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1.
MMWR Morb Mortal Wkly Rep ; 73(22): 507-513, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38843078

ABSTRACT

In 2022, a global mpox outbreak occurred, primarily affecting gay and bisexual men who have sex with men (GBMSM). To screen for mpox's reemergence and investigate potentially unsuspected cases among non-GBMSM, prospective surveillance of patients aged ≥3 months with an mpox-compatible rash (vesicular, pustular, ulcerated, or crusted) was conducted at 13 U.S. emergency departments (EDs) during June-December 2023. Demographic, historical, and illness characteristics were collected using questionnaires and electronic health records. Lesions were tested for monkeypox virus using polymerase chain reaction. Among 196 enrolled persons, the median age was 37.5 years (IQR = 21.0-53.5 years); 39 (19.9%) were aged <16 years, and 108 (55.1%) were male. Among all enrollees, 13 (6.6%) were GBMSM. Overall, approximately one half (46.4%) and one quarter (23.5%) of enrolled persons were non-Hispanic White and non-Hispanic Black or African American, respectively, and 38.8% reported Hispanic or Latino (Hispanic) ethnicity. Unstable housing was reported by 21 (10.7%) enrollees, and 24 (12.2%) lacked health insurance. The prevalence of mpox among ED patients evaluated for an mpox-compatible rash was 1.5% (95% CI = 0.3%-4.4%); all persons with a confirmed mpox diagnosis identified as GBMSM and reported being HIV-negative, not being vaccinated against mpox, and having engaged in sex with one or more partners met through smartphone dating applications. No cases were identified among women, children, or unhoused persons. Clinicians should remain vigilant for mpox and educate persons at risk for mpox about modifying behaviors that increase risk and the importance of receiving 2 appropriately spaced doses of JYNNEOS vaccine to prevent mpox.


Subject(s)
Emergency Service, Hospital , Exanthema , Mpox (monkeypox) , Humans , Male , United States/epidemiology , Adult , Female , Young Adult , Middle Aged , Emergency Service, Hospital/statistics & numerical data , Adolescent , Exanthema/epidemiology , Mpox (monkeypox)/epidemiology , Disease Outbreaks , Population Surveillance , Prospective Studies
2.
Small ; 19(51): e2300617, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37104829

ABSTRACT

Multiplexed computational sensing with a point-of-care serodiagnosis assay to simultaneously quantify three biomarkers of acute cardiac injury is demonstrated. This point-of-care sensor includes a paper-based fluorescence vertical flow assay (fxVFA) processed by a low-cost mobile reader, which quantifies the target biomarkers through trained neural networks, all within <15 min of test time using 50 µL of serum sample per patient. This fxVFA platform is validated using human serum samples to quantify three cardiac biomarkers, i.e., myoglobin, creatine kinase-MB, and heart-type fatty acid binding protein, achieving less than 0.52 ng mL-1 limit-of-detection for all three biomarkers with minimal cross-reactivity. Biomarker concentration quantification using the fxVFA that is coupled to neural network-based inference is blindly tested using 46 individually activated cartridges, which shows a high correlation with the ground truth concentrations for all three biomarkers achieving >0.9 linearity and <15% coefficient of variation. The competitive performance of this multiplexed computational fxVFA along with its inexpensive paper-based design and handheld footprint makes it a promising point-of-care sensor platform that can expand access to diagnostics in resource-limited settings.


Subject(s)
Deep Learning , Point-of-Care Systems , Humans , Fluorescence , Biomarkers
3.
PLoS Biol ; 18(3): e3000652, 2020 03.
Article in English | MEDLINE | ID: mdl-32191697

