Stefan Riedel - Academia.edu (original) (raw)
Papers by Stefan Riedel
Journal of Clinical Microbiology, Sep 20, 2021
W hile the incidence of coronavirus disease (COVID)-associated pulmonary aspergillosis (CAPA) in ... more W hile the incidence of coronavirus disease (COVID)-associated pulmonary aspergillosis (CAPA) in COVID-19 patients admitted to the intensive care unit (ICU) in Europe is widely published (incidence up to 30%) (1), data on CAPA from the United States is lacking or has not been well described (2, 3). During the first surge of COVID-19 (March to August 2020), members of the Fungal Diagnostic Laboratories Consortium (FDLC) were formally asked if they had recovered Aspergillus species in respiratory specimens from patients with confirmed COVID-19 after ICU admission (4). Only 8 of the 23 FDLC member laboratory sites (35%) responded in the affirmative. Cumulatively, data from 33 patients who were admitted to the ICU and/or intubated in the ICU setting were identified at four academic medical centers (among a total of 1,633 ICU patients) and were collected and summarized (Table 1). The overall incidence was 2%. Based on the most recent CAPA case definition (3, 5), 17 cases were considered to be possible CAPA, and 16 cases were determined to be probable CAPA. The mean age was 63.2 (range, 38 to 85), 55% were male, 42% were white, and 58% had hypertension. Only 9 (27%) patients were immunosuppressed at the time of COVID-19 diagnosis, but 16 (48%) patients received immunosuppression therapy during COVID-19 treatment. Overall, 20 cases (61%) were treated with antifungals (75% in probable CAPA, 47% in possible CAPA). Mortality was 67% overall (75% in probable CAPA cases; 59% in possible CAPA cases). The median time of first isolation of Aspergillus spp. from respiratory tract specimens was 13 days after ICU admission (range, 0 to 35 days). A. fumigatus was the most common species (79%), followed by A. niger (15%), A. flavus (3%), and A. parasiticus (3%). These Aspergillus spp. were initially recovered from the following sources: endotracheal tube aspirate (61%), tracheal aspirate (12%), sputum (21%), and bronchoalveolar lavage (BAL) fluid (21%). Testing for serum galactomannan (GM) (Platelia EIA, Bio-Rad) was performed in 23 cases (70%). Only four cases (17%) tested positive, yielding a positive rate of 28.6% (4/ 14) for probable CAPA. This is consistent with other published reports (6, 7). Only 7 cases (21%) had BAL samples collected, of which BAL GM was not even ordered in 4 cases (57%), and of the 3 cases that underwent BAL GM testing, two were positive (GM index 6.16, 3.52). Serum 1,3-beta-D-glucan (BDG) (Fungitell, Associated of Cape Cod, Inc.) testing was available for 23 cases (70%); 8 (35%) were positive, yielding a positive rate of 50% (7/14) for probable CAPA cases.
Journal of Antimicrobial Chemotherapy, Jan 27, 2019
Background: The emergence of Neisseria gonorrhoeae resistant to all currently available antimicro... more Background: The emergence of Neisseria gonorrhoeae resistant to all currently available antimicrobial therapies poses a dire public health threat. New antimicrobial agents with activity against N. gonorrhoeae are urgently needed. Apramycin is an aminocyclitol aminoglycoside with broad-spectrum in vitro activity against MDR Gramnegative pathogens and Staphylococcus aureus. However, its activity against N. gonorrhoeae has not been described. Objectives: The activity spectrum of apramycin against a collection of MDR N. gonorrhoeae was assessed. Isolates tested included those susceptible and resistant to the structurally distinct aminocyclitol, spectinomycin. Results: The modal MICs for apramycin and spectinomycin were 16 mg/L and 32 mg/L, respectively. The epidemiological cutoff (ECOFF) for apramycin was 64 mg/L. No strains among 77 tested had an MIC above this ECOFF, suggesting very low levels of acquired apramycin resistance. In time-kill analysis, apramycin demonstrated rapid bactericidal activity comparable to that of spectinomycin. Conclusions: Apramycin has broad-spectrum, rapidly bactericidal activity against N. gonorrhoeae. Future pharmacokinetic and pharmacodynamic studies will be needed to determine whether apramycin and/or apramycin derivatives hold promise as new therapeutics for N. gonorrhoeae infection.
