Publications by authors named "David J Ecker"

81 Publications

Telehealth: from the abstract to necessity to competency.

FASEB Bioadv 2021 Jan 19. Epub 2021 Jan 19.

University of Colorado School of Medicine Aurora Colorado USA.

The COVID-19 pandemic caused significant disruption in medical education. With disruption comes the opportunity for innovation. Telehealth had been growing rapidly in many fields of medicine prior to the pandemic, however, the necessities of social distancing, scarcity of personal protective equipment, and mandates to prevent unnecessary exposures for healthcare workers and patients alike, brought opportunities for the exponential expansion of telehealth. With expansion of telehealth services came the need to expand curriculum in telehealth to prepare medical students to return to vastly transformed clinical settings as well as prepare them for a future clinical landscape likely to incorporate telehealth to a much greater degree. The University of Colorado School of Medicine (CUSOM) rapidly developed a course in telehealth to prepare students for this changing clinical environment. Simultaneously, a faculty development curriculum was created to support clinical faculty new to telehealth in basic skills and teaching in a virtual environment. Lastly, adaptations were made to the summative Clinical Practice Exam administered to students at the completion of clerkships to incorporate telehealth. Recognizing the importance of achieving competence in telehealth, the CUSOM has taken steps to invest in the development of comprehensive and integrated telehealth curricula. Many creative and innovative solutions have been adopted in the wake of this pandemic to allow medical education to continue despite many hurdles and barriers; many of these will not persist past the pandemic. However, we expect telehealth clinical skills and the curricula developed to support them to remain relevant long past the time when the COVID-19 pandemic has faded into history.
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http://dx.doi.org/10.1096/fba.2020-00098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8013382PMC
January 2021

Molecular Microbiological and Immune Characterization of a Cohort of Patients Diagnosed with Early Lyme Disease.

J Clin Microbiol 2020 12 17;59(1). Epub 2020 Dec 17.

The Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

Lyme disease is a tick-borne infection caused by the bacteria Current diagnosis of early Lyme disease relies heavily on clinical criteria, including the presence of an erythema migrans rash. The sensitivity of current gold-standard diagnostic tests relies upon antibody formation, which is typically delayed and thus of limited utility in early infection. We conducted a study of blood and skin biopsy specimens from 57 patients with a clinical diagnosis of erythema migrans. Samples collected at the time of diagnosis were analyzed using an ultrasensitive, PCR-based assay employing an isothermal amplification step and multiple primers. In 75.4% of patients, we directly detected one or more genotypes in the skin. Two-tier testing showed that 20 (46.5%) of those found to be PCR positive remained serologically negative at both acute and convalescent time points. Multiple genotypes were found in three (8%) of those where a specific genotype could be identified. The 13 participants who lacked PCR and serologic evidence for exposure to could be differentiated as a group from PCR-positive participants by their levels of several immune markers as well as by clinical descriptors such as the number of acute symptoms and the pattern of their erythema migrans rash. These results suggest that within a Mid-Atlantic cohort, patient subgroups can be identified using PCR-based direct detection approaches. This may be particularly useful in future research such as vaccine trials and public health surveillance of tick-borne disease patterns.
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http://dx.doi.org/10.1128/JCM.00615-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771464PMC
December 2020

An Antisense Oligonucleotide Leads to Suppressed Transcription of Hdac2 and Long-Term Memory Enhancement.

Mol Ther Nucleic Acids 2020 Mar 27;19:1399-1412. Epub 2020 Feb 27.

Department of Pharmacology, Vanderbilt University, Nashville, TN, USA. Electronic address:

Knockout of the memory suppressor gene histone deacetylase 2 (Hdac2) in mice elicits cognitive enhancement, and drugs that block HDAC2 have potential as therapeutics for disorders affecting memory. Currently available HDAC2 catalytic activity inhibitors are not fully isoform specific and have short half-lives. Antisense oligonucleotides (ASOs) are drugs that elicit extremely long-lasting, specific inhibition through base pairing with RNA targets. We utilized an ASO to reduce Hdac2 messenger RNA (mRNA) in mice and determined its longevity, specificity, and mechanism of repression. A single injection of the Hdac2-targeted ASO in the central nervous system produced persistent reduction in HDAC2 protein and Hdac2 mRNA levels for 16 weeks. It enhanced object location memory for 8 weeks. RNA sequencing (RNA-seq) analysis of brain tissues revealed that the repression was specific to Hdac2 relative to related Hdac isoforms, and Hdac2 reduction caused alterations in the expression of genes involved in extracellular signal-regulated kinase (ERK) and memory-associated immune signaling pathways. Hdac2-targeted ASOs also suppress a nonpolyadenylated Hdac2 regulatory RNA and elicit direct transcriptional suppression of the Hdac2 gene through stalling RNA polymerase II. These findings identify transcriptional suppression of the target gene as a novel mechanism of action of ASOs.
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http://dx.doi.org/10.1016/j.omtn.2020.01.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047133PMC
March 2020

Molecular Testing of Serial Blood Specimens from Patients with Early Lyme Disease during Treatment Reveals Changing Coinfection with Mixtures of Borrelia burgdorferi Genotypes.