ABSTRACT

The rise in carbapenem-resistant Enterobacteriaceae (CRE) infections has created a global health emergency, underlining the critical need to develop faster diagnostics to treat swiftly and correctly. Although rapid pathogen-identification (ID) tests are being developed, gold-standard antibiotic susceptibility testing (AST) remains unacceptably slow (1-2 d), and innovative approaches for rapid phenotypic ASTs for CREs are urgently needed. Motivated by this need, in this manuscript we tested the hypothesis that upon treatment with ß-lactam antibiotics, susceptible Enterobacteriaceae isolates would become sufficiently permeabilized, making some of their DNA accessible to added polymerase and primers. Further, we hypothesized that this accessible DNA would be detectable directly by isothermal amplification methods that do not fully lyse bacterial cells. We build on these results to develop the polymerase-accessibility AST (pol-aAST), a new phenotypic approach for ß-lactams, the major antibiotic class for gram-negative infections. We test isolates of the 3 causative pathogens of CRE infections using ceftriaxone (CRO), ertapenem (ETP), and meropenem (MEM) and demonstrate agreement with gold-standard AST. Importantly, pol-aAST correctly categorized resistant isolates that are undetectable by current genotypic methods (negative for ß-lactamase genes or lacking predictive genotypes). We also test contrived and clinical urine samples. We show that the pol-aAST can be performed in 30 min sample-to-answer using contrived urine samples and has the potential to be performed directly on clinical urine specimens.


Subject(s)
Anti-Bacterial Agents/pharmacology , Carbapenem-Resistant Enterobacteriaceae/drug effects , DNA, Bacterial/metabolism , DNA-Directed DNA Polymerase/metabolism , beta-Lactams/pharmacology , Carbapenem-Resistant Enterobacteriaceae/genetics , Carbapenem-Resistant Enterobacteriaceae/isolation & purification , Enterobacteriaceae/drug effects , Enterobacteriaceae/genetics , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/urine , Genotype , Humans , Microbial Sensitivity Tests , Phenotype , Reproducibility of Results , Time Factors , beta-Lactamases/genetics
4.
Clin Infect Dis ; 74(2): 271-277, 2022 01 29.
Article in English | MEDLINE | ID: mdl-33939799

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused one of the worst pandemics in recent history. Few reports have revealed that SARS-CoV-2 was spreading in the United States as early as the end of January. In this study, we aimed to determine if SARS-CoV-2 had been circulating in the Los Angeles (LA) area at a time when access to diagnostic testing for coronavirus disease 2019 (COVID-19) was severely limited. METHODS: We used a pooling strategy to look for SARS-CoV-2 in remnant respiratory samples submitted for regular respiratory pathogen testing from symptomatic patients from November 2019 to early March 2020. We then performed sequencing on the positive samples. RESULTS: We detected SARS-CoV-2 in 7 specimens from 6 patients, dating back to mid-January. The earliest positive patient, with a sample collected on January 13, 2020 had no relevant travel history but did have a sibling with similar symptoms. Sequencing of these SARS-CoV-2 genomes revealed that the virus was introduced into the LA area from both domestic and international sources as early as January. CONCLUSIONS: We present strong evidence of community spread of SARS-CoV-2 in the LA area well before widespread diagnostic testing was being performed in early 2020. These genomic data demonstrate that SARS-CoV-2 was being introduced into Los Angeles County from both international and domestic sources in January 2020.


Subject(s)
COVID-19 , SARS-CoV-2 , Diagnostic Techniques and Procedures , Humans , Los Angeles/epidemiology , Retrospective Studies
5.
BMC Genomics ; 23(1): 260, 2022 Apr 04.
Article in English | MEDLINE | ID: mdl-35379194

ABSTRACT

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks. METHODS: The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020. RESULTS: We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region. CONCLUSION: Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.


Subject(s)
COVID-19 , COVID-19/epidemiology , Disease Outbreaks , Genomics , Humans , Los Angeles/epidemiology , SARS-CoV-2/genetics
6.
J Clin Microbiol ; 60(2): e0136621, 2022 02 16.
Article in English | MEDLINE | ID: mdl-34851679

