Background Patients with bloodstream infections (BSIs) due to carbapenem-resistant Enterobacteriaceae (CRE) have long delays until receipt of appropriate antimicrobial therapy and high mortality rates. Rapid molecular diagnostics and... more
Background Patients with bloodstream infections (BSIs) due to carbapenem-resistant Enterobacteriaceae (CRE) have long delays until receipt of appropriate antimicrobial therapy and high mortality rates. Rapid molecular diagnostics and novel therapies, such as ceftazidime–avibactam (CAZ-AVI), offer promise to improve outcomes, but their clinical impact is unclear. Methods We conducted an observational study of patients with CRE BSI from January 2016 to June 2018 at 8 New York and New Jersey medical centers. Patient demographics, comorbidities, clinical presentations, diagnostic methods, and treatments were compared between patients who died within 30 days of BSI onset and survivors. Independent risk factors for mortality were identified using logistic regression. We then compared time to receipt of active antimicrobial therapy between patients whose positive blood culture bottles underwent testing for the Klebsiella pneumoniae carbapenemase gene (blaKPC PCR) and patients where this te...
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Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change... more
Background: The merging of two divergent genomes during hybridization can result in the remodeling of parental gene expression in hybrids. A molecular basis underling expression change in hybrid is regulatory divergence, which may change with the parental genetic divergence. However, there still no unanimous conclusion for this hypothesis. Results : Three species of Camellia with a range of genetic divergence and their F 1 hybrids were used to study the effect of parental genetic divergence on gene expression and regulatory patterns in hybrids by RNA-sequencing and allele-specific gene expression analysis. We found that though the proportion of differentially expressed genes (DEGs) between the hybrids and their parents did not increase, a greater proportion of DEGs would be non-additively (especially transgressively) expressed in the hybrids as genomes between the parents become more divergent . In addition, the proportion of genes with significant evidence of cis -regulatory diverg...
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Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and... more
Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% ( n = 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorr...
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This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of and species compared... more
This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of and species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the , , and complexes and within the and groups could be differentiated. Among the 312 isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex...
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Next generation sequencing of sixharboringandisolates collected from a tertiary care hospital in China revealed significant sequence variations in the regions flanking thegene. While sequence variations significantly affect the expression... more
Next generation sequencing of sixharboringandisolates collected from a tertiary care hospital in China revealed significant sequence variations in the regions flanking thegene. While sequence variations significantly affect the expression and promoter activity of, thegene expressions do not correlate with thecolistin resistance levels, which warrants further in-depth investigations.
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Here we completely sequenced fourmcr-1-haboring plasmids, isolated from two ESBL-producingEscherichia coliand two carbapenemase-producingKlebsiella pneumoniaeclinical isolates. Themcr-1-harboring plasmids, pMCR1-IncX4, from an ST2248E.... more
Here we completely sequenced fourmcr-1-haboring plasmids, isolated from two ESBL-producingEscherichia coliand two carbapenemase-producingKlebsiella pneumoniaeclinical isolates. Themcr-1-harboring plasmids, pMCR1-IncX4, from an ST2248E. coliand two ST25K. pneumoniae, were identical, belonging to the IncX4 incompatibility group, while the plasmid (pMCR1-IncI2) from an ST2085E. colibelongs to the IncI2 group. A 2.6 kb nearly identicalmcr-1-pap2element was found to be shared by allmcr-1-carring plasmids.
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Molecular Microbiology: Diagnostic Principles and Practice . Second Edition. Edited by David H. Persing , Fred C. Tenover , Yi-Wei Tang , Frederick S. Nolte , Randall T. Hayden , and Alex van Belkum . Washington (DC): ASM Press. $179.95. xvi + 936 p. + 12 pl.; ill.; index. ISBN: 978-1-55581-497-7...more
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The mechanisms for increased risk of chronic kidney disease (CKD) in obesity remain unclear. The renin-angiotensin system is implicated in the pathogenesis of both adiposity and CKD. We investigated whether the angiotensin type 1 (AT1)... more
The mechanisms for increased risk of chronic kidney disease (CKD) in obesity remain unclear. The renin-angiotensin system is implicated in the pathogenesis of both adiposity and CKD. We investigated whether the angiotensin type 1 (AT1) receptor, composed of dominant AT1a and less expressed AT1b in wild-type (WT) mice, modulates development and progression of kidney injury in a high-fat diet (HFD)-induced obesity model. WT mice had increased body weight, body fat, and insulin levels and decreased adiponectin levels after 24 wk of a high-fat diet. Identically fed AT1a knockout (AT1aKO) mice gained weight similarly to WT mice, but had lower body fat and higher plasma cholesterol. Both obese AT1aKO and obese WT mice had increased visceral fat and kidney macrophage infiltration, with more proinflammatory M1 macrophage markers as well as increased mesangial expansion and tubular vacuolization, compared with lean mice. These abnormalities were heightened in the obese AT1aKO mice, with down...