Antimicrob Agents Chemother 2019 07 24;63(7). Epub 2019 Jun 24.

Ibis Biosciences, an Abbott Company, Carlsbad, California, USA.

is the etiological agent of Lyme disease. In the current study, we used direct-detection PCR and electrospray ionization mass spectrometry to monitor and genotype isolates from serially collected whole-blood specimens from patients clinically diagnosed with early Lyme disease before and during 21 days of antibiotic therapy. isolates were detected up to 3 weeks after the initiation of antibiotic treatment, with ratios of coinfecting genotypes changing over time.
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http://dx.doi.org/10.1128/AAC.00237-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591639PMC
July 2019

In Reply to Elder.

Acad Med 2018 11;93(11):1601-1602

Assistant professor of medicine, assistant director of education, Hospital Medicine Group, and director, Foundations of Doctoring Curriculum, Integrated Clinicians Course, and Clinical Practice Exam, University of Colorado School of Medicine, Aurora, Colorado; Assistant dean for curriculum, University of Michigan Medical School, Ann Arbor, Michigan. Professor of medicine and director, Ruth L. Gottesman Clinical Skills Center and Introduction to Clinical Medicine Program, Albert Einstein College of Medicine, Bronx, New York.

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http://dx.doi.org/10.1097/ACM.0000000000002424DOI Listing
November 2018

Broad-range survey of vector-borne pathogens and tick host identification of Ixodes ricinus from Southern Czech Republic.

FEMS Microbiol Ecol 2017 11;93(11)

Ibis Biosciences Inc., Abbott Laboratories, 2251 Faraday Ave, Ste 150, Carlsbad, CA 92008, USA.

Ixodes ricinus ticks are vectors of numerous human and animal pathogens. They are host generalists able to feed on more than 300 vertebrate species. The prevalence of tick-borne pathogens is influenced by host-vector-pathogen interactions that results in spatial distribution of infection risk. Broad-range polymerase chain reaction electrospray ionization mass spectrometry (PCR/ESI-MS) was used to analyze 435 I. ricinus nymphs from four localities in the south of the Czech Republic for the species identification of tick-borne pathogens. Borrelia burgdorferi sensu lato spirochetes were the most common pathogen detected in the ticks; 21% of ticks were positive for a single genospecies and 2% were co-infected with two genospecies. Other tick-borne pathogens detected included Rickettsia helvetica (3.9%), R. monacensis (0.2%), Anaplasma phagocytophilum (2.8%), Babesia venatorum (0.9%), and Ba. microti (0.5%). The vertebrate host of the ticks was determined using PCR followed by reverse line blot hybridization from the tick's blood-meal remnants. The host was identified for 61% of ticks. DNA of two hosts was detected in 16% of samples with successful host identification. The majority of ticks had fed on artiodactyls (50.7%) followed by rodents (28.6%) and birds (7.8%). Other host species were wild boar, deer, squirrels, field mice and voles.
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http://dx.doi.org/10.1093/femsec/fix129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812510PMC
November 2017

Step Up-Not On-The Step 2 Clinical Skills Exam: Directors of Clinical Skills Courses (DOCS) Oppose Ending Step 2 CS.

Acad Med 2018 05;93(5):693-698

D.J. Ecker is assistant professor of medicine, assistant director of education, Hospital Medicine Group, and director, Integrated Clinicians Course, University of Colorado School of Medicine, Aurora, Colorado, and chair, Advocacy and Advancement Subcommittee, Directors of Clinical Skills Courses (DOCS); ORCID: http://orcid.org/0000-0002-1530-0079. F.B. Milan is professor of medicine and director, Ruth L. Gottesman Clinical Skills Center and Introduction to Clinical Medicine Program, Albert Einstein College of Medicine, Bronx, New York, and president, Directors of Clinical Skills Courses (DOCS). T. Cassese is associate professor of medical science and director, Clinical Arts and Sciences Course, Frank H. Netter MD School of Medicine, Quinnipiac University, North Haven, Connecticut, and president-elect, Directors of Clinical Skills Courses (DOCS). J.M. Farnan is assistant dean, Curricular Innovation and Evaluation, associate professor of medicine, and director, Clinical Skills Education, University of Chicago Pritzker School of Medicine, Chicago, Illinois, and secretary, Directors of Clinical Skills Courses (DOCS); ORCID: http://orcid.org/0000-0002-1138-9416. W.S. Madigosky is associate professor of family medicine and director, Foundations of Doctoring Curriculum, University of Colorado School of Medicine, Aurora, Colorado, and chair, Nominations Subcommittee, Directors of Clinical Skills Courses (DOCS); ORCID: http://orcid.org/0000-0003-0714-4114. F.S. Massie Jr is professor of medicine, director, Introduction to Clinical Medicine Curriculum, and director, Clinical Skills Scholars Program, University of Alabama School of Medicine, Birmingham, Alabama, and past president (2014-2015), Directors of Clinical Skills Courses (DOCS). P. Mendez is associate dean, Clinical Curriculum, associate professor of medicine, and director, Clinical Skills Program, University of Miami Miller School of Medicine, Miami, Florida, and representative, Southern Group on Educational Affairs, Directors of Clinical Skills Courses (DOCS). S. Obadia is associate dean, Clinical Education and Services, associate professor of internal medicine, and codirector, Medical Skills Courses, A.T. Still University, School of Osteopathic Medicine, Mesa, Arizona, and chair, Program Planning Subcommittee, Directors of Clinical Skills Courses (DOCS). R.K. Ovitsh is assistant dean, Clinical Competencies, and assistant professor of pediatrics, State University of New York Downstate School of Medicine, Brooklyn, New York, and representative, Northeast Group on Educational Affairs, Directors of Clinical Skills Courses (DOCS). R. Silvestri is assistant professor of medicine and site director, Practice of Medicine Clinical Skills Course, Harvard Medical School, Boston, Massachusetts, and chair, Research Subcommittee, Directors of Clinical Skills Courses (DOCS). T. Uchida is associate professor of medicine and medical education and director, Clinical Skills Education, Northwestern University Feinberg School of Medicine, Chicago, Illinois, and treasurer, Directors of Clinical Skills Courses (DOCS). M. Daniel is assistant dean, Curriculum, and assistant professor of emergency medicine and learning and health sciences, University of Michigan Medical School, Ann Arbor, Michigan, and past president (2015-2016), Directors of Clinical Skills Courses (DOCS); ORCID: http://orcid.org/0000-0001-8961-7119.