Background: Fungal infection is a rare but life threatening finding in burn patients. While most ... more Background: Fungal infection is a rare but life threatening finding in burn patients. While most current literature focuses on incidence, risk, and mortality of fungal burn wound infections, the topics of surveillance and prevention are largely ignored. The Johns Hopkins Burn Center is a ten-bed regional burn center that sees over 400 admissions annually. In our burn center patients undergo regular wound inspection and wound cultures are obtained based on clinical suspicion. Additionally, patients with burns greater than 40% total body surface area (TBSA) receive oral fluconazole for antifungal prophylaxis starting day three of hospital admission. In this study we describe the incidence and characterization of non-candida fungal (NCF) cultures in a regional burn center over a five year period. Methods: We retrospectively reviewed all patients admitted to a dedicated burn intensive care unit (BICU) from 2008 to 2012. Wounds were inspected daily, and cultures collected based on the cl...
doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by pee... more doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
Journal of Clinical Microbiology, Jun 1, 2006
The BACTEC 9240 blood culture system with a standard aerobic medium, Plus Aerobic/F, was compared... more The BACTEC 9240 blood culture system with a standard aerobic medium, Plus Aerobic/F, was compared to the BacT/Alert system with a platelet-specific medium, BPA, as a means for detecting bacterial contamination of platelet preparations. One hundred thirteen platelet units seeded with low levels of different bacteria were examined with both systems. In 93 instances, growth was detected first in the BACTEC system; in 12 cases, growth registered first in the BacT/Alert system. Among all comparisons, growth was detected, on average, 1.7 h sooner with the BACTEC system. The differences in length of time to detection were statistically significant.
Frontiers in Immunology, Oct 28, 2022
proposition has potential implications for immunogen design, and provides strategies to elicit pa... more proposition has potential implications for immunogen design, and provides strategies to elicit pan-neutAbs from natural B1-like cells. Refinements in future immunization protocols might further boost long-term cross-protection, even at the mucosal level, against clinical manifestations of COVID-19.
Frontiers in Cellular and Infection Microbiology, Oct 16, 2020
Dermatophytoses account for nearly a quarter of all fungal infections worldwide. These difficult ... more Dermatophytoses account for nearly a quarter of all fungal infections worldwide. These difficult to treat infections of the skin, hair, and nails, are growing more resistant to conventional antifungal treatments, and when treatable, often require prolonged therapeutic regimens. For centuries, essential oils have been used to treat a variety of ailments. In this study, we evaluated the clinical effects in vitro of 65 essential oils and 21 essential oil blends against various clinical species/strains of dermatophytes from two primary genera, Microsporum and Trichophyton. Our aim: To determine the overall activity of a wide range of essential oils against a number of clinical strains of dermatophytes. For all assays, 16 clinically derived species/strains of dermatophytes were used. The activity of each essential oil was assessed using a modified disk-diffusion assay over a period of 21 days of incubation vs. standard antifungal drugs. Subsequently, we determined the minimum inhibitory dilution possible for the most potent essential oils and performed combination testing to determine if synergy could be demonstrated with sub-inhibitory concentrations. We also assessed the effect of repeated vs. single applications. Of all the essential oils tested, cassia, cilantro, cinnamon, thyme, and oregano were the most potent along with one blend, DDR Prime; all genera/species tested were completely inhibited for 21 days following a single application. Many of the other oils tested exhibited temporal differences in activity where significant inhibition was observed ≤10 days of incubation which declined by day 21. Synergistic combinations were achieved with oregano and cilantro, cassia, or cinnamon bark; rose and cassia were also synergistic. Repeat application maintained complete inhibition for citronella, lemon myrtle, and litsea out to 21 days, but not lemon grass or On Guard. More study is necessary to understand the ways essential oils inhibit the growth of dermatophytes. Comprehensive research aimed at understanding the mechanism of action of essential oils and their components may provide the basis for a natural alternative to topical antifungal drugs. Such research could be envisioned to target optimal combinations and determine the timing between applications to provide for maximum inhibition of recurrence or growth.
The COVID-19 pandemic has presented unique diagnostic challenges including the need to store and ... more The COVID-19 pandemic has presented unique diagnostic challenges including the need to store and test large number of samples for clinical and research studies. While SARS CoV-2 diagnosis relies on RT-qPCR and antigen testing, live virus culture remains an important surrogate for viral “infectiousness”, as we previously described in “SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load and Viral Culture Testing on a Large Sample Cohort” (Clin Microbiol Infect, 2022,PMC9293398). Live virus isolation and characterization has also been important to the SARS CoV-2 research community, to assess viral fitness, cellular tropism, and live virus neutralization, particularly with the emergence of new variants. Many clinical and research studies make use of samples that are frozen in transport media and investigated at later dates. The effect of freezing on RT-qPCR results is well established. However, the effect of freeze-thaw on viral via...
Frontiers in Immunology
Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, r... more Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, repeated infections in both unvaccinated and vaccinated populations remain a major global health challenge. Because of mutation-mediated immune escape by variants-of-concern (VOC), approved neutralizing antibodies (neutAbs) effective against the original strains have been rendered non-protective. Identification and characterization of mutation-independent pan-neutralizing antibody responses are therefore essential for controlling the pandemic. Here, we characterize and discuss the origins of SARS-CoV-2 neutAbs, arising from either natural infection or following vaccination. In our study, neutAbs in COVID-19 patients were detected using the combination of two lateral flow immunoassay (LFIA) tests, corroborated by plaque reduction neutralization testing (PRNT). A point-of-care neutAb LFIA, NeutraXpress™, was validated using serum samples from historical pre-COVID-19 negative controls, patie...