Research Interests: Endocrinology, Biology, Kidney diseases, Macrophages, Adipose tissue, and 15 moreInternal Medicine, Kidney, Insulin, Hemodynamics, Cholesterol, Animals, Male, Medical Physiology, Adiponectin, Body Weight, Biological markers, Macrophage Polarization, Dietary fats, Adiposity, and Inflammation Mediators
Increased plasminogen activator inhibitor-1 (PAI-1) is linked to obesity and insulin resistance. However, the functional role of PAI-1 in adipocytes is unknown. This study was designed to investigate effects and underlying mechanisms of... more
Increased plasminogen activator inhibitor-1 (PAI-1) is linked to obesity and insulin resistance. However, the functional role of PAI-1 in adipocytes is unknown. This study was designed to investigate effects and underlying mechanisms of PAI-1 on glucose uptake in adipocytes and on adipocyte differentiation. Using primary cultured adipocytes from PAI-1+/+and PAI-1−/−mice, we found that PAI-1 deficiency promoted adipocyte differentiation, enhanced basal and insulin-stimulated glucose uptake, and protected against tumor necrosis factor-α-induced adipocyte dedifferentiation and insulin resistance. These beneficial effects were associated with upregulated glucose transporter 4 at basal and insulin-stimulated states and upregulated peroxisome proliferator-activated receptor-γ (PPARγ) and adiponectin along with downregulated resistin mRNA in differentiated PAI-1−/−vs. PAI-1+/+adipocytes. Similarly, inhibition of PAI-1 with a neutralizing anti-PAI-1 antibody in differentiated 3T3-L1 adipocy...
Research Interests: Endocrinology, Biology, Medicine, Gene expression, Biological Sciences, and 15 moreCell Differentiation, Internal Medicine, Glucose, Insulin, Mice, Animals, Male, Monoclonal Antibodies, Adiponectin, Resistin, Adipocytes, Adipocyte, Plasminogen Activator Inhibitor, Medical and Health Sciences, and Collagen type I
OXA-48-producing Enterobacteriaceae have extensively spread throughout Europe and other global regions, but remain uncommon in North and South America, and in some Asian countries (1, 2).….
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Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures,... more
Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.
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Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and... more
Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO) in early 2020. Results As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein ter...
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1 National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China, 2 Key Laboratory of Respiratory Disease... more
1 National Health Commission (NHC) Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China, 2 Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, 3 Department of Medical Affairs, Danaher Diagnostic Platform/Cepheid (China), New York, NY, United States, 4 State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which... more
The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistic...
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As one of the most recent additions to the syndromic testing landscape, the ePlex® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics,... more
As one of the most recent additions to the syndromic testing landscape, the ePlex® platform by GenMark Diagnostics is a system that combines the manufacturer's signature electrochemical detection technology with updated microfluidics, providing a new option for multiplex testing that is both rapid and requires minimal hands-on steps. In this review, we detail the ePlex platform and its current/future syndromic panels, with a particular focus on the respiratory pathogen panel – the platform's first assay to undergo clinical trials and receive regulatory approval in the USA. By keeping informed of these ever-expanding laboratory options, clinicians and microbiologists can stay positioned at the forefront of infectious disease diagnosis.
