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Article ; Online: A Comparison of Culture Results and Visual Acuity in Contact Lens Related Microbial Keratitis.

Hart, Jenna N / Lu, Ming-Chen / Tracey, Breanna M / Miller, Keith D / Lephart, Paul R / Mian, Shahzad I / Woodward, Maria A

Current eye research

2024 Volume 49, Issue 1, Page(s) 39–45

Abstract: Purpose: Evaluate the effect of corneal and contact lens-related (CLR) culture results on visual acuity (VA) in patients with microbial keratitis (MK).: Methods: MK patients with corneal and CLR cultures were identified in the University of Michigan ... ...

Abstract	Purpose: Evaluate the effect of corneal and contact lens-related (CLR) culture results on visual acuity (VA) in patients with microbial keratitis (MK). Methods: MK patients with corneal and CLR cultures were identified in the University of Michigan electronic health record from August 2012 to April 2022. Test results were classified as laboratory-positive or laboratory-negative. Linear regression was used to examine trends of VA and associations between changes in VA (differences of VA at 90-day and baseline VA) and corneal and CLR culture results, after adjustment for baseline VA. One-sample t-tests were used to test if the slope estimates were different from zero. Results: MK patients ( Conclusions: Positive CLR cultures are associated with significant improvement in VA over time. These additional cultures can provide guidance on appropriate antimicrobial selection, especially when corneal cultures are negative.
MeSH term(s)	Humans ; Female ; Middle Aged ; Male ; Corneal Ulcer/diagnosis ; Corneal Ulcer/drug therapy ; Eye Infections, Bacterial/diagnosis ; Eye Infections, Bacterial/drug therapy ; Retrospective Studies ; Keratitis/diagnosis ; Contact Lenses ; Visual Acuity
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	82079-9
ISSN	1460-2202 ; 0271-3683
ISSN (online)	1460-2202
ISSN	0271-3683
DOI	10.1080/02713683.2023.2269322
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Article ; Online: Factors Associated With Laboratory Test Negativity Following a Transition in Specimen Collection in Microbial Keratitis Cases.

Miller, Keith D / Toiv, Avi / Deng, Callie / Lu, Ming-Chen / Niziol, Leslie M / Hart, Jenna N / Sherman, Eric / Mian, Shahzad I / Lephart, Paul R / Sugar, Alan / Kang, Linda / Woodward, Maria A

Current eye research

2024 Volume 49, Issue 4, Page(s) 339–344

Abstract: Purpose: Negative laboratory results make targeting microbial keratitis treatment difficult. We investigated factors associated with laboratory negativity in patients with microbial keratitis in the context of a transition to a new specimen collection ... ...

Abstract	Purpose: Negative laboratory results make targeting microbial keratitis treatment difficult. We investigated factors associated with laboratory negativity in patients with microbial keratitis in the context of a transition to a new specimen collection method. Methods: Microbial keratitis patients with associated laboratory tests were identified in the electronic health record of a tertiary care facility from August 2012 to April 2022. Patient demographics and laboratory results were obtained. Random sampling of 50% of charts was performed to assess the impact of the ocular history and pretreatment measures. The relationship between probability of negative laboratory results with demographics, ocular history, pretreatment measures, and utilization of a new specimen collection method (i.e. ESwab) was evaluated by multivariable logistic regression. Results: Of 3395 microbial keratitis patients identified, 31% ( Conclusion: More microbial keratitis associated laboratory tests are being taken over time. Over 60% of tests were negative by 2022. Factors associated with negative laboratory test results included pretreatment with antibiotics and specimens collected with the new collection method.
MeSH term(s)	Humans ; Corneal Ulcer/drug therapy ; Retrospective Studies ; Keratitis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Specimen Handling ; Risk Factors ; Eye Infections, Bacterial/diagnosis ; Eye Infections, Bacterial/drug therapy
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	82079-9
ISSN	1460-2202 ; 0271-3683
ISSN (online)	1460-2202
ISSN	0271-3683
DOI	10.1080/02713683.2023.2294700
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Article ; Online: Microbial Keratitis Isolates at a Midwestern Tertiary Eye Care Center.