ABSTRACT

In the absence of antimicrobial susceptibility data, the institutional antibiogram is a valuable tool to guide clinicians in the empirical treatment of infections. However, there is a misunderstanding about how best to prepare cumulative antimicrobial susceptibility testing reports (CASTRs) to guide empirical therapy (e.g., routine antibiogram) versus monitoring antimicrobial resistance, with the former following guidance from the Clinical and Laboratory Standards Institute (CLSI) and the latter from the Centers for Disease Control and Prevention's National Healthcare Safety Network (NHSN). These criteria vary markedly in their exclusion or inclusion of isolates cultured repeatedly from the same patient. We compared rates of nonsusceptibility (NS) using annual data from a large teaching health care system subset to isolates eligible by either NHSN criteria or CLSI criteria. For a panel of the three most prevalent Gram-negative pathogens in combination with clinically relevant antimicrobial agents (or priority pathogen-agent combinations [PPACs]), we found that the inclusion of duplicate isolates by NHSN criteria yielded higher NS rates than when CLSI criteria (for which duplicate isolates are not included) were applied. Patients with duplicate isolates may not be representative of antimicrobial resistance within a population. For this reason, users of CASTR data should carefully consider that the criteria used to generate these reports can impact resulting NS rates and, therefore, maintain the distinction between CASTRs created for different purposes.


Subject(s)
Anti-Bacterial Agents , Laboratories, Clinical , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Delivery of Health Care , Drug Resistance, Bacterial , Humans , Microbial Sensitivity Tests
7.
Clin Infect Dis ; 72(2): 239-245, 2021 01 27.
Article in English | MEDLINE | ID: mdl-31942944

ABSTRACT

BACKGROUND: Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice. METHODS: We performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 United States institutions over 1.5 years. Comprehensive records review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established. RESULTS: A total of 82 Karius tests were evaluated from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50 of 82 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), and no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only 1 was associated with clinical impact. CONCLUSIONS: The real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods, and discern how best to integrate mNGS into current testing algorithms.


Subject(s)
Cell-Free Nucleic Acids , Communicable Diseases , Adult , Child , Communicable Diseases/diagnosis , High-Throughput Nucleotide Sequencing , Humans , Metagenomics , Plasma , Retrospective Studies , Sensitivity and Specificity
8.
Clin Infect Dis ; 73(1): e39-e46, 2021 07 01.
Article in English | MEDLINE | ID: mdl-32374822

ABSTRACT

BACKGROUND: Rapid blood culture diagnostics are of unclear benefit for patients with gram-negative bacilli (GNB) bloodstream infections (BSIs). We conducted a multicenter, randomized, controlled trial comparing outcomes of patients with GNB BSIs who had blood culture testing with standard-of-care (SOC) culture and antimicrobial susceptibility testing (AST) vs rapid organism identification (ID) and phenotypic AST using the Accelerate Pheno System (RAPID). METHODS: Patients with positive blood cultures with Gram stains showing GNB were randomized to SOC testing with antimicrobial stewardship (AS) review or RAPID with AS. The primary outcome was time to first antibiotic modification within 72 hours of randomization. RESULTS: Of 500 randomized patients, 448 were included (226 SOC, 222 RAPID). Mean (standard deviation) time to results was faster for RAPID than SOC for organism ID (2.7 [1.2] vs 11.7 [10.5] hours; P < .001) and AST (13.5 [56] vs 44.9 [12.1] hours; P < .001). Median (interquartile range [IQR]) time to first antibiotic modification was faster in the RAPID arm vs the SOC arm for overall antibiotics (8.6 [2.6-27.6] vs 14.9 [3.3-41.1] hours; P = .02) and gram-negative antibiotics (17.3 [4.9-72] vs 42.1 [10.1-72] hours; P < .001). Median (IQR) time to antibiotic escalation was faster in the RAPID arm vs the SOC arm for antimicrobial-resistant BSIs (18.4 [5.8-72] vs 61.7 [30.4-72] hours; P = .01). There were no differences between the arms in patient outcomes. CONCLUSIONS: Rapid organism ID and phenotypic AST led to faster changes in antibiotic therapy for gram-negative BSIs. CLINICAL TRIALS REGISTRATION: NCT03218397.