Recently, a student-initiated movement to end the United States Medical Licensing Examination Step 2 Clinical Skills and the Comprehensive Osteopathic Medical Licensing Examination Level 2-Performance Evaluation has gained momentum. These are the only national licensing examinations designed to assess clinical skills competence in the stepwise process through which physicians gain licensure and certification. Therefore, the movement to end these examinations and the ensuing debate merit careful consideration. The authors, elected representatives of the Directors of Clinical Skills Courses, an organization comprising clinical skills educators in the United States and beyond, believe abolishing the national clinical skills examinations would have a major negative impact on the clinical skills training of medical students, and that forfeiting a national clinical skills competency standard has the potential to diminish the quality of care provided to patients. In this Perspective, the authors offer important additional background information, outline key concerns regarding the consequences of ending these national clinical skills examinations, and provide recommendations for moving forward: reducing the costs for students, exploring alternatives, increasing the value and transparency of the current examinations, recognizing and enhancing the strengths of the current examinations, and engaging in a national dialogue about the issue.
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http://dx.doi.org/10.1097/ACM.0000000000001874DOI Listing
May 2018

Tcf4 Regulates Synaptic Plasticity, DNA Methylation, and Memory Function.

Cell Rep 2016 09 25;16(10):2666-2685. Epub 2016 Aug 25.

Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address:

Human haploinsufficiency of the transcription factor Tcf4 leads to a rare autism spectrum disorder called Pitt-Hopkins syndrome (PTHS), which is associated with severe language impairment and development delay. Here, we demonstrate that Tcf4 haploinsufficient mice have deficits in social interaction, ultrasonic vocalization, prepulse inhibition, and spatial and associative learning and memory. Despite learning deficits, Tcf4(+/-) mice have enhanced long-term potentiation in the CA1 area of the hippocampus. In translationally oriented studies, we found that small-molecule HDAC inhibitors normalized hippocampal LTP and memory recall. A comprehensive set of next-generation sequencing experiments of hippocampal mRNA and methylated DNA isolated from Tcf4-deficient and WT mice before or shortly after experiential learning, with or without administration of vorinostat, identified "memory-associated" genes modulated by HDAC inhibition and dysregulated by Tcf4 haploinsufficiency. Finally, we observed that Hdac2 isoform-selective knockdown was sufficient to rescue memory deficits in Tcf4(+/-) mice.
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http://dx.doi.org/10.1016/j.celrep.2016.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710002PMC
September 2016

The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood.

PLoS One 2016 6;11(7):e0158186. Epub 2016 Jul 6.

Ibis Biosciences, an Abbott Company, Carlsbad, California, United States of America.

Unlabelled: Bloodstream infection (BSI) and sepsis are rising in incidence throughout the developed world. The spread of multi-drug resistant organisms presents increasing challenges to treatment. Surviving BSI is dependent on rapid and accurate identification of causal organisms, and timely application of appropriate antibiotics. Current culture-based methods used to detect and identify agents of BSI are often too slow to impact early therapy and may fail to detect relevant organisms in many positive cases. Existing methods for direct molecular detection of microbial DNA in blood are limited in either sensitivity (likely the result of small sample volumes) or in breadth of coverage, often because the PCR primers and probes used target only a few specific pathogens. There is a clear unmet need for a sensitive molecular assay capable of identifying the diverse bacteria and yeast associated with BSI directly from uncultured whole blood samples. We have developed a method of extracting DNA from larger volumes of whole blood (5 ml per sample), amplifying multiple widely conserved bacterial and fungal genes using a mismatch- and background-tolerant PCR chemistry, and identifying hundreds of diverse organisms from the amplified fragments on the basis of species-specific genetic signatures using electrospray ionization mass spectrometry (PCR/ESI-MS). We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. The assay generated matching results in 80% of culture-positive cases (86% when common contaminants were excluded from the analysis), and twice the total number of positive detections. The described method is capable of providing organism identifications directly from uncultured blood in less than 8 hours.