Kang, Linda / Lu, Ming-Chen / Niziol, Leslie M / Greenwald, Miles F / Mian, Shahzad I / Thibodeau, Alexa / Pawar, Mercy / Lephart, Paul R / Woodward, Maria A

Cornea

2023 Volume 42, Issue 12, Page(s) 1488–1496

Abstract: Purpose: The aim of the study was to describe the pathogen, antimicrobial susceptibility, and trends over time of microbial keratitis (MK) at a Midwestern tertiary eye center.: Methods: Patients with MK were identified in the electronic health record ...

Abstract	Purpose: The aim of the study was to describe the pathogen, antimicrobial susceptibility, and trends over time of microbial keratitis (MK) at a Midwestern tertiary eye center. Methods: Patients with MK were identified in the electronic health record from August 2012 to December 2021. Diagnostic laboratory tests with an MK diagnosis were identified and classified as laboratory positive or laboratory negative. Laboratory-positive infections were categorized as bacterial (gram-positive, gram-negative, or acid-fast bacilli), fungal, viral, Acanthamoeba , or polymicrobial. Antimicrobial susceptibilities were obtained. Trends over time were assessed using linear regression. Results: Of 3288 patients with MK identified, 1012 (30.8%) had laboratory tests performed. Laboratory-positive infections (n = 499, 49.3%) were bacterial in 73.5% (n = 367) of cases, fungal in 7.8% (n = 39), viral in 1.6% (n = 8), Acanthamoeba in 1.4% (n = 7), and polymicrobial in 15.6% (n = 78). Of bacterial infections, 70% (n = 257) were gram-positive, with coagulase-negative Staphylococcus (CoNS; 31%) and Staphylococcus aureus ( S. aureus 23%) as the most common pathogens. Bacteria were acid-fast bacilli in 1.9% (n = 7) of cases and gram-negative in 28.1% (n = 103), with Pseudomonas aeruginosa as the predominant pathogen (47.7%). S. aureus showed antibiotic resistance from 0% (vancomycin and gentamicin) to 50% (erythromycin); CoNS from 0% (vancomycin, gentamicin, and moxifloxacin) to 64% (erythromycin). The rate of laboratory-negative MK significantly increased over time (slope estimate = 2.1% per year, P = 0.034). Rates of bacterial, fungal, viral, Acanthamoeba , and polymicrobial infections were stable over time (all slope P > 0.05). Conclusions: Bacterial keratitis accounted for most MK cases. Gram-positive bacteria were the most common isolates. CoNS and S. aureus were universally susceptible to vancomycin. Rates of MK infection types were stable over time.
MeSH term(s)	Humans ; Anti-Bacterial Agents/therapeutic use ; Vancomycin ; Staphylococcus aureus ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Keratitis/microbiology ; Bacteria ; Eye Infections, Bacterial/microbiology ; Gentamicins ; Erythromycin ; Retrospective Studies
Chemical Substances	Anti-Bacterial Agents ; Vancomycin (6Q205EH1VU) ; Gentamicins ; Erythromycin (63937KV33D)
Language	English
Publishing date	2023-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	604826-2
ISSN	1536-4798 ; 0277-3740
ISSN (online)	1536-4798
ISSN	0277-3740
DOI	10.1097/ICO.0000000000003198
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Zs.A 1790: Show issues

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Article: Predicting Direct-Specimen SARS-CoV-2 Assay Performance Using Residual Patient Samples.

Schroeder, Lee F / Bachman, Michael A / Idoni, Allison / Gegenheimer-Holmes, Jennifer / Kronick, Steven L / Valdez, Riccardo / Lephart, Paul R

The journal of applied laboratory medicine

2021 Volume 7, Issue 3, Page(s) 661–673

Abstract: Background: Diagnostic sensitivities of point-of-care SARS-CoV-2 assays depend on specimen type and population-specific viral loads. Evaluation of these assays require "direct" specimens from paired-swab studies rather than more accessible residual ... ...