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term se... more The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dram...
Journal of Ancient Diseases & Preventive Remedies, 2013
The history of tuberculosis (TB) is intricately connected to the history of humanity. The disease... more The history of tuberculosis (TB) is intricately connected to the history of humanity. The disease is considered one of the oldest infectious diseases afflicting mankind. Its history is that of colorful, often vibrant descriptions and interpretations, in the attempt of human societies to demystify the origins, causality, and course of this grave and lethal disease, and in the ultimate pursuit of finding a cure. The discovery of the tubercle bacillus on March 24 th 1882, by Robert Koch, led to an unprecedented increase in international research efforts, ultimately resulting in the development of a vaccine and many potent antimicrobial agents and treatment regimens. However, the course of history is often not without some irony, commonly perceived as being unpredictable by those who find themselves immersed in history's path. In this sense, and despite the advances that were made in diagnostics and treatment during the past 70 years, TB continues to challenge mankind on numerous levels even today. The most recent emergence of multidrug-resistant and extensively-drug-resistant strains of Mycobacterium tuberculosis is only a small but significant reflection of the ongoing challenges in the attempt of eradicating this disease. Here we provide a review of the historic aspects of TB leading to a discussion of the current state of the approach to antituberculous treatment, including the aspects of microbiology, diagnostics, antimicrobial therapy, and public health. A Brief Review of History from Prehistoric Evidence to the Modern World As stated above, Tuberculosis (TB) is one of the most deadly, but also J o u r n a l of Infec ti o u s D is eases & P r e v en tive M e d i c in e
Journal of Clinical Microbiology, 2021
Fungal infections are a rising threat to our immunocompromised patient population, as well as oth... more Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics.
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injur... more The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients’ demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung,...
BackgroundThe continued need for molecular testing for SARS-CoV-2 and potential for self-collecte... more BackgroundThe continued need for molecular testing for SARS-CoV-2 and potential for self-collected saliva as an alternative to nasopharyngeal (NP) swabs for sample acquisition led us to compare saliva to NP swabs in an outpatient setting, without restrictions to avoid food, drink, smoking, or tooth-brushing.MethodsA total of 385 pairs of NP and saliva specimens were obtained, the majority from individuals presenting for initial evaluation, and were tested on two high-sensitivity RT-PCR platforms: the Abbott m2000 and Abbott Alinity m (both with limits of detection [LoD] of 100 copies of viral RNA/mL).ResultsConcordance between saliva and NP was excellent overall (Cohen’s κ=0.93), for both initial and followup testing, for both platforms, and for specimens treated with guanidinium transport medium as preservative as well as for untreated saliva (κ=0.88-0.95). Viral loads were on average 16x higher in NP specimens than saliva specimens, suggesting that only the relatively small fracti...
Nature, 2021
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets COVID-19, which is cause... more COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure 1-4 , but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63 + intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments. The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection ranges from asymptomatic infection to severe coronavirus disease 2019 (COVID-19) and death. The leading cause of mortality is acute lung injury and acute respiratory distress syndrome, or direct complications with multiple organ failure 1-4. Clinical deterioration in acute illness leads to ineffective viral clearance and collateral tissue damage 1-5. Severe COVID-19 is also accompanied by an inappropriate pro-inflammatory host immune response and a diminished antiviral interferon response 6-8. Many molecular and cellular questions related to COVID-19 pathophysiology remain unanswered, including how cell composition and gene programs shift, which cells are infected, and how associated genetic loci drive disease. Autopsies are crucial to understanding severe COVID-19 pathophysiology 9-12 , but comprehensive genomic studies are challenged by long post-mortem intervals (PMIs). Here, we developed a large cross-body COVID-19 autopsy biobank of 420 autopsy specimens, spanning 11 organs, and used it to generate a single-cell atlas of lung, kidney, liver and heart associated with COVID-19 and a lung spatial atlas, in a subset of 14-18 donors per organ. Our atlases provide crucial insights into the pathogenesis of severe COVID-19. A COVID-19 autopsy cohort and biobank We assembled an autopsy cohort of 20 male and 12 female donors, of various ages (>30->89 years), racial/ethnic backgrounds, intermittent mandatory ventilation (IMV) periods (0-30 days) and days from symptom start to death (Fig. 1a, Supplementary Table 1). A biobank was created with a subset of 17 donors. From most donors, we collected at least lung, heart and liver tissue (Fig. 1a, Extended Data Fig. 1a, Supplementary Methods), preserving specimens for single-cell and spatial analysis. We optimized single-cell and single-nucleus RNA sequencing (sc/snRNA-Seq) protocols for Biosafety Level 3 and NanoString GeoMx workflows to spatially profile RNA from different tissue compartments by cell composition or viral RNA (Supplementary Methods). A cell census of the COVID-19 lung Automatic annotation defined 28 subsets of parenchymal, endothelial and immune cells (Fig. 2a, Supplementary Table 2, Supplementary
Baylor University Medical Center Proceedings, 2006
International Journal of STD & AIDS, 2018
Antimicrobial resistance (AMR) to gonorrhoea is a threat to global health security. There have be... more Antimicrobial resistance (AMR) to gonorrhoea is a threat to global health security. There have been concerns expressed that countries with high rates of disease have poor surveillance. The objectives of the study were to determine the AMR patterns of Neisseria gonorrhoeae clinical isolates to antimicrobial agents in patients with HIV or high risk of HIV acquisition, to compare the concordance of disk diffusion and agar dilution as methods for determining AMR to N. gonorrhoeae, and to describe methodological challenges to carrying out AMR testing. The study was conducted at an HIV outpatient service for at-risk populations and an outreach clinic for commercial sex workers in Kampala. Patients were offered a sexually transmitted infection screen using a polymerase chain reaction (PCR)-based assay. Samples positive for gonorrhoea were cultured. Antimicrobial susceptibility testing was performed using disk diffusion and isolates were sent to a reference laboratory for agar dilution dire...