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Fecal calprotectin (fCPT) has been used as a surrogate marker for assessment of intestinal inflammation. We explore the utility of fCPT values as a diagnostic aid in cancer patients with suspected Clostridium difficile infection (CDI). A... more
Fecal calprotectin (fCPT) has been used as a surrogate marker for assessment of intestinal inflammation. We explore the utility of fCPT values as a diagnostic aid in cancer patients with suspected Clostridium difficile infection (CDI). A total of 232 stool specimens submitted for GeneXpert C. difficile PCR testing were included in the study. All specimens were tested for fCPT and toxin/GDH antigens. Clinical severity of CDI cases was determined by the IDSA/SHEA criteria. Significant differences of median fCPT values between CDI (n = 117, Median 183.6 μg/g) and non-CDI (n = 115, 145.6 μg/g, p = 0.006) patients were seen. In CDI patents, significantly lower fCPT values were found in patients with mild to moderate (n = 95, 182.1 μg/g) than those with severe and severe to complicated (n = 22, 218.5 μg/g, p = 0.014) scores, and among those that were toxin positive (n = 24, 200.2 μg/g) vs. toxin negative (n = 86, 182.8 μg/g, p = 0.044). Despite this overall trend, wide variations in fCPT ...
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The accuracy and robustness of the VITEK® MS V3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) system was evaluated by identifying mycobacteria from automated liquid media systems using... more
The accuracy and robustness of the VITEK® MS V3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) system was evaluated by identifying mycobacteria from automated liquid media systems using patient samples. This is the first report demonstrating that proteins within the liquid media, its supplements, and decontamination reagents for non-sterile patient samples do not generate misidentification or false positive results when using the VITEK MS V3.0 system. Prior to testing with patient samples, a seeded study was conducted to challenge the accuracy of the VITEK MS to identify mycobacteria from liquid media through mimicking a clinical workflow. A total of 77 strains representing 21 species, seeded in simulated sputum, were decontaminated and inoculated into BACT/ALERT®MP liquid culture medium, incubated until positivity, and identified using VITEK MS. A total of 383 liquid cultures were tested of which 379 (99%) identified correctly to the...
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Clostridium difficile is a leading cause of antibiotic-associated diarrhea worldwide. The diagnosis of C. difficile infection (CDI) requires both clinical manifestations and a positive laboratory test for C. difficile and/or its toxins.... more
Clostridium difficile is a leading cause of antibiotic-associated diarrhea worldwide. The diagnosis of C. difficile infection (CDI) requires both clinical manifestations and a positive laboratory test for C. difficile and/or its toxins. While antibiotic therapy is the treatment of choice for CDI, there are relatively few classes of effective antibiotics currently available. Therefore, the development of novel antibiotics and/or alternative treatment strategies for CDI has received a great deal of attention in recent years. A number of emerging agents such as cadazolid, surotomycin, ridinilazole, and bezlotoxumab have demonstrated activity against C. difficile; some of these have been approved for limited clinical use and some are in clinical trials. In addition, other approaches such as early and accurate diagnosis of CDI as well as disease prevention are important for clinical management. While the toxigenic culture and the cell cytotoxicity neutralization assay are still recognize...
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Rapid identification of respiratory pathogens such as influenza viruses A (FluA), B (FluB) and respiratory syncytial virus (RSV) reduces unnecessary antimicrobial use and enhances infection control practice. We performed a comparative... more
Rapid identification of respiratory pathogens such as influenza viruses A (FluA), B (FluB) and respiratory syncytial virus (RSV) reduces unnecessary antimicrobial use and enhances infection control practice. We performed a comparative evaluation of three molecular methods; 1) ARIES Flu A/B & RSV, 2) Xpert Xpress Flu/RSV and 3) Cobas Flu A/B & RSV. The clinical performance of the three methods was evaluated using 200 remnant nasopharyngeal swab (NPS) specimens against a combined reference standard. The limits of detection (LODs) of the ARIES and the Xpert Xpress assays were determined using titer-known FluA, FluB, and RSV control strains. The 95% limits of detection were between 1.702 and 0.0003 TCID50 with no significant differences revealed among the three assays. Perfect qualitative detection agreement was obtained in the reproducibility study. The Cobas failed at the first run on 13 clinical specimens, resulting in an invalid rate of 6.5%. Sensitivities and specificities for all ...