Abstract	Background: Diagnostic sensitivities of point-of-care SARS-CoV-2 assays depend on specimen type and population-specific viral loads. Evaluation of these assays require "direct" specimens from paired-swab studies rather than more accessible residual specimens in viral transport media (VTM). Methods: Residual VTM and limit-of-detection studies were conducted on Abbott ID NOW™ COVID-19, Quidel Sofia 2™ SARS Antigen FIA, and DiaSorin Simplexa™ COVID-19 Direct assays, with cycle threshold (CT) adjustments to approximate direct-specimen testing based on gene-target doubling each PCR cycle. Logistic regression was used to model assay performance by specimen CT. These models were applied to CT distributions of symptomatic and asymptomatic populations presenting to emergency services to predict the percentage of specimens that would be detected by each assay. A 96-sample paired-swab study was conducted to confirm model results. Results: When using direct nasopharyngeal samples and fit with either VTM or limit-of-detection data, percent positivities for ID NOW (symptomatic 94.9%/97.4%; asymptomatic 88.4.0%/89.6%) and Simplexa (symptomatic 97.8%/97.2%; asymptomatic 91.1%/90.8%) were predicted to be similar. Likewise, percent positivities for ID NOW with direct nasal specimens (symptomatic 77.8%; asymptomatic 64.5%) and, fit with VTM data, Sofia 2 with direct nasopharyngeal specimens (symptomatic 76.6%, asymptomatic 60.3%) were similar. The paired-swab study comparing direct nasopharyngeal specimens on ID NOW and nasopharyngeal VTM specimens on Simplexa showed 99% concordance. Conclusions: Assay performance can be modeled as dependent on viral load, fit using laboratory bench study results, and adjusted to account for direct-specimen testing. When using nasopharyngeal specimens, direct testing on Abbott ID NOW and VTM testing on DiaSorin Simplexa have similar performance.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Disease Progression ; Humans ; Nasopharynx ; SARS-CoV-2 ; Sensitivity and Specificity
Language	English
Publishing date	2021-11-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2576-9456
ISSN	2576-9456
DOI	10.1093/jalm/jfab159
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Article ; Online: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type.

Lephart, Paul R / Bachman, Michael A / LeBar, William / McClellan, Scott / Barron, Karen / Schroeder, Lee / Newton, Duane W

Diagnostic microbiology and infectious disease

2020 Volume 99, Issue 1, Page(s) 115200

Abstract: The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA and were validated by laboratories and utilized clinically, all within a ... ...

Abstract	The COVID-19 pandemic in the United States created a unique situation where multiple molecular SARS-CoV-2 diagnostic assays rapidly received Emergency Use Authorization by the FDA and were validated by laboratories and utilized clinically, all within a period of a few weeks. We compared the performance of four of these assays that were evaluated for use at our institution: Abbott RealTime m2000 SARS-CoV-2 Assay, DiaSorin Simplexa COVID-19 Direct, Cepheid Xpert Xpress SARS-CoV-2, and Abbott ID NOW COVID-19. Nasopharyngeal and nasal specimens were collected from 88 ED and hospital-admitted patients and tested by the four methods in parallel to compare performance. ID NOW performance stood out as significantly worse than the other 3 assays despite demonstrating comparable analytic sensitivity. Further study determined that the use of a nasal swab compared to a nylon flocked nasopharyngeal swab, as well as use in a population chronically vs. acutely positive for SARS-CoV-2, were substantial factors.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Nucleic Acid Testing/methods ; COVID-19 Nucleic Acid Testing/standards ; Emergency Service, Hospital ; Hospitals, University ; Humans ; Inpatients ; Limit of Detection ; Nasopharynx/virology ; Nose/virology ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Sensitivity and Specificity ; United States/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-09-03
Publishing country	United States
Document type	Comparative Study ; Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2020.115200
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Zs.A 1845: Show issues

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Article ; Online: The Verigene dilemma: gram-negative polymicrobial bloodstream infections and clinical decision making.

Claeys, Kimberly C / Heil, Emily L / Pogue, Jason M / Lephart, Paul R / Johnson, J Kristie

Diagnostic microbiology and infectious disease

2018 Volume 91, Issue 2, Page(s) 144–146

Abstract: Verigene Blood-Culture Gram-Negative (GN) results in rapid identification of key GNs in bloodstream infections. Its use clinically is limited by low sensitivity in polymicrobial GN infections and concerns for inappropriate antibiotic modification. In a ... ...