Disclaimer: The IRIDICA BAC BSI Assay is not available in the United States.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158186PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934770PMC
July 2017

Rapid Molecular Diagnostics, Antibiotic Treatment Decisions, and Developing Approaches to Inform Empiric Therapy: PRIMERS I and II.

Clin Infect Dis 2016 Jan 25;62(2):181-9. Epub 2015 Sep 25.

Department of Medicine, Case Western Reserve University School of Medicine Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio.

Background: Rapid molecular diagnostic (RMD) platforms may lead to better antibiotic use. Our objective was to develop analytical strategies to enhance the interpretation of RMDs for clinicians.

Methods: We compared the performance characteristics of 4 RMD platforms for detecting resistance against β-lactams in 72 highly resistant isolates of Escherichia coli and Klebsiella pneumoniae (PRIMERS I). Subsequently, 2 platforms were used in a blinded study in which a heterogeneous collection of 196 isolates of E. coli and K. pneumoniae (PRIMERS II) were examined. We evaluated the genotypic results as predictors of resistance or susceptibility against β-lactam antibiotics. We designed analytical strategies and graphical representations of platform performance, including discrimination summary plots and susceptibility and resistance predictive values, that are readily interpretable by practitioners to inform decision-making.

Results: In PRIMERS I, the 4 RMD platforms detected β-lactamase (bla) genes and identified susceptibility or resistance in >95% of cases. In PRIMERS II, the 2 platforms identified susceptibility against extended-spectrum cephalosporins and carbapenems in >90% of cases; however, against piperacillin/tazobactam, susceptibility was identified in <80% of cases. Applying the analytical strategies to a population with 15% prevalence of ceftazidime-resistance and 5% imipenem-resistance, RMD platforms predicted susceptibility in >95% of cases, while prediction of resistance was 69%-73% for ceftazidime and 41%-50% for imipenem.

Conclusions: RMD platforms can help inform empiric β-lactam therapy in cases where bla genes are not detected and the prevalence of resistance is known. Our analysis is a first step in bridging the gap between RMDs and empiric treatment decisions.
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http://dx.doi.org/10.1093/cid/civ837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690483PMC
January 2016

Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species.

PLoS One 2015 16;10(9):e0135828. Epub 2015 Sep 16.

Ibis Biosciences, an Abbott Company, Carlsbad CA, United States of America.

Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called 'Candidatus Cryptoplasma californiense'. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135828PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574436PMC
May 2016

Rapid Diagnosis of Infection in the Critically Ill, a Multicenter Study of Molecular Detection in Bloodstream Infections, Pneumonia, and Sterile Site Infections.

Crit Care Med 2015 Nov;43(11):2283-91

1Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium. 2Division of Critical Care, University College London Hospitals NIHR Biomedical Research Centre and Bloomsbury Institute of Intensive Care Medicine, University College Hospital, London, United Kingdom. 3Department of Anesthesiology and Critical Care, Val de Grâce Military Hospital, Paris, France. 4Intensive Care Unit, Department of Anesthesiology, Pharmacology and Intensive Care, University Hospitals of Geneva, Geneva, Switzerland. 5Barts and The London School of Medicine and Dentistry, Queen Mary University of London and Barts Health NHS Trust, London, United Kingdom. 6Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany. 71st Clinic of Anaesthesia and Intensive Care of Warsaw Medical University, Warsaw, Poland. 8Genomic Research Laboratory, Department of Internal Medicine, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland. 9Department of Microbiology, Saint Louis University Hospital, Paris, France. 10Abbott GmbH & Co. KG, Wiesbaden, Germany. 11Ibis Biosciences, Abbott, Carlsbad, CA.

Objective: Early identification of causative microorganism(s) in patients with severe infection is crucial to optimize antimicrobial use and patient survival. However, current culture-based pathogen identification is slow and unreliable such that broad-spectrum antibiotics are often used to insure coverage of all potential organisms, carrying risks of overtreatment, toxicity, and selection of multidrug-resistant bacteria. We compared the results obtained using a novel, culture-independent polymerase chain reaction/electrospray ionization-mass spectrometry technology with those obtained by standard microbiological testing and evaluated the potential clinical implications of this technique.

Design: Observational study.

Setting: Nine ICUs in six European countries.

Patients: Patients admitted between October 2013 and June 2014 with suspected or proven bloodstream infection, pneumonia, or sterile fluid and tissue infection were considered for inclusion.

Interventions: None.