Journal of Ancient Diseases & Preventive Remedies, 2014
Plague has been without doubt one of the most important and devastating epidemic diseases of mank... more Plague has been without doubt one of the most important and devastating epidemic diseases of mankind. During the past decade, this disease has received much attention because of its potential use as an agent of biowarfare and bioterrorism. However, while it is easy to forget its importance in the 21 st century and view the disease only as a historic curiosity, relegating it to the sidelines of infectious diseases, plague is clearly an important and re-emerging infectious disease. In today's world, it is easy to focus on its potential use as a bioweapon, however, one must also consider that there is still much to learn about the pathogenicity and enzoonotic transmission cycles connected to the natural occurrence of this disease. Plague is still an important, naturally occurring disease as it was 1,000 years ago. This review highlights some of the important aspects of the disease throughout history with a discussion of the current situation of naturally occurring plague in the 21 st century.
Respiratory Medicine, 2017
Background: Pneumonia is a leading cause of morbidity and mortality in children worldwide; howeve... more Background: Pneumonia is a leading cause of morbidity and mortality in children worldwide; however, its diagnosis can be challenging, especially in settings where skilled clinicians or standard imaging are unavailable. We sought to determine the diagnostic accuracy of lung ultrasound when compared to radiographically-confirmed clinical pediatric pneumonia. Methods: Between January 2012 and September 2013, we consecutively enrolled children aged 2e59 months with primary respiratory complaints at the outpatient clinics, emergency department, and inpatient wards of the Instituto Nacional de Salud del Niño in Lima, Peru. All participants underwent clinical evaluation by a pediatrician and lung ultrasonography by one of three general practitioners. We also consecutively enrolled children without respiratory symptoms. Children with respiratory symptoms had a chest radiograph. We obtained ancillary laboratory testing in a subset. Results: Final clinical diagnoses included 453 children with pneumonia, 133 with asthma, 103 with bronchiolitis, and 143 with upper respiratory infections. In total, CXR confirmed the diagnosis in 191 (42%) of 453 children with clinical pneumonia. A consolidation on lung ultrasound, which is our primary endpoint for pneumonia, had a sensitivity of 88.5%, specificity of 100%, and an area under-the-curve of 0.94 (95% CI 0.92e0.97) when compared to radiographically-confirmed clinical pneumonia. When any abnormality on lung ultrasound was compared to radiographically-confirmed clinical pneumonia the sensitivity increased to 92.2% and the specificity decreased to 95.2%, with an area under-the-curve of 0.94 (95% CI 0.91e0.96). Conclusions: Lung ultrasound had high diagnostic accuracy for the diagnosis of radiographicallyconfirmed pneumonia. Added benefits of lung ultrasound include rapid testing and high inter-rater agreement. Lung ultrasound may serve as an alternative tool for the diagnosis of pediatric pneumonia.
Journal of Clinical Laboratory Analysis, 2016
Objectives: Assessment of specimen rejection rates is an important laboratory quality measure for... more Objectives: Assessment of specimen rejection rates is an important laboratory quality measure for laboratories because of a potential negative impact on patient care. Here, we examined reasons for specimen rejection at a single, tertiary care healthcare institution and propose a framework for designing an efficient intervention. Methods: During a 1-year period, we identified all specimens rejected at our hospital and performed an analysis of a wide range of associated variables: reason for rejection, patient location, type of phlebotomist, tests ordered, priority status, collection container used, transport time. Results: Clotted and hemolyzed specimens accounted for the majority of rejected specimens, but significant differences in reasons for specimen rejection existed between patient care areas. Eighty-five percent of rejected specimens came from the Emergency Department and eight other inpatient care areas. Registered nurses drew approximately 85% of rejected specimens, while laboratory phlebotomy staff drew only 4%. Conclusions: While hemolysis and clotting are primary causes for specimen rejection, collection of all available data regarding specimen rejection data is essential for laboratories determining which factors are most significant causes of specimen rejection.