Abstract	Verigene Blood-Culture Gram-Negative (GN) results in rapid identification of key GNs in bloodstream infections. Its use clinically is limited by low sensitivity in polymicrobial GN infections and concerns for inappropriate antibiotic modification. In a retrospective review of 1003 blood culture sets, the incidence of missed GNs was infrequent, <4%, with the potential to negatively impact the management of GN BSIs in <2% of cases.
MeSH term(s)	Bacteremia/diagnosis ; Bacteremia/microbiology ; Blood Culture ; Clinical Decision-Making/methods ; Coinfection/diagnosis ; Coinfection/microbiology ; Gram-Negative Bacteria ; Gram-Negative Bacterial Infections/diagnosis ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Molecular Diagnostic Techniques ; Oligonucleotide Array Sequence Analysis ; Retrospective Studies ; Sensitivity and Specificity
Language	English
Publishing date	2018-02-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2018.01.012
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Article: Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic.

Fairfax, Marilynn R / Lephart, Paul R / Salimnia, Hossein

Frontiers in microbiology

2014 Volume 5, Page(s) 254

Abstract: Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals. The incidence of human infections is underestimated partly due to confusion with viridans ... ...

Abstract	Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals. The incidence of human infections is underestimated partly due to confusion with viridans streptococci and partly due to difficulty making a definitive identification, even if the organism is recognized to belong to another genus, owing to the inability of commercial organism systems to identify it. We report our experiences identifying W. confusa isolated from two immune-compromised patients, both of whom developed sepsis with this organism. Two MicroScan gram positive combination panels, could not identify the organism because they did not have W. confusa in their data bases, but did not provide a false identification. Other laboratorians have reported failure to identify or false identifications of W. confusa with other commercial systems. W. confusa is in the data base of the RapID™ Str panel (Remel), which gave three incorrect, high probability results (≥95%). 16S rDNA sequencing identified the isolates as W. confusa. Maldi-Tof, performed by two of our reference laboratories, also correctly identified both isolates. Use of W. confusa as a probiotic should be approached with caution because its true incidence as an opportunisitic pathogen is unknown.
Language	English
Publishing date	2014-06-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2014.00254
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Article ; Online: Donor to recipient transmission of SARS-CoV-2 by lung transplantation despite negative donor upper respiratory tract testing.

Kaul, Daniel R / Valesano, Andrew L / Petrie, Joshua G / Sagana, Rommel / Lyu, Dennis / Lin, Jules / Stoneman, Emily / Smith, Lane M / Lephart, Paul / Lauring, Adam S

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

2021 Volume 21, Issue 8, Page(s) 2885–2889

Abstract: We describe a case of proven transmission of SARS-CoV-2 from lung donor to recipient. The donor had no clinical history or findings suggestive of infection with SARS-CoV-2 and tested negative by reverse transcriptase polymerase chain reaction (RT-PCR) on ...

Abstract	We describe a case of proven transmission of SARS-CoV-2 from lung donor to recipient. The donor had no clinical history or findings suggestive of infection with SARS-CoV-2 and tested negative by reverse transcriptase polymerase chain reaction (RT-PCR) on a nasopharyngeal (NP) swab obtained within 48 h of procurement. Lower respiratory tract testing was not performed. The recipient developed fever, hypotension, and pulmonary infiltrates on posttransplant day (PTD) 3, and RT-PCR testing for SARS-CoV-2 on an NP swab specimen was non-reactive, but positive on bronchoalveolar lavage (BAL) fluid. One thoracic surgeon present during the transplantation procedure developed COVID-19. Sequence analysis of isolates from donor BAL fluid (obtained at procurement), the recipient, and the infected thoracic surgeon proved donor origin of recipient and health-care worker (HCW) infection. No other organs were procured from this donor. Transplant centers and organ procurement organizations should perform SARS-CoV-2 testing of lower respiratory tract specimens from potential lung donors, and consider enhanced personal protective equipment for HCWs involved in lung procurement and transplantation.
MeSH term(s)	COVID-19 ; COVID-19 Testing ; Humans ; Lung ; Lung Transplantation/adverse effects ; SARS-CoV-2
Language	English
Publishing date	2021-03-15
Publishing country	United States
Document type	Case Reports
ZDB-ID	2060594-8
ISSN	1600-6143 ; 1600-6135
ISSN (online)	1600-6143
ISSN	1600-6135
DOI	10.1111/ajt.16532
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Zs.A 5542: Show issues

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Article: Effect of the major repeat sequence on mitotic recombination in Candida albicans.