Measurements And Main Results: We tested 616 bloodstream infection, 185 pneumonia, and 110 sterile fluid and tissue specimens from 529 patients. From the 616 bloodstream infection samples, polymerase chain reaction/electrospray ionization-mass spectrometry identified a pathogen in 228 cases (37%) and culture in just 68 (11%). Culture was positive and polymerase chain reaction/electrospray ionization-mass spectrometry negative in 13 cases, and both were negative in 384 cases, giving polymerase chain reaction/electrospray ionization-mass spectrometry a sensitivity of 81%, specificity of 69%, and negative predictive value of 97% at 6 hours from sample acquisition. The distribution of organisms was similar with both techniques. Similar observations were made for pneumonia and sterile fluid and tissue specimens. Independent clinical analysis of results suggested that polymerase chain reaction/electrospray ionization-mass spectrometry technology could potentially have resulted in altered treatment in up to 57% of patients.

Conclusions: Polymerase chain reaction/electrospray ionization-mass spectrometry provides rapid pathogen identification in critically ill patients. The ability to rule out infection within 6 hours has potential clinical and economic benefits.
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http://dx.doi.org/10.1097/CCM.0000000000001249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603364PMC
November 2015

CMS Reimbursement Reform.

J Gen Intern Med 2015 Nov;30(11):1587

Department of Internal Medicine Division of Pulmonary and Critical Care Medicine, University of South Florida, Tampa, FL, USA.

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http://dx.doi.org/10.1007/s11606-015-3464-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617944PMC
November 2015

Prevalence of Borrelia miyamotoi in Ixodes ticks in Europe and the United States.

Emerg Infect Dis 2014 Oct;20(10):1678-82

Borrelia miyamotoi, a relapsing fever-related spirochete transmitted by Ixodes ticks, has been recently shown to be a human pathogen. To characterize the prevalence of this organism in questing Ixodes ticks, we tested 2,754 ticks for a variety of tickborne pathogens by PCR and electrospray-ionization mass spectrometry. Ticks were collected from California, New York, Connecticut, Pennsylvania, and Indiana in the United States and from Germany and the Czech Republic in Europe from 2008 through 2012. In addition, an isolate from Japan was characterized. We found 3 distinct genotypes, 1 for North America, 1 for Europe, and 1 for Japan. We found B. miyamotoi infection in ticks in 16 of the 26 sites surveyed, with infection prevalence as high as 15.4%. These results show the widespread distribution of the pathogen, indicating an exposure risk to humans in areas where Ixodes ticks reside.
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http://dx.doi.org/10.3201/eid2010.131583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193165PMC
October 2014

Broad-range survey of tick-borne pathogens in Southern Germany reveals a high prevalence of Babesia microti and a diversity of other tick-borne pathogens.

Vector Borne Zoonotic Dis 2014 Aug;14(8):584-91

1 Ibis Biosciences an Abbott company , Carlsbad, California.

Abstract Ticks harbor numerous pathogens of significance to human and animal health. A better understanding of the pathogens carried by ticks in a given geographic area can alert health care providers of specific health risks leading to better diagnosis and treatments. In this study, we tested 226 Ixodes ricinis ticks from Southern Germany using a broad-range PCR and electrospray ionization mass spectrometry assay (PCR/ESI-MS) designed to identify tick-borne bacterial and protozoan pathogens in a single test. We found 21.2% of the ticks tested carried Borrelia burgdorferi sensu lato consisting of diverse genospecies; a surprisingly high percentage of ticks were infected with Babesia microti (3.5%). Other organisms found included Borrelia miyamotoi, Rickettsia helvetica, Rickettsia monacensis, and Anaplasma phagocytophilum. Of further significance was our finding that more than 7% of ticks were infected with more than one pathogen or putative pathogen.
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http://dx.doi.org/10.1089/vbz.2013.1498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117270PMC
August 2014

Germ catcher.

Authors:
David J Ecker

Sci Am 2014 Jun;310(6):50-5

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http://dx.doi.org/10.1038/scientificamerican0614-50DOI Listing
June 2014

Improved sensitivity for molecular detection of bacterial and Candida infections in blood.

J Clin Microbiol 2014 Sep 20;52(9):3164-74. Epub 2014 Jun 20.

Ibis Biosciences, Inc., Carlsbad, California, USA

The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.
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http://dx.doi.org/10.1128/JCM.00801-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313132PMC
September 2014

Rapid PCR/ESI-MS-based molecular genotyping of Staphylococcus aureus from nasal swabs of emergency department patients.

BMC Infect Dis 2014 Jan 9;14:16. Epub 2014 Jan 9.

Department of Community Health and Prevention, Drexel University School of Public Health, Philadelphia, PA, USA.

Background: A limitation of both culture-based and molecular methods of screening for staphylococcal infection is that current tests determine only the presence or absence of colonization with no information on the colonizing strain type. A technique that couples polymerase chain reaction to mass spectrometry (PCR/ESI-MS) has recently been developed and an assay validated to identify and genotype S. aureus and coagulase-negative staphylococci (CoNS).

Methods: This study was conducted to determine the rates, risk factors, and molecular genotypes of colonizing Staphylococcus aureus in adult patients presenting to an inner-city academic emergency department. Participants completed a structured questionnaire to assess hospital and community risks for infection with methicillin-resistant S. aureus (MRSA). Nasal swabs were analyzed by PCR/ESI-MS to identify and genotype S. aureus and CoNS.