Journal of Clinical Microbiology, Sep 20, 2021
W hile the incidence of coronavirus disease (COVID)-associated pulmonary aspergillosis (CAPA) in ... more W hile the incidence of coronavirus disease (COVID)-associated pulmonary aspergillosis (CAPA) in COVID-19 patients admitted to the intensive care unit (ICU) in Europe is widely published (incidence up to 30%) (1), data on CAPA from the United States is lacking or has not been well described (2, 3). During the first surge of COVID-19 (March to August 2020), members of the Fungal Diagnostic Laboratories Consortium (FDLC) were formally asked if they had recovered Aspergillus species in respiratory specimens from patients with confirmed COVID-19 after ICU admission (4). Only 8 of the 23 FDLC member laboratory sites (35%) responded in the affirmative. Cumulatively, data from 33 patients who were admitted to the ICU and/or intubated in the ICU setting were identified at four academic medical centers (among a total of 1,633 ICU patients) and were collected and summarized (Table 1). The overall incidence was 2%. Based on the most recent CAPA case definition (3, 5), 17 cases were considered to be possible CAPA, and 16 cases were determined to be probable CAPA. The mean age was 63.2 (range, 38 to 85), 55% were male, 42% were white, and 58% had hypertension. Only 9 (27%) patients were immunosuppressed at the time of COVID-19 diagnosis, but 16 (48%) patients received immunosuppression therapy during COVID-19 treatment. Overall, 20 cases (61%) were treated with antifungals (75% in probable CAPA, 47% in possible CAPA). Mortality was 67% overall (75% in probable CAPA cases; 59% in possible CAPA cases). The median time of first isolation of Aspergillus spp. from respiratory tract specimens was 13 days after ICU admission (range, 0 to 35 days). A. fumigatus was the most common species (79%), followed by A. niger (15%), A. flavus (3%), and A. parasiticus (3%). These Aspergillus spp. were initially recovered from the following sources: endotracheal tube aspirate (61%), tracheal aspirate (12%), sputum (21%), and bronchoalveolar lavage (BAL) fluid (21%). Testing for serum galactomannan (GM) (Platelia EIA, Bio-Rad) was performed in 23 cases (70%). Only four cases (17%) tested positive, yielding a positive rate of 28.6% (4/ 14) for probable CAPA. This is consistent with other published reports (6, 7). Only 7 cases (21%) had BAL samples collected, of which BAL GM was not even ordered in 4 cases (57%), and of the 3 cases that underwent BAL GM testing, two were positive (GM index 6.16, 3.52). Serum 1,3-beta-D-glucan (BDG) (Fungitell, Associated of Cape Cod, Inc.) testing was available for 23 cases (70%); 8 (35%) were positive, yielding a positive rate of 50% (7/14) for probable CAPA cases.
Journal of Antimicrobial Chemotherapy, Jan 27, 2019
Background: The emergence of Neisseria gonorrhoeae resistant to all currently available antimicro... more Background: The emergence of Neisseria gonorrhoeae resistant to all currently available antimicrobial therapies poses a dire public health threat. New antimicrobial agents with activity against N. gonorrhoeae are urgently needed. Apramycin is an aminocyclitol aminoglycoside with broad-spectrum in vitro activity against MDR Gramnegative pathogens and Staphylococcus aureus. However, its activity against N. gonorrhoeae has not been described. Objectives: The activity spectrum of apramycin against a collection of MDR N. gonorrhoeae was assessed. Isolates tested included those susceptible and resistant to the structurally distinct aminocyclitol, spectinomycin. Results: The modal MICs for apramycin and spectinomycin were 16 mg/L and 32 mg/L, respectively. The epidemiological cutoff (ECOFF) for apramycin was 64 mg/L. No strains among 77 tested had an MIC above this ECOFF, suggesting very low levels of acquired apramycin resistance. In time-kill analysis, apramycin demonstrated rapid bactericidal activity comparable to that of spectinomycin. Conclusions: Apramycin has broad-spectrum, rapidly bactericidal activity against N. gonorrhoeae. Future pharmacokinetic and pharmacodynamic studies will be needed to determine whether apramycin and/or apramycin derivatives hold promise as new therapeutics for N. gonorrhoeae infection.
Background: Fungal infection is a rare but life threatening finding in burn patients. While most ... more Background: Fungal infection is a rare but life threatening finding in burn patients. While most current literature focuses on incidence, risk, and mortality of fungal burn wound infections, the topics of surveillance and prevention are largely ignored. The Johns Hopkins Burn Center is a ten-bed regional burn center that sees over 400 admissions annually. In our burn center patients undergo regular wound inspection and wound cultures are obtained based on clinical suspicion. Additionally, patients with burns greater than 40% total body surface area (TBSA) receive oral fluconazole for antifungal prophylaxis starting day three of hospital admission. In this study we describe the incidence and characterization of non-candida fungal (NCF) cultures in a regional burn center over a five year period. Methods: We retrospectively reviewed all patients admitted to a dedicated burn intensive care unit (BICU) from 2008 to 2012. Wounds were inspected daily, and cultures collected based on the cl...
doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by pee... more doi: medRxiv preprint NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
Journal of Clinical Microbiology, Jun 1, 2006
The BACTEC 9240 blood culture system with a standard aerobic medium, Plus Aerobic/F, was compared... more The BACTEC 9240 blood culture system with a standard aerobic medium, Plus Aerobic/F, was compared to the BacT/Alert system with a platelet-specific medium, BPA, as a means for detecting bacterial contamination of platelet preparations. One hundred thirteen platelet units seeded with low levels of different bacteria were examined with both systems. In 93 instances, growth was detected first in the BACTEC system; in 12 cases, growth registered first in the BacT/Alert system. Among all comparisons, growth was detected, on average, 1.7 h sooner with the BACTEC system. The differences in length of time to detection were statistically significant.
Frontiers in Immunology, Oct 28, 2022
proposition has potential implications for immunogen design, and provides strategies to elicit pa... more proposition has potential implications for immunogen design, and provides strategies to elicit pan-neutAbs from natural B1-like cells. Refinements in future immunization protocols might further boost long-term cross-protection, even at the mucosal level, against clinical manifestations of COVID-19.
Frontiers in Cellular and Infection Microbiology, Oct 16, 2020
Dermatophytoses account for nearly a quarter of all fungal infections worldwide. These difficult ... more Dermatophytoses account for nearly a quarter of all fungal infections worldwide. These difficult to treat infections of the skin, hair, and nails, are growing more resistant to conventional antifungal treatments, and when treatable, often require prolonged therapeutic regimens. For centuries, essential oils have been used to treat a variety of ailments. In this study, we evaluated the clinical effects in vitro of 65 essential oils and 21 essential oil blends against various clinical species/strains of dermatophytes from two primary genera, Microsporum and Trichophyton. Our aim: To determine the overall activity of a wide range of essential oils against a number of clinical strains of dermatophytes. For all assays, 16 clinically derived species/strains of dermatophytes were used. The activity of each essential oil was assessed using a modified disk-diffusion assay over a period of 21 days of incubation vs. standard antifungal drugs. Subsequently, we determined the minimum inhibitory dilution possible for the most potent essential oils and performed combination testing to determine if synergy could be demonstrated with sub-inhibitory concentrations. We also assessed the effect of repeated vs. single applications. Of all the essential oils tested, cassia, cilantro, cinnamon, thyme, and oregano were the most potent along with one blend, DDR Prime; all genera/species tested were completely inhibited for 21 days following a single application. Many of the other oils tested exhibited temporal differences in activity where significant inhibition was observed ≤10 days of incubation which declined by day 21. Synergistic combinations were achieved with oregano and cilantro, cassia, or cinnamon bark; rose and cassia were also synergistic. Repeat application maintained complete inhibition for citronella, lemon myrtle, and litsea out to 21 days, but not lemon grass or On Guard. More study is necessary to understand the ways essential oils inhibit the growth of dermatophytes. Comprehensive research aimed at understanding the mechanism of action of essential oils and their components may provide the basis for a natural alternative to topical antifungal drugs. Such research could be envisioned to target optimal combinations and determine the timing between applications to provide for maximum inhibition of recurrence or growth.
The COVID-19 pandemic has presented unique diagnostic challenges including the need to store and ... more The COVID-19 pandemic has presented unique diagnostic challenges including the need to store and test large number of samples for clinical and research studies. While SARS CoV-2 diagnosis relies on RT-qPCR and antigen testing, live virus culture remains an important surrogate for viral “infectiousness”, as we previously described in “SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load and Viral Culture Testing on a Large Sample Cohort” (Clin Microbiol Infect, 2022,PMC9293398). Live virus isolation and characterization has also been important to the SARS CoV-2 research community, to assess viral fitness, cellular tropism, and live virus neutralization, particularly with the emergence of new variants. Many clinical and research studies make use of samples that are frozen in transport media and investigated at later dates. The effect of freezing on RT-qPCR results is well established. However, the effect of freeze-thaw on viral via...
Frontiers in Immunology
Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, r... more Despite the initially reported high efficacy of vaccines directed against ancestral SARS-CoV-2, repeated infections in both unvaccinated and vaccinated populations remain a major global health challenge. Because of mutation-mediated immune escape by variants-of-concern (VOC), approved neutralizing antibodies (neutAbs) effective against the original strains have been rendered non-protective. Identification and characterization of mutation-independent pan-neutralizing antibody responses are therefore essential for controlling the pandemic. Here, we characterize and discuss the origins of SARS-CoV-2 neutAbs, arising from either natural infection or following vaccination. In our study, neutAbs in COVID-19 patients were detected using the combination of two lateral flow immunoassay (LFIA) tests, corroborated by plaque reduction neutralization testing (PRNT). A point-of-care neutAb LFIA, NeutraXpress™, was validated using serum samples from historical pre-COVID-19 negative controls, patie...