Lephart, Paul R / Magee, Paul T

Genetics

2006 Volume 174, Issue 4, Page(s) 1737–1744

Abstract: The major repeat sequence (MRS) is known to play a role in karyotypic variation in Candida albicans. The MRS affects karyotypic variation by expanding and contracting internal repeats, by altering the frequency of chromosome loss, and by serving as a ... ...

Abstract	The major repeat sequence (MRS) is known to play a role in karyotypic variation in Candida albicans. The MRS affects karyotypic variation by expanding and contracting internal repeats, by altering the frequency of chromosome loss, and by serving as a hotspot for chromosome translocation. We proposed that the effects of the MRS on translocation could be better understood by examination of the effect of the MRS on a similar event, mitotic recombination between two chromosome homologs. We examined the frequency of mitotic recombination across an MRS of average size (approximately 50 kb) as well as the rate of recombination in a 325-kb stretch of DNA adjacent to the MRS. Our results indicate that mitotic recombination frequencies across the MRS were not enhanced compared to the frequencies measured across the 325-kb region adjacent to the MRS. Mitotic recombination events were found to occur throughout the 325-kb region analyzed as well as within the MRS itself. This analysis of mitotic recombination frequencies across a large portion of chromosome 5 is the first large-scale analysis of mitotic recombination done in C. albicans and indicates that mitotic recombination frequencies are similar to the rates found in Saccharomyces cerevisiae.
MeSH term(s)	Blotting, Southern ; Candida albicans/genetics ; Chromosome Mapping ; Chromosomes, Fungal/genetics ; DNA, Fungal ; Karyotyping ; Mitosis ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid
Chemical Substances	DNA, Fungal
Language	English
Publishing date	2006-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.106.063271
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Zs.B 767: Show issues

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Article: Minimizing Time to Optimal Antimicrobial Therapy for Enterobacteriaceae Bloodstream Infections: A Retrospective, Hypothetical Application of Predictive Scoring Tools vs Rapid Diagnostics Tests.

Cwengros, Laura N / Mynatt, Ryan P / Timbrook, Tristan T / Mitchell, Robert / Salimnia, Hossein / Lephart, Paul / Pogue, Jason M

Open forum infectious diseases

2020 Volume 7, Issue 8, Page(s) ofaa278

Abstract: Background: Bloodstream infections (BSIs) due to ceftriaxone (CRO)-resistant Enterobacteriaceae are associated with delays in time to appropriate therapy and worse outcomes compared with infections due to susceptible isolates. However, treating all at- ... ...

Abstract	Background: Bloodstream infections (BSIs) due to ceftriaxone (CRO)-resistant Enterobacteriaceae are associated with delays in time to appropriate therapy and worse outcomes compared with infections due to susceptible isolates. However, treating all at-risk patients with empiric carbapenem therapy risks overexposure. Strategies are needed to appropriately balance these competing interests. The purpose of this study was to compare 4 methods for achieving this balance. Methods: This was a retrospective hypothetical observational study of patients at the Detroit Medical Center with monomicrobial BSIs due to Results: Four hundred fifty-one Enterobacteriaceae BSIs were included, 73 (16%) of which were CRO-resistant. Verigene accurately predicted ceftriaxone susceptibility for 97% of isolates, compared with 70%-81% using the scoring tools ( Conclusions: Verigene significantly outperformed published ESBL scoring tools for identifying CRO-resistant Enterobacteriaceae BSI. Institutions should validate scoring tools before implementation. Stewardship programs should consider adoption of rapid diagnostic tests to optimize early therapy.
Language	English
Publishing date	2020-07-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofaa278
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