Results: Of 200 patients evaluated, 59 were colonized with S. aureus; 27 of these were methicillin-resistant strains. Twenty-four of the 59 S. aureus carriers were co-colonized with a CoNS and 140 of the 200 patients were colonized exclusively with CoNS. The molecular genotypes of the 59 S. aureus strains were diverse; 21 unique molecular genotypes belonging to seven major clonal complexes were identified. Eighty-five of 200 patients carried strains with high-level mupirocin resistance. Of these eighty-five participants, 4 were colonized exclusively with S. aureus, 16 were co-colonized with S. aureus and CoNS, and 65 were colonized exclusively with CoNS.

Conclusion: The prevalence of S. aureus and methicillin-resistant S. aureus colonization in a random sample of patients seeking care in Emergency Department was 29.5% and 13.5%, respectively. A substantial fraction of the S. aureus-colonized patients were co-colonized with CoNS and high-level mupirocin-resistant CoNS. Determining the molecular genotype of S. aureus during intake screening may prove valuable in the future if certain molecular genotypes become associated with increased infection risk.
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http://dx.doi.org/10.1186/1471-2334-14-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937163PMC
January 2014

Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry.

J Clin Virol 2014 Feb 27;59(2):115-9. Epub 2013 Nov 27.

Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China. Electronic address:

Background: Rapid detection and identification of viruses are important for early diagnosis and effective surveillance of hand, foot, and mouth disease (HFMD). We described a novel assay using multilocus PCR and reverse transcription-PCR coupled with electrospray ionization mass spectrometry (RT-PCR/ESI-MS) to simultaneously detect and identify human enterovirus A-D, adenovirus A-F, human herpesvirus 1-8, parvovirus B19 and polyomavirus.

Objectives: To evaluate the accuracy and efficacy of the RT-PCR/ESI-MS method, to detect and type enterovirus from specimens of clinical diagnosed HFMD patients.

Study Design: In this study, 152 specimens of clinically diagnosed HFMD patients were studied by the assay using RT-PCR/ESI-MS method. The detection and typing of enterovirus by RT-PCR/ESI-MS were compared with results from reference molecular methods.

Results: The assay detected enteroviruses in 97 (63.8%) specimens, resulting in a sensitivity of 93.8% (95% CI: 91.8-95.7%) and a specificity of 87.5% (95% CI: 84.8-90.2%) compared with a reference clinical diagnostic test. Most enterovirus genotypes (65/84; 77%) determined by the platform were consistent with 5' UTR sequence analysis, and most misidentifications resulted from the virus library, which could be further improved by updating the enterovirus database. In addition to enteroviruses, herpesviruses, polyomaviruses, adenoviruses and human rhinoviruses were detected and identified in 55 (36%) HFMD specimens by RT-PCR/ESI-MS.

Conclusion: With the capability of high throughput and detection and typing of multiple clinically relevant viruses simultaneously, RT-PCR/ESI-MS can be a rapid and robust laboratory tool for identifying viral pathogens.
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http://dx.doi.org/10.1016/j.jcv.2013.11.007DOI Listing
February 2014

Achieving molecular diagnostics for Lyme disease.

Expert Rev Mol Diagn 2013 Nov;13(8):875-83

Ibis Biosciences Inc., an Abbott Company, 2251 Faraday Ave, Carlsbad, CA 92008, USA.

Early Lyme disease is often difficult to diagnose. Left untreated, symptoms can last for many years leading to chronic health problems. Serological tests for the presence of antibodies that react to Borrelia burgdorferi antigens are generally used to support a clinical diagnosis. Due to the biologically delayed antibody response, serology is negative in many patients in the initial 3 weeks after infection and a single test cannot be used to demonstrate active disease, although certain specialized tests provide strong correlation. Because of these limitations there exists a need for better diagnostics for Lyme disease that can detect Borrelia genomic material at the onset of symptoms.
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http://dx.doi.org/10.1586/14737159.2013.850418DOI Listing
November 2013

The value and validation of broad spectrum biosensors for diagnosis and biodefense.

Virulence 2013 Nov 9;4(8):752-8. Epub 2013 Oct 9.

Ibis Biosciences; An Abbott Company; Carlsbad, CA USA.

Broad spectrum biosensors capable of identifying diverse organisms are transitioning from the realm of research into the clinic. These technologies simultaneously capture signals from a wide variety of biological entities using universal processes. Specific organisms are then identified through bioinformatic signature-matching processes. This is in contrast to currently accepted molecular diagnostic technologies, which utilize unique reagents and processes to detect each organism of interest. This paradigm shift greatly increases the breadth of molecular diagnostic tools with little increase in biochemical complexity, enabling simultaneous diagnostic, epidemiologic, and biothreat surveillance capabilities at the point of care. This, in turn, offers the promise of increased biosecurity and better antimicrobial stewardship. Efficient realization of these potential gains will require novel regulatory paradigms reflective of the generalized, information-based nature of these assays, allowing extension of empirical data obtained from readily available organisms to support broader reporting of rare, difficult to culture, or extremely hazardous organisms.
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http://dx.doi.org/10.4161/viru.26652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925709PMC
November 2013

Enhanced diagnostic yields of bacteremia and candidemia in blood specimens by PCR-electrospray ionization mass spectrometry.