The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term se... more The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dram...
Journal of Ancient Diseases & Preventive Remedies, 2013
The history of tuberculosis (TB) is intricately connected to the history of humanity. The disease... more The history of tuberculosis (TB) is intricately connected to the history of humanity. The disease is considered one of the oldest infectious diseases afflicting mankind. Its history is that of colorful, often vibrant descriptions and interpretations, in the attempt of human societies to demystify the origins, causality, and course of this grave and lethal disease, and in the ultimate pursuit of finding a cure. The discovery of the tubercle bacillus on March 24 th 1882, by Robert Koch, led to an unprecedented increase in international research efforts, ultimately resulting in the development of a vaccine and many potent antimicrobial agents and treatment regimens. However, the course of history is often not without some irony, commonly perceived as being unpredictable by those who find themselves immersed in history's path. In this sense, and despite the advances that were made in diagnostics and treatment during the past 70 years, TB continues to challenge mankind on numerous levels even today. The most recent emergence of multidrug-resistant and extensively-drug-resistant strains of Mycobacterium tuberculosis is only a small but significant reflection of the ongoing challenges in the attempt of eradicating this disease. Here we provide a review of the historic aspects of TB leading to a discussion of the current state of the approach to antituberculous treatment, including the aspects of microbiology, diagnostics, antimicrobial therapy, and public health. A Brief Review of History from Prehistoric Evidence to the Modern World As stated above, Tuberculosis (TB) is one of the most deadly, but also J o u r n a l of Infec ti o u s D is eases & P r e v en tive M e d i c in e
Journal of Clinical Microbiology, 2021
Fungal infections are a rising threat to our immunocompromised patient population, as well as oth... more Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics.
The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injur... more The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients’ demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung,...
BackgroundThe continued need for molecular testing for SARS-CoV-2 and potential for self-collecte... more BackgroundThe continued need for molecular testing for SARS-CoV-2 and potential for self-collected saliva as an alternative to nasopharyngeal (NP) swabs for sample acquisition led us to compare saliva to NP swabs in an outpatient setting, without restrictions to avoid food, drink, smoking, or tooth-brushing.MethodsA total of 385 pairs of NP and saliva specimens were obtained, the majority from individuals presenting for initial evaluation, and were tested on two high-sensitivity RT-PCR platforms: the Abbott m2000 and Abbott Alinity m (both with limits of detection [LoD] of 100 copies of viral RNA/mL).ResultsConcordance between saliva and NP was excellent overall (Cohen’s κ=0.93), for both initial and followup testing, for both platforms, and for specimens treated with guanidinium transport medium as preservative as well as for untreated saliva (κ=0.88-0.95). Viral loads were on average 16x higher in NP specimens than saliva specimens, suggesting that only the relatively small fracti...
Nature, 2021
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets COVID-19, which is cause... more COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure 1-4 , but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63 + intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments. The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection ranges from asymptomatic infection to severe coronavirus disease 2019 (COVID-19) and death. The leading cause of mortality is acute lung injury and acute respiratory distress syndrome, or direct complications with multiple organ failure 1-4. Clinical deterioration in acute illness leads to ineffective viral clearance and collateral tissue damage 1-5. Severe COVID-19 is also accompanied by an inappropriate pro-inflammatory host immune response and a diminished antiviral interferon response 6-8. Many molecular and cellular questions related to COVID-19 pathophysiology remain unanswered, including how cell composition and gene programs shift, which cells are infected, and how associated genetic loci drive disease. Autopsies are crucial to understanding severe COVID-19 pathophysiology 9-12 , but comprehensive genomic studies are challenged by long post-mortem intervals (PMIs). Here, we developed a large cross-body COVID-19 autopsy biobank of 420 autopsy specimens, spanning 11 organs, and used it to generate a single-cell atlas of lung, kidney, liver and heart associated with COVID-19 and a lung spatial atlas, in a subset of 14-18 donors per organ. Our atlases provide crucial insights into the pathogenesis of severe COVID-19. A COVID-19 autopsy cohort and biobank We assembled an autopsy cohort of 20 male and 12 female donors, of various ages (>30->89 years), racial/ethnic backgrounds, intermittent mandatory ventilation (IMV) periods (0-30 days) and days from symptom start to death (Fig. 1a, Supplementary Table 1). A biobank was created with a subset of 17 donors. From most donors, we collected at least lung, heart and liver tissue (Fig. 1a, Extended Data Fig. 1a, Supplementary Methods), preserving specimens for single-cell and spatial analysis. We optimized single-cell and single-nucleus RNA sequencing (sc/snRNA-Seq) protocols for Biosafety Level 3 and NanoString GeoMx workflows to spatially profile RNA from different tissue compartments by cell composition or viral RNA (Supplementary Methods). A cell census of the COVID-19 lung Automatic annotation defined 28 subsets of parenchymal, endothelial and immune cells (Fig. 2a, Supplementary Table 2, Supplementary
Baylor University Medical Center Proceedings, 2006
International Journal of STD & AIDS, 2018
Antimicrobial resistance (AMR) to gonorrhoea is a threat to global health security. There have be... more Antimicrobial resistance (AMR) to gonorrhoea is a threat to global health security. There have been concerns expressed that countries with high rates of disease have poor surveillance. The objectives of the study were to determine the AMR patterns of Neisseria gonorrhoeae clinical isolates to antimicrobial agents in patients with HIV or high risk of HIV acquisition, to compare the concordance of disk diffusion and agar dilution as methods for determining AMR to N. gonorrhoeae, and to describe methodological challenges to carrying out AMR testing. The study was conducted at an HIV outpatient service for at-risk populations and an outreach clinic for commercial sex workers in Kampala. Patients were offered a sexually transmitted infection screen using a polymerase chain reaction (PCR)-based assay. Samples positive for gonorrhoea were cultured. Antimicrobial susceptibility testing was performed using disk diffusion and isolates were sent to a reference laboratory for agar dilution dire...