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Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allows prompt and specific treatment. We optimized the specimen processing to maximize the limit of detection (LOD) by matrix-assisted... more
Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allows prompt and specific treatment. We optimized the specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile and supernatant spotted onto the target plate were 15 mL, 3 μL and 3 μL, respectively, yielding a LOD of 1.0×10(5) colony-forming units/mL. Among the total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were respectively positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV...
Research Interests: Algorithms, Chemistry, Chromatography, Mass Spectrometry, Medicine, and 15 moreClinical Microbiology, Biological Sciences, Humans, Escherichia coli, Female, Male, Bacteria, Urinalysis, Formic Acid, Urinary System, Enterococcus faecalis, Sensitivity and Specificity, Klebsiella pneumoniae, Medical and Health Sciences, and limit of detection
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Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex II V2.0 kit and explored factors influencing its sensitivity.... more
Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex II V2.0 kit and explored factors influencing its sensitivity. Nasopharyngeal swab (NPS) specimens were prospectively collected from pediatric inpatients with lower respiratory tract infections at the time of admission in the Shenzhen Children's Hospital from May 2009 to April 2010. Total nucleic acids were extracted using the EZ1 system (Qiagen, Germany) and 17 respiratory viruses and genotypes including influenza A virus (FluA), FluB, parainfluenza virus 1 (PIV1), PIV2, PIV3, PIV4, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinoviruses (RhV), enteroviruses (EnV), human bocaviruses (hBoV), adenoviruses (AdV), four coronaviruses (229E, OC43, NL63 and HKU1), and FluA 2009 pandemic H1N1(H1N1-p) were detected and identified by the ResPlex II kit. In parallel, 16 real-time TaqMan quantita...
Research Interests: Biology, Virology, Medicine, Humans, Child, and 15 moreVirus, Female, Male, Infant, Human Metapneumovirus, Respiratory Tract Infections, influenza A virus, Multiplex, Rhinovirus, Sensitivity and Specificity, Virus diseases, Enterovirus, Child preschool, reverse transcriptase polymerase chain reaction, and multiplex polymerase chain reaction
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Research Interests: Immunology, Biology, Infectious Diseases, Medicine, Biological Sciences, and 15 moreHumans, Mice, Female, Animals, Monoclonal Antibodies, Animal Model, Infectious, Efficiency, Antibody, Monoclonal Antibody, Intranasal Administration, immunoglobulin G, Immunoglobulin A, Lower Respiratory Tract Infection, and Medical and Health Sciences
High rates and transmission of multidrug-resistant (MDR) tuberculosis (TB) have been associated with the Mycobacterium tuberculosis complex (MTBC) Beijing lineage, pointing to the importance of pathogen genetic factors for the modulation... more
High rates and transmission of multidrug-resistant (MDR) tuberculosis (TB) have been associated with the Mycobacterium tuberculosis complex (MTBC) Beijing lineage, pointing to the importance of pathogen genetic factors for the modulation of infection outcome and epidemiology. We present here an in-depth analysis of the population structure of MTBC strains from the Republic of Georgia, a high-incidence setting at the Black Sea Coast. Phylogenetic lineages were identified based on 24-locus MIRU-VNTR (for mycobacterial interspersed repetitive unit-variable number tandem repeat) and spoligotyping analysis. Clusters of strains with identical genotyping profiles were determined as an indicator for the rate of recent transmission. Among the 183 M. tuberculosis isolates investigated, the most prominent lineage found was Beijing (26%), followed by the LAM (18%), Ural (12%), and Haarlem (5%) strains. A closely related previously undefined phylogenetic group (62 strains) showed a genotyping pa...