J Clin Microbiol 2013 Nov 21;51(11):3535-41. Epub 2013 Aug 21.

Ibis Biosciences, Carlsbad, California, USA.

A prospective study was performed to determine the value of direct molecular testing of whole blood for detecting the presence of culturable and unculturable bacteria and yeasts in patients with suspected bloodstream infections. A total of 464 adult and pediatric patients with positive blood cultures matched with 442 patients with negative blood cultures collected during the same period were recruited during a 10-month study. PCR amplification coupled with electrospray ionization mass spectrometry (PCR-ESI-MS) plus blood culture reached an overall agreement of 78.6% in the detection and species-level identification of bacterial and candidal pathogens. Of 33 culture-negative/PCR-ESI-MS-positive specimens, 31 (93.9%) were judged to be truly bacteremic and/or candidemic based on a medical chart review and analytical metrics. Among the 15 culture-positive specimens in which PCR-ESI-MS detected additional bacterial or yeast species, 66.7% and 20.0% of the additional positive specimens by PCR-ESI-MS were judged to be truly or possibly bacteremic and/or candidemic, respectively. Direct analysis of blood samples by PCR-ESI-MS rapidly detects bacterial and yeast pathogens in patients with bloodstream infections. When used in conjunction with blood culture, PCR-ESI-MS enhances the diagnostics of septicemia by shortening test turnaround time and improving yields.
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http://dx.doi.org/10.1128/JCM.00876-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889730PMC
November 2013

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

J Clin Microbiol 2013 Oct 24;51(10):3263-9. Epub 2013 Jul 24.

University of Maryland, School of Medicine, Baltimore, Maryland, USA.

Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens.
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http://dx.doi.org/10.1128/JCM.01342-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811648PMC
October 2013

"Salvage microbiology": detection of bacteria directly from clinical specimens following initiation of antimicrobial treatment.

PLoS One 2013 25;8(6):e66349. Epub 2013 Jun 25.

University of Illinois School of Medicine, Department of Medicine, Peoria, Illinois, United States of America.

Background: PCR coupled with electrospray ionization mass spectrometry (ESI-MS) is a diagnostic approach that has demonstrated the capacity to detect pathogenic organisms from culture negative clinical samples after antibiotic treatment has been initiated. [1] We describe the application of PCR/ESI-MS for detection of bacteria in original patient specimens that were obtained after administration of antibiotic treatment in an open investigation analysis.

Methods: We prospectively identified cases of suspected bacterial infection in which cultures were not obtained until after the initiation of antimicrobial treatment. PCR/ESI-MS was performed on 76 clinical specimens that were submitted for conventional microbiology testing from 47 patients receiving antimicrobial treatment.

Findings: In our series, 72% (55/76) of cultures obtained following initiation of antimicrobial treatment were non-diagnostic (45 negative cultures; and 10 respiratory specimens with normal flora (5), yeast (4), or coagulase-negative staphylococcus (1)). PCR/ESR-MS detected organisms in 83% (39/47) of cases and 76% (58/76) of the specimens. Bacterial pathogens were detected by PCR/ESI-MS in 60% (27/45) of the specimens in which cultures were negative. Notably, in two cases of relapse of prosthetic knee infections in patients on chronic suppressive antibiotics, the previous organism was not recovered in tissue cultures taken during extraction of the infected knee prostheses, but was detected by PCR/ESI-MS.

Conclusion: Molecular methods that rely on nucleic acid amplification may offer a unique advantage in the detection of pathogens collected after initiation of antimicrobial treatment and may provide an opportunity to target antimicrobial therapy and "salvage" both individual treatment regimens as well as, in select cases, institutional antimicrobial stewardship efforts.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066349PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692526PMC
February 2014

Broad-spectrum biosensor capable of detecting and identifying diverse bacterial and Candida species in blood.

J Clin Microbiol 2013 Aug 12;51(8):2670-8. Epub 2013 Jun 12.

Ibis Biosciences, A Division of Abbott, Carlsbad, California, USA.

We describe an assay which uses broad-spectrum, conserved-site PCR paired with mass spectrometry analysis of amplicons (PCR/electrospray ionization-mass spectrometry [ESI-MS]) to detect and identify diverse bacterial and Candida species in uncultured specimens. The performance of the assay was characterized using whole-blood samples spiked with low titers of 64 bacterial species and 6 Candida species representing the breadth of coverage of the assay. The assay had an average limit of detection of 100 CFU of bacteria or Candida per milliliter of blood, and all species tested yielded limits of detection between 20 and 500 CFU per milliliter. Over 99% of all detections yielded correct identifications, whether they were obtained at concentrations well above the limit of detection or at the lowest detectable concentrations. This study demonstrates the ability of broad-spectrum PCR/ESI-MS assays to detect and identify diverse organisms in complex natural matrices that contain high levels of background DNA.
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http://dx.doi.org/10.1128/JCM.00966-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719611PMC
August 2013

Molecular genotyping of Acinetobacter spp. isolated in Arizona, USA, using multilocus PCR and mass spectrometry.