Subject(s)
Bacteremia , Gram-Negative Bacterial Infections , Anti-Bacterial Agents/therapeutic use , Bacteremia/diagnosis , Bacteremia/drug therapy , Blood Culture , Gram-Negative Bacteria , Gram-Negative Bacterial Infections/diagnosis , Gram-Negative Bacterial Infections/drug therapy , Humans , Microbial Sensitivity Tests
9.
Emerg Infect Dis ; 27(8): 2215-2218, 2021.
Article in English | MEDLINE | ID: mdl-34287130

ABSTRACT

We describe a case of endogenous endophthalmitis caused by sequence type 66-K2 hypervirulent Klebsiella pneumoniae in a diabetic patient with no travel history outside the United States. Genomic analysis showed the pathogen has remained highly conserved, retaining >98% genetic similarity to the original strain described in Indonesia in 1935.


Subject(s)
Endophthalmitis , Klebsiella Infections , Endophthalmitis/diagnosis , Endophthalmitis/epidemiology , Humans , Indonesia , Klebsiella Infections/diagnosis , Klebsiella pneumoniae/genetics , United States/epidemiology , Virulence Factors
10.
Emerg Infect Dis ; 27(4): 1223-1227, 2021.
Article in English | MEDLINE | ID: mdl-33755003

ABSTRACT

Candida auris is an emerging multidrug-resistant yeast. We describe an ongoing C. auris outbreak that began in October 2019 in Los Angeles, California, USA. We used genomic analysis to determine that isolates from 5 of 6 patients belonged to clade III; 4 isolates were closely related.


Subject(s)
Candida , Candidiasis , Antifungal Agents , Genomics , Humans , Los Angeles , Microbial Sensitivity Tests
11.
J Clin Microbiol ; 59(7): e0043121, 2021 06 18.
Article in English | MEDLINE | ID: mdl-33903168

ABSTRACT

Patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be diagnosed by PCR during acute infection or later in their clinical course by detection of virus-specific antibodies. While in theory complementary, both PCR and serologic tests have practical shortcomings. A retrospective study was performed in order to further define these limitations in a clinical context and to determine how to best utilize these tests in a coherent fashion. A total of 3,075 patients underwent both PCR and serology tests at University of California, Los Angeles (UCLA), in the study period. Among these, 2,731 (89%) had no positive tests at all, 73 (2%) had a positive PCR test and only negative serology tests, 144 (5%) had a positive serology test and only negative PCR tests, and 127 (4%) had positive PCR and serology tests. Approximately half of the patients with discordant results (i.e., PCR positive and serology negative or vice versa) had mistimed tests in reference to the course of their disease. PCR-positive patients who were asymptomatic or pregnant were less likely to generate a detectable humoral immune response to SARS-CoV-2. On a quantitative level, the log number of days between symptom onset and PCR test was positively correlated with cycle threshold (CT) values. However, there was no apparent relationship between PCR CT and serologic (arbitrary units per milliliter) results.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Humans , Los Angeles , Polymerase Chain Reaction , Retrospective Studies , Serologic Tests
12.
Anaerobe ; 71: 102421, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34314867

ABSTRACT

Catabacter hongkongensis, an increasingly recognized bacteria in clinical samples, was identified by direct metagenomic sequencing of positive blood culture fluid from a 55-year-old patient with colonic perforation. The bacteremia was cleared by both antibiotic treatment and surgical intervention. This is the first case report of C. hongkongensis infection in the US.


Subject(s)
Bacteremia/microbiology , Clostridiales/genetics , Clostridiales/isolation & purification , Anti-Bacterial Agents/therapeutic use , Bacteremia/blood , Bacteremia/drug therapy , Bacteremia/surgery , Blood Culture , Clostridiales/classification , Clostridiales/drug effects , Female , Humans , Metagenomics , Middle Aged , Phylogeny , Sequence Analysis, DNA
13.
Article in English | MEDLINE | ID: mdl-31527031