Research Interests: Biology, Medicine, Molecular Epidemiology, Clinical Microbiology, Biological Sciences, and 15 moreHumans, Mycobacterium tuberculosis, Female, Clinical, Male, Bacteria, Cluster Analysis, DNA fingerprinting, Aged, Middle Aged, Genotype, Adult, Genotyping, Democratic Republic of Georgia, and Medical and Health Sciences
Mycobacterium tuberculosis that is resistant to both isoniazid (INH) and rifampin (RIF) is spreading. It has become a public health problem in part because the standard culture methods used to determine the appropriate treatment regimen... more
Mycobacterium tuberculosis that is resistant to both isoniazid (INH) and rifampin (RIF) is spreading. It has become a public health problem in part because the standard culture methods used to determine the appropriate treatment regimen for patients often take months following the presumptive diagnosis of tuberculosis. Furthermore, the misidentification of nontuberculosis mycobacteria (NTM) in patients presumably suffering from tuberculosis results in additional human and health care costs. The mechanisms of resistance for several drugs used to treat Mycobacterium tuberculosis are well understood and therefore should be amenable to determination by rapid molecular methods. We describe here the use of PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) in an assay that simultaneously determines INH and RIF resistance in Mycobacterium tuberculosis and identifies and determines the species of NTMs. The assay panel included 16 primer pairs in eight multiplexed reactio...
Research Interests: Microbiology, Biology, Medicine, Clinical Microbiology, Biological Sciences, and 15 moreSouth Africa, Tuberculosis, Humans, Mycobacterium tuberculosis, Mycobacterium, New York City, Clinical, Drug Resistance, Polymerase Chain Reaction, Liquid Chromatography / Electrospray Ionization Mass Spectrometry, Isoniazid, Ethambutol, Democratic Republic of Georgia, Medical and Health Sciences, and Rifampin
Robinsoniella peoriensis was recently identified as a Gram-positive, spore-forming, anaerobic rod originally isolated from swine manure storage pits. We describe here a case of R. peoriensis bacteremia in a 42-year-old male with... more
Robinsoniella peoriensis was recently identified as a Gram-positive, spore-forming, anaerobic rod originally isolated from swine manure storage pits. We describe here a case of R. peoriensis bacteremia in a 42-year-old male with pancreatic cancer. The identification was confirmed by unique phenotypic profiles and partial 16S rRNA gene sequences.
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The Bruker Biotyper and BD Phoenix systems were evaluated for identification of 1,024 bacterial urinary tract isolates. The Biotyper and Phoenix systems correctly identified 99.9% and 99.5% to the genus level and 99.1% and 98.5% to the... more
The Bruker Biotyper and BD Phoenix systems were evaluated for identification of 1,024 bacterial urinary tract isolates. The Biotyper and Phoenix systems correctly identified 99.9% and 99.5% to the genus level and 99.1% and 98.5% to the species level, respectively. Both systems provide reliable results, and the Biotyper system offers a rapid tool for urine bacterial isolate identification.
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Current methods for identification of yeast from blood cultures may take several days after these microorganisms have been observed by Gram stain smears from positive blood cultures. We explored the use of a matrix-assisted laser... more
Current methods for identification of yeast from blood cultures may take several days after these microorganisms have been observed by Gram stain smears from positive blood cultures. We explored the use of a matrix-assisted laser desorption ionization (MALDI) Biotyper system in combination with Sepsityper specimen processing and Microflex analysis for improved detection and identification of yeast species directly from positive blood culture specimens demonstrating yeast-like organisms by Gram stain. The limit of detection of yeast species in blood culture medium was determined to be 5.9 × 10 5 CFU, with intra- and interstrain coefficients of variation of 1.8 to 3.6% and 2.9%, respectively. A total of 42 yeast-containing positive blood culture specimens were processed, and the identification results were compared to those obtained by routinely used phenotypic methods. Specimens with discrepant results between the Biotyper and phenotypic methods were identified on the basis of intern...
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Background: Respiratory viruses have become increasingly recognized as serious causes of morbidity and mortality in immunocompromised patients. Rapid and sensitive detection of respiratory viruses is essential for early diagnosis and... more
Background: Respiratory viruses have become increasingly recognized as serious causes of morbidity and mortality in immunocompromised patients. Rapid and sensitive detection of respiratory viruses is essential for early diagnosis and administration of appropriate antiviral therapy as well as for effective implementation of infection control measures.Methods: We compared the performance of two commercial assays, the xTAG RVP FAST (Luminex Diagnostics, Toronto, Canada) and the FilmArray RVP (FA RVP, Idaho Technology, Salt Lake City, Utah) in pediatric patients at Memorial Sloan-Kettering Cancer Center. These assays detect the following viruses: respiratory syncytial virus, influenza A and B, parainfluenza 1, 2, 3, 4, human metapneumovirus, adenovirus, enterovirus-rhinovirus, coronaviruses NL63, HKU1, 229E and OC43 and bocavirus. We tested a total of 358 respiratory specimens from 173 pediatric patients previously tested by direct fluorescence assay (DFA) and viral culture.Results: The...