J Med Microbiol 2013 Sep 5;62(Pt 9):1295-1300. Epub 2013 Jun 5.

Northern Arizona University, Center for Microbial Genetics and Genomics, Flagstaff, AZ 86011, USA.

Acinetobacter spp. are a diverse group of Gram-negative bacteria frequently implicated in nosocomial infections. Genotypic methods have been instrumental in studying Acinetobacter, but few offer high resolution, rapid turnaround time, technical ease and high inter-laboratory reproducibility, which has hampered understanding of disease incidence, transmission patterns and diversity within this genus. Here, we further evaluated multilocus PCR electrospray ionization/mass spectrometry (PCR/ESI-MS), a method that is simple and robust, and provides both species characterization and strain-level resolution of Acinetobacter spp. on a single platform. We examined 125 Acinetobacter isolates from 21 hospitals, laboratories and medical centres spanning four counties in Arizona, USA, using PCR/ESI-MS. We compared PCR/ESI-MS with an in-house amplified fragment length polymorphism (AFLP) genotyping scheme. PCR/ESI-MS demonstrated that Acinetobacter spp. from Arizonan hospitals had similar species and strain distributions to other US civilian hospitals. Furthermore, we showed that the PCR/ESI-MS and AFLP genotypes were highly congruent, with the former having the advantages of robust inter-laboratory reproducibility, rapid turnaround time and simple experimental set-up and data analysis. PCR/ESI-MS is an effective and high-throughput platform for strain typing of Acinetobacter baumannii and for identification of other Acinetobacter spp., including the emerging nosocomial pathogens Acinetobacter pittii and Acinetobacter nosocomialis.
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http://dx.doi.org/10.1099/jmm.0.052381-0DOI Listing
September 2013

Rapid diagnosis of bloodstream infections with PCR followed by mass spectrometry.

PLoS One 2013 23;8(4):e62108. Epub 2013 Apr 23.

Microbiology Department, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.

Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062108PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633912PMC
November 2013

Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis.

J Dairy Sci 2013 Jun 12;96(6):3611-20. Epub 2013 Apr 12.

Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Bovine mastitis, an inflammatory disease of the mammary gland, is one of the most costly diseases affecting the dairy industry. The treatment and prevention of this disease is linked heavily to the use of antibiotics in agriculture and early detection of the primary pathogen is essential to control the disease. Milk samples (n=67) from cows suffering from mastitis were analyzed for the presence of pathogens using PCR electrospray-ionization mass spectrometry (PCR/ESI-MS) and were compared with standard culture diagnostic methods. Concurrent identification of the primary mastitis pathogens was obtained for 64% of the tested milk samples, whereas divergent results were obtained for 27% of the samples. The PCR/ESI-MS failed to identify some of the primary pathogens in 18% of the samples, but identified other pathogens as well as microorganisms in samples that were negative by culture. The PCR/ESI-MS identified bacteria to the species level as well as yeasts and molds in samples that contained a mixed bacterial culture (9%). The sensitivity of the PCR/ESI-MS for the most common pathogens ranged from 57.1 to 100% and the specificity ranged from 69.8 to 100% using culture as gold standard. The PCR/ESI-MS also revealed the presence of the methicillin-resistant gene mecA in 16.2% of the milk samples, which correlated with the simultaneous detection of staphylococci including Staphylococcus aureus. We demonstrated that PCR/ESI-MS, a more rapid diagnostic platform compared with bacterial culture, has the significant potential to serve as an important screening method in the diagnosis of bovine clinical mastitis and has the capacity to be used in infection control programs for both subclinical and clinical disease.
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http://dx.doi.org/10.3168/jds.2012-6124DOI Listing
June 2013

PCR followed by electrospray ionization mass spectrometry for broad-range identification of fungal pathogens.

J Clin Microbiol 2013 Mar 9;51(3):959-66. Epub 2013 Jan 9.

Ibis Biosciences, Abbott Laboratories, Carlsbad, California, USA.

Invasive fungal infections are a significant cause of morbidity and mortality among immunocompromised patients. Early and accurate identification of these pathogens is central to direct therapy and to improve overall outcome. PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) was evaluated as a novel means for identification of fungal pathogens. Using a database grounded by 60 ATCC reference strains, a total of 394 clinical fungal isolates (264 molds and 130 yeasts) were analyzed by PCR/ESI-MS; results were compared to phenotypic identification, and discrepant results were sequence confirmed. PCR/ESI-MS identified 81.4% of molds to either the genus or species level, with concordance rates of 89.7% and 87.4%, respectively, to phenotypic identification. Likewise, PCR/ESI-MS was able to identify 98.4% of yeasts to either the genus or species level, agreeing with 100% of phenotypic results at both the genus and species level. PCR/ESI-MS performed best with Aspergillus and Candida isolates, generating species-level identification in 94.4% and 99.2% of isolates, respectively. PCR/ESI-MS is a promising new technology for broad-range detection and identification of medically important fungal pathogens that cause invasive mycoses.
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http://dx.doi.org/10.1128/JCM.02621-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592073PMC
March 2013