Journal of Ancient Diseases & Preventive Remedies, 2014
Plague has been without doubt one of the most important and devastating epidemic diseases of mank... more Plague has been without doubt one of the most important and devastating epidemic diseases of mankind. During the past decade, this disease has received much attention because of its potential use as an agent of biowarfare and bioterrorism. However, while it is easy to forget its importance in the 21 st century and view the disease only as a historic curiosity, relegating it to the sidelines of infectious diseases, plague is clearly an important and re-emerging infectious disease. In today's world, it is easy to focus on its potential use as a bioweapon, however, one must also consider that there is still much to learn about the pathogenicity and enzoonotic transmission cycles connected to the natural occurrence of this disease. Plague is still an important, naturally occurring disease as it was 1,000 years ago. This review highlights some of the important aspects of the disease throughout history with a discussion of the current situation of naturally occurring plague in the 21 st century.
Respiratory Medicine, 2017
Background: Pneumonia is a leading cause of morbidity and mortality in children worldwide; howeve... more Background: Pneumonia is a leading cause of morbidity and mortality in children worldwide; however, its diagnosis can be challenging, especially in settings where skilled clinicians or standard imaging are unavailable. We sought to determine the diagnostic accuracy of lung ultrasound when compared to radiographically-confirmed clinical pediatric pneumonia. Methods: Between January 2012 and September 2013, we consecutively enrolled children aged 2e59 months with primary respiratory complaints at the outpatient clinics, emergency department, and inpatient wards of the Instituto Nacional de Salud del Niño in Lima, Peru. All participants underwent clinical evaluation by a pediatrician and lung ultrasonography by one of three general practitioners. We also consecutively enrolled children without respiratory symptoms. Children with respiratory symptoms had a chest radiograph. We obtained ancillary laboratory testing in a subset. Results: Final clinical diagnoses included 453 children with pneumonia, 133 with asthma, 103 with bronchiolitis, and 143 with upper respiratory infections. In total, CXR confirmed the diagnosis in 191 (42%) of 453 children with clinical pneumonia. A consolidation on lung ultrasound, which is our primary endpoint for pneumonia, had a sensitivity of 88.5%, specificity of 100%, and an area under-the-curve of 0.94 (95% CI 0.92e0.97) when compared to radiographically-confirmed clinical pneumonia. When any abnormality on lung ultrasound was compared to radiographically-confirmed clinical pneumonia the sensitivity increased to 92.2% and the specificity decreased to 95.2%, with an area under-the-curve of 0.94 (95% CI 0.91e0.96). Conclusions: Lung ultrasound had high diagnostic accuracy for the diagnosis of radiographicallyconfirmed pneumonia. Added benefits of lung ultrasound include rapid testing and high inter-rater agreement. Lung ultrasound may serve as an alternative tool for the diagnosis of pediatric pneumonia.
Journal of Clinical Laboratory Analysis, 2016
Objectives: Assessment of specimen rejection rates is an important laboratory quality measure for... more Objectives: Assessment of specimen rejection rates is an important laboratory quality measure for laboratories because of a potential negative impact on patient care. Here, we examined reasons for specimen rejection at a single, tertiary care healthcare institution and propose a framework for designing an efficient intervention. Methods: During a 1-year period, we identified all specimens rejected at our hospital and performed an analysis of a wide range of associated variables: reason for rejection, patient location, type of phlebotomist, tests ordered, priority status, collection container used, transport time. Results: Clotted and hemolyzed specimens accounted for the majority of rejected specimens, but significant differences in reasons for specimen rejection existed between patient care areas. Eighty-five percent of rejected specimens came from the Emergency Department and eight other inpatient care areas. Registered nurses drew approximately 85% of rejected specimens, while laboratory phlebotomy staff drew only 4%. Conclusions: While hemolysis and clotting are primary causes for specimen rejection, collection of all available data regarding specimen rejection data is essential for laboratories determining which factors are most significant causes of specimen rejection.