01–0.88; P = 0.0381). Conclusions: These findings suggest that the use of ACE-I and ARB is not associated with adverse outcomes and may be associated with improved outcomes in COVID-19, which is immediately relevant to care of the many patients on these medications.

Background Bartonella henselae and Bartonella quintana are the etiologic agents of cat scratch disease (CSD) and “trench fever”, respectively. Both are important causes of culture-negative endocarditis and fever of unknown origin (FUO). The diagnosis of Bartonella infections is limited by (1) the nonspecific, protean manifestations of the disease and its broad differential diagnosis; (2) the fastidious nature of Bartonella spp., leading to rare detections with traditional culture based methods; (3) the insensitivity and poor specificity of Bartonella serologies. Rapid, non-invasive diagnosis of Bartonella through next-generation sequencing (NGS) of plasma microbial cell-free DNA (mcfDNA) offers a means to overcome these limitations. Here we describe the diagnosis of 23 Bartonella infections in children from August 2017 – December 2020 using plasma mcfDNA NGS. Methods The Karius Test (KT), developed and validated in Karius’ CLIA certified/CAP accredited lab, detects mcfDNA in plasma. After mcfDNA is extracted and NGS performed, human reads are removed, and remaining sequences are aligned to a curated database of > 1400 organisms. McfDNA from organisms present above a statistical threshold are reported and quantified in molecules/μL (MPM). Clinical information was included from data submitted with the requisition or obtained at the time of reporting from clinical consultations with the provider. Results KT detected Bartonella henselae mcfDNA in 22 cases and Bartonella quintana in 1. Detections included 10 cases of endocarditis (7 prosthetic valve), 12 cases of CSD/FUO, and a single case of osteomyelitis. Glomerulonephritis was reported in 5 the cases of endocarditis. Six cases had splenic involvement; three had hepatic involvement. History of cat exposure was elicited in 8 cases. The mean MPMs was highest for prosthetic valve endocarditis (mean 47,272 +/- 67,526) followed by native valve endocarditis (3,881 +/- 2,458), FUO/CSD (1,922 +/- 3,416), and osteomyelitis (119 +/- 0) (p Conclusion Open-ended, plasma-based NGS for mcfDNA provides a rapid, non-invasive method to diagnose diverse clinical manifestations of invasive pediatric Bartonella infection against a competing broad differential diagnosis. The quantification of mcfDNA may further help in differentiating the various clinical syndromes caused by Bartonella. Finally, serial monitoring to trend MPMs may serve as an indicator of burden of infection, provide a means to monitor treatment efficacy and ultimately help define the length of therapy for optimal outcomes. All detections are Bartonella henselae except for one case of *Bartonella quintana (prosthetic valve endocarditis). MPM=molecules/μL; GN=glomerulonephritis, LN=lymph node involvement, FUO=fever of unknown origin, CSD=cat scratch disease

Much remains unknown about Mycobacterium tuberculosis transmission. Seminal experimental studies from the 1950s demonstrated that airborne expulsion of droplet nuclei from an infectious tuberculosis (TB) patient is the primary route of transmission. However, these findings did not rule out other routes of M. tuberculosis transmission. We reviewed historical scientific evidence from the late 19th/early 20th century and contemporary studies investigating the presence, persistence and infectiousness of environmental M. tuberculosis. We found both experimental and epidemiological evidence supporting the presence and viability of M. tuberculosis in multiple natural and built environments for months to years, presumably following contamination by a human source. Furthermore, several studies confirm M. tuberculosis viability and virulence in the environment using guinea pig and mouse models. Most of this evidence was historical; however, several recent studies have reported consistent findings of M. tuberculosis detection and viability in the environment using modern methods. Whether M. tuberculosis in environments represents an infectious threat to humans requires further investigation; this may represent an untapped source of data with which to further understand M. tuberculosis transmission. We discuss potential opportunities for harnessing these data to generate new insights into TB transmission in congregate settings.

Much remains unknown about Mycobacterium tuberculosis transmission. Seminal experimental studies from the 1950s demonstrated that airborne expulsion of droplet nuclei from an infectious tuberculosis (TB) patient is the primary route of transmission. However, these findings did not rule out other routes of M. tuberculosis transmission. We reviewed historical scientific evidence from the late 19th/early 20th century and contemporary studies investigating the presence, persistence and infectiousness of environmental M. tuberculosis. We found both experimental and epidemiological evidence supporting the presence and viability of M. tuberculosis in multiple natural and built environments for months to years, presumably following contamination by a human source. Furthermore, several studies confirm M. tuberculosis viability and virulence in the environment using guinea pig and mouse models. Most of this evidence was historical; however, several recent studies have reported consistent findings of M. tuberculosis detection and viability in the environment using modern methods. Whether M. tuberculosis in environments represents an infectious threat to humans requires further investigation; this may represent an untapped source of data with which to further understand M. tuberculosis transmission. We discuss potential opportunities for harnessing these data to generate new insights into TB transmission in congregate settings.