ABSTRACT

We report here a fatal case of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in a renal transplant patient without a travel history in the prior year, from whom 2 genetically different CRKP (sequence type 14 [ST14] and ST2497) strains carrying the same plasmids and antimicrobial resistance genes, including blaNDM-1, blaOXA-232, blaCTX-M-15, armA, and tet(D), were isolated from blood and the abdominal cavity. The isolates were susceptible to colistin, tigecycline, eravacycline, and cefiderocol, which was used to treat the CRKP in combination with ceftazidime-avibactam and polymyxin B and resulted in bacterial clearance. Despite the aggressive treatment, the patient died of ischemic colitis and multiorgan failure.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Klebsiella Infections/drug therapy , Klebsiella pneumoniae/drug effects , beta-Lactamases/genetics , Aged , Coinfection , Female , Humans , Kidney Transplantation/adverse effects , Klebsiella Infections/mortality , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Methyltransferases/genetics , Microbial Sensitivity Tests , Plasmids/genetics
14.
J Clin Microbiol ; 58(12)2020 11 18.
Article in English | MEDLINE | ID: mdl-32967898

ABSTRACT

Seasonal influenza virus is associated with high morbidity and mortality especially in vulnerable patient populations. Here, we demonstrate the novel use of Sofia influenza A+B fluorescent immunoassay (FIA), a rapid antigen-based influenza point-of-care test (POCT), combined with Virena software for automatic deidentified tracking of influenza activity across the Los Angeles area and for predicting surges of influenza cases in the emergency department (ED). We divided outpatient clinics into 6 geographic zones and compared weekly influenza activity. In the outpatient setting, there were 1,666 and 274 influenza A and influenza B positives, respectively, across the 2018 to 2019 influenza season and 1,857 and 1,449 influenza A and influenza B positives, respectively, during the 2019 to 2020 influenza season, with zone-specific differences observed. Moreover, we found that a rapid increase in outpatient influenza was followed by an influx in influenza-positive cases in the ED, offering a 1- to 3-week warning sign for ED influx of triple or quadruple the number of influenza cases compared to the prior week. Sofia influenza A+B FIA allows for surveillance of real-time deidentified influenza activity. Tracking of such data may serve as a valuable region-specific influenza indicator and predictor to guide infection prevention measures in both the outpatient and hospital settings. High-impact interventions include designating areas for waiting rooms for influenza-like illnesses, altering staff scheduling in anticipation of surges, and securing sufficient personal protective equipment and antivirals during the height of influenza season.


Subject(s)
Delivery of Health Care, Integrated , Influenza, Human , Emergency Service, Hospital , Humans , Influenza, Human/diagnosis , Los Angeles/epidemiology , Outpatients
15.
J Clin Microbiol ; 58(1)2019 12 23.
Article in English | MEDLINE | ID: mdl-31619532

ABSTRACT

Meropenem-vaborbactam (MEV) is a novel carbapenem-beta-lactamase inhibitor combination antibiotic approved by the U.S. Food and Drug Administration (FDA) for treatment of complicated urinary tract infections, including pyelonephritis, in adults. In this study, we evaluated the performance of Etest MEV (bioMérieux, Marcy l'Etoile, France) compared to that of broth microdilution for 629 Enterobacterales and 163 Pseudomonas aeruginosa isolates. According to CLSI/FDA breakpoints, 13 Enterobacterales isolates (12 clinical and 1 challenge) were resistant to MEV. Overall, Etest MEV demonstrated 92.4% essential agreement (EA), 99.2% category agreement (CA), 0% very major errors (VME), 0% major errors (ME), and 0.8% minor errors (mE) with clinical and challenge isolates of Enterobacterales Individual species demonstrated EA rates of ≥80%, with the exception of Proteus mirabilis, for which clinical and challenge isolates demonstrated 34.3% EA, 97.1% CA, 0% ME, and 2.9% mE, precluding the use of Etest MEV with this species. Excluding P. mirabilis, MEV Etest MEV demonstrated 95.8% EA, 99.3% CA, 0% VME, 0% ME, and 0.7% mE with Enterobacterales isolates. When evaluated using European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, Etest MEV performance with clinical (16 MEV resistant) and challenge (12 MEV resistant) isolates of Enterobacterales (excluding P. mirabilis) and P. aeruginosa demonstrated an unacceptably high VME rate of 7.1% despite 95.2% EA, 99.2% CA, and 0.5% ME compared to the reference method. In conclusion, we report that Etest MEV is accurate and reproducible for MEV susceptibility testing for P. aeruginosa and Enterobacterales, with the exception of P. mirabilis, using CLSI/FDA breakpoints. Etest MEV should not be used with P. mirabilis due to unacceptable analytical performance.