Research Interests: Adolescent, Medicine, Clinical Microbiology, Biological Sciences, Humans, and 15 moreChild, Female, Male, Infant, Cancer Care Facilities, Human Metapneumovirus, Neoplasms, Respiratory Tract Infections, Multiplex, Molecular Diagnostic Techniques, Rhinovirus, Sensitivity and Specificity, Child preschool, Human Bocavirus, and Medical and Health Sciences
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Throughout her career, Dr. Marie L. Landry has brought a unique combination of actionable medical intelligence, charisma, and energy to the field of clinical virology and infectious diseases.…
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Purpose Donor-derived infection (DDI) has become an important factor affecting the prognosis of lung transplantation patients. The risks versus benefits of using donor organs infected with multidrug-resistant organisms (MDRO), especially... more
Purpose Donor-derived infection (DDI) has become an important factor affecting the prognosis of lung transplantation patients. The risks versus benefits of using donor organs infected with multidrug-resistant organisms (MDRO), especially carbapenem-resistant organisms (CRO), are frequently debated. Traditional microbial culture and antimicrobial susceptibility testing at present fail to meet the needs of quick CRO determination for donor lungs before acquisition. In this study, we explored a novel screening method by using Xpert® Carba-R assay for CRO in donor lungs in a real-time manner to reduce CRO-associated DDI mortality. Methods This study was registered on chictr.org.cn (ChiCTR2100053687) on November 2021. In the Xpert Carba-R screening group, donor lungs were screened for CRO infection by the Xpert Carba-R test on bronchoalveolar fluid (BALF) before acquisition. If the result was negative, donor lung acquisition and subsequent lung transplantation were performed. In the thir...
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Identification of coryneform bacteria to the species level is important in certain circumstances for differentiating contamination and/or colonization from infection, which influences decisions regarding clinical intervention. However,... more
Identification of coryneform bacteria to the species level is important in certain circumstances for differentiating contamination and/or colonization from infection, which influences decisions regarding clinical intervention. However, methods currently used in clinical microbiology laboratories for the species identification of coryneform bacteria are often inadequate. We evaluated the MicroSeq 500 16S bacterial sequencing kit (Perkin-Elmer Biosystems, Foster City, Calif.), which is designed to sequence the first 527 bp of the 16S rRNA gene for bacterial identification, by using 52 coryneform gram-positive bacilli from clinical specimens isolated from January through June 1993 at the Mayo Clinic. Compared to conventional and supplemented phenotypic methods, MicroSeq provided concordant results for identification to the genus level for all isolates. At the species level, MicroSeq provided concordant results for 27 of 42 (64.3%) Corynebacterium isolates and 5 of 6 (83.3%) Corynebacte...
Research Interests: Microbiology, Biology, Medicine, Sequence Analysis, Clinical Microbiology, and 14 moreBiological Sciences, Identification, Humans, Gram Positive, Clinical, Bacteria, Actinomycetales, Genotype, Corynebacterium, Ribosomal DNA, Bacilli, Nucleotide sequence, Medical and Health Sciences, and Microbacterium
Heterogeneity among Aspergillus fumigatus isolates results in unique virulence potential and inflammatory responses. How these isolates drive specific immune responses and how this affects fungally induced lung damage and disease outcome... more
Heterogeneity among Aspergillus fumigatus isolates results in unique virulence potential and inflammatory responses. How these isolates drive specific immune responses and how this affects fungally induced lung damage and disease outcome are unresolved. We demonstrate that the highly virulent CEA10 strain is able to rapidly germinate within the immunocompetent lung environment, inducing greater lung damage, vascular leakage, and interleukin 1α (IL-1α) release than the low-virulence Af293 strain, which germinates with a lower frequency in this environment. Importantly, the clearance of CEA10 was consequently dependent on IL-1α, in contrast to Af293. The release of IL-1α occurred by a caspase 1/11- and P2XR7-independent mechanism but was dependent on calpain activity. Our finding that early fungal conidium germination drives greater lung damage and IL-1α-dependent inflammation is supported by three independent experimental lines. First, pregermination of Af293 prior to in vivo challen...