Subject(s)
Anti-Bacterial Agents/pharmacology , Boronic Acids/pharmacology , Disk Diffusion Antimicrobial Tests , Enterobacteriaceae/drug effects , Meropenem/pharmacology , Pseudomonas aeruginosa/drug effects , Drug Combinations , Humans , Reproducibility of Results
16.
Anal Chem ; 90(15): 8881-8888, 2018 08 07.
Article in English | MEDLINE | ID: mdl-30004217

ABSTRACT

We present an approach to estimate the concentration of a biomolecule in a solution by sampling several nanoliter-scale volumes and determining if the volumes contain any biomolecules. In this method, varying volume fractions (nanoliter-scale) of a sample of nucleic acids are introduced to an array of uniform volume reaction wells (100 µL), which are then fluorescently imaged to determine if signal is above a threshold after nucleic acid amplification, all without complex instrumentation. The nanoliter volumes are generated and introduced using the simple positioning of a permanent magnet, and imaging is performed with a cellphone-based fluorescence detection scheme, both methods suitable for limited-resource settings. We use the length of time a magnetic field is applied to generate a calibrated number of nanoliter ferrodrops of sample mixed with ferrofluid at a step emulsification microfluidic junction. Each dose of ferrodrops is then transferred into larger microliter scale reaction wells on chip through a simple shift of the external magnet. Nucleic acid amplification is achieved using loop-mediated isothermal amplification (LAMP). By repeating each nanoliter dosage a number of times to calculate the probability of a positive signal at each dosage, we can use a binomial probability distribution to estimate the sample nucleic acid concentration. Using this approach we demonstrate detection of lambda DNA molecules down to 25 copies per microliter. The ability to dose separate nanoliter-scale volumes of a low-volume sample across wells in this platform is suited for multiplexed assays. This platform has the potential to be applied to a range of diseases by mixing a sample with magnetic nanoparticles.


Subject(s)
DNA/analysis , Magnetite Nanoparticles/chemistry , Microfluidic Analytical Techniques/instrumentation , Nucleic Acid Amplification Techniques/instrumentation , Emulsions/chemistry , Equipment Design , Microfluidic Analytical Techniques/economics , Nucleic Acid Amplification Techniques/economics , Sample Size
17.
J Virol ; 89(5): 2520-9, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25505064

ABSTRACT

UNLABELLED: Nipah virus (NiV) is a deadly emerging enveloped paramyxovirus that primarily targets human endothelial cells. Endothelial cells express the innate immune effector galectin-1 that we have previously shown can bind to specific N-glycans on the NiV envelope fusion glycoprotein (F). NiV-F mediates fusion of infected endothelial cells into syncytia, resulting in endothelial disruption and hemorrhage. Galectin-1 is an endogenous carbohydrate-binding protein that binds to specific glycans on NiV-F to reduce endothelial cell fusion, an effect that may reduce pathophysiologic sequelae of NiV infection. However, galectins play multiple roles in regulating host-pathogen interactions; for example, galectins can promote attachment of HIV to T cells and macrophages and attachment of HSV-1 to keratinocytes but can also inhibit influenza entry into airway epithelial cells. Using live Nipah virus, in the present study, we demonstrate that galectin-1 can enhance NiV attachment to and infection of primary human endothelial cells by bridging glycans on the viral envelope to host cell glycoproteins. In order to exhibit an enhancing effect, galectin-1 must be present during the initial phase of virus attachment; in contrast, addition of galectin-1 postinfection results in reduced production of progeny virus and syncytium formation. Thus, galectin-1 can have dual and opposing effects on NiV infection of human endothelial cells. While various roles for galectin family members in microbial-host interactions have been described, we report opposing effects of the same galectin family member on a specific virus, with the timing of exposure during the viral life cycle determining the outcome. IMPORTANCE: Nipah virus is an emerging pathogen that targets endothelial cells lining blood vessels; the high mortality rate (up to 70%) in Nipah virus infections results from destruction of these cells and resulting catastrophic hemorrhage. Host factors that promote or prevent Nipah virus infection are not well understood. Endogenous human lectins, such as galectin-1, can function as pattern recognition receptors to reduce infection and initiate immune responses; however, lectins can also be exploited by microbes to enhance infection of host cells. We found that galectin-1, which is made by inflamed endothelial cells, can both promote Nipah virus infection of endothelial cells by "bridging" the virus to the cell, as well as reduce production of progeny virus and reduce endothelial cell fusion and damage, depending on timing of galectin-1 exposure. This is the first report of spatiotemporal opposing effects of a host lectin for a virus in one type of host cell.


Subject(s)
Endothelial Cells/physiology , Endothelial Cells/virology , Galectin 1/metabolism , Giant Cells/virology , Host-Pathogen Interactions , Nipah Virus/physiology , Virus Internalization , Cells, Cultured , Endothelial Cells/immunology , Galectin 1/immunology , Humans , Nipah Virus/immunology
19.
J Clin Microbiol ; 53(7): 2349-52, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25926486

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has revolutionized the identification of clinical bacterial and yeast isolates. However, data describing the reproducibility of MALDI-TOF MS for microbial identification are scarce. In this study, we show that MALDI-TOF MS-based microbial identification is highly reproducible and can tolerate numerous variables, including differences in testing environments, instruments, operators, reagent lots, and sample positioning patterns. Finally, we reveal that samples of bacterial and yeast isolates prepared for MALDI-TOF MS identification can be repeatedly analyzed without compromising organism identification.


Subject(s)
Bacteria/chemistry , Bacteria/classification , Microbiological Techniques/methods , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Yeasts/chemistry , Yeasts/classification , Humans , Reproducibility of Results , Specimen Handling/methods
20.
Transplant Proc ; 56(7): 1683-1690, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39174391

ABSTRACT

BACKGROUND: Mucorales infections continue to cause significant morbidity and mortality in immunocompromised hosts despite the advent of new approaches for diagnosis and treatment of fungal infections. We aimed to evaluate risk factors and outcomes of Mucorales infection in solid organ transplant, hematopoietic cell transplant, and chimeric antigen receptor T-cell therapy recipients. METHODS: This single-center retrospective study included solid organ transplant, hematopoietic cell transplant, and chimeric antigen receptor T-cell patients with cultures positive for Mucorales. RESULTS: Forty-three patients were included for analysis; 34 solid organ transplant (79%) and 9 hematopoietic stem cell transplant or chimeric antigen receptor T-cell (21%). Infection with Mucorales occurred a median of 184 days after transplant. At the time of diagnosis, 36 patients were on antifungal prophylaxis with the majority receiving posaconazole (53%). Thirty-three had clinically significant disease; 30 received definitive anti-Mucorales therapy and 3 empiric antifungal therapy. Isavuconazole was the most common azole used for treatment in monotherapy recipients. All-cause mortality was 64% and, of these deaths, 18 (75%) were directly related to Mucormycosis. The highest mortality was seen in disseminated and intra-abdominal disease (100%), followed by pulmonary disease (50%). There was no significant association with mortality and transplant type or number of immunosuppressive agents. CONCLUSION: Mucormycosis is an important cause of morbidity and mortality in immunocompromised patients. Breakthrough infection was not uncommon in this study. Data regarding the incidence of infection at approximately 6 months after transplantation can inform prophylaxis and treatment regimens. The spectrum of antifungal regimens used reflects the lack of consensus on ideal regimens for these organisms and a need for more studies.


Subject(s)
Antifungal Agents , Hematopoietic Stem Cell Transplantation , Mucorales , Mucormycosis , Organ Transplantation , Humans , Retrospective Studies , Risk Factors , Hematopoietic Stem Cell Transplantation/adverse effects , Middle Aged , Mucormycosis/epidemiology , Male , Female , Organ Transplantation/adverse effects , Adult , Antifungal Agents/therapeutic use , Receptors, Chimeric Antigen , Immunocompromised Host , Aged , Treatment Outcome
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