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Previous work has shown that environmental and clinical isolates of Aspergillus fumigatus represent a diverse population that occupies a variety of niches, has extensive genetic diversity, and exhibits virulence heterogeneity in a number... more
Previous work has shown that environmental and clinical isolates of Aspergillus fumigatus represent a diverse population that occupies a variety of niches, has extensive genetic diversity, and exhibits virulence heterogeneity in a number of animal models of invasive pulmonary aspergillosis (IPA). However, mechanisms explaining differences in virulence among A. fumigatus isolates remain enigmatic. Here, we report a significant difference in virulence of two common lab strains, CEA10 and AF293, in the murine triamcinolone immunosuppression model of IPA, in which we previously identified severe low oxygen microenvironments surrounding fungal lesions. Therefore, we hypothesize that the ability to thrive within these lesions of low oxygen promotes virulence of A. fumigatus in this model. To test this hypothesis, we performed in vitro fitness and in vivo virulence analyses in the triamcinolone murine model of IPA with 14 environmental and clinical isolates of A. fumigatus . Among these is...
Research Interests: Microbiology, Medical Sciences, Medical Microbiology, Biology, Medicine, and 15 moreVirulence, Medical Immunology, Humans, Mice, Animals, Aspergillus fumigatus, Genotype, Triamcinolone, Oxygen, Genetic variation, Genetic Fitness, Mbio, Medicine and Health Sciences, Cellular Microenvironment, and Aspergillosis
The spread of the plasmid-mediated colistin resistance gene, mcr-1, into carbapenem-resistant Enterobacteriaceae (CRE) clinical isolates poses a significant threat to global health. Here we report the identification of three... more
The spread of the plasmid-mediated colistin resistance gene, mcr-1, into carbapenem-resistant Enterobacteriaceae (CRE) clinical isolates poses a significant threat to global health. Here we report the identification of three mcr-1-harboring carbapenem-resistant Escherichia coli, collected from three patients in two provinces in China. Our results show that mcr-1-harboring CRE have started to spread in different hospitals in China. In addition, this study describes the first report of chromosomal integration of mcr-1 in a carbapenem-resistant E. coli.
Research Interests: Microbiology, Medical Microbiology, Biology, China, Medicine, and 12 moreHospitals, Escherichia coli, Enterobacteriaceae, Anti-Bacterial Agents, Colistin, Carbapenem, Carbapenems, McR, Microbial Sensitivity Tests, Plasmid, Pharmacology and pharmaceutical sciences, and Carbapenem-Resistant Enterobacteriaceae
We implemented hospital information system (HIS) alerts to deter unnecessary test orders for ova and parasite (O&P) exams and Clostridium difficile polymerase chain reaction (PCR). The HIS alerts decreased non-compliant O&P orders (orders... more
We implemented hospital information system (HIS) alerts to deter unnecessary test orders for ova and parasite (O&P) exams and Clostridium difficile polymerase chain reaction (PCR). The HIS alerts decreased non-compliant O&P orders (orders after > 72 h of hospitalization) from 49.8% to 30.9, an overall decrease of 19% and reduced non-compliant C. difficile PCR orders (orders < 7 days after a previous positive result) from 30.6% to 19.2%, an overall decrease of 31.9%.
Research Interests:
We explored the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for identification of Fusobacterium nucleatum subspecies. MALDI-TOF MS spectra of five F. nucleatum subspecies ( animalis ,... more
We explored the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) for identification of Fusobacterium nucleatum subspecies. MALDI-TOF MS spectra of five F. nucleatum subspecies ( animalis , fusiforme , nucleatum , polymorphum , and vincentii ) were analyzed and divided into four distinct clusters, including subsp. animalis , nucleatum , polymorphum , and fusiforme / vincentii . MALDI-TOF MS with the modified SARAMIS database further correctly identified 28 of 34 F. nucleatum clinical isolates to the subspecies level.