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Article ; Online: Updates in Prevention, Diagnosis, and Management of Infections Among Solid Organ Transplant Recipients.

Imlay, Hannah / Hanson, Kimberly E

Infectious disease clinics of North America

2023 Volume 37, Issue 3, Page(s) xiii–xv

MeSH term(s)	Humans ; Antiviral Agents ; Organ Transplantation/adverse effects ; Transplant Recipients
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Editorial
ZDB-ID	1077676-x
ISSN	1557-9824 ; 0891-5520
ISSN (online)	1557-9824
ISSN	0891-5520
DOI	10.1016/j.idc.2023.06.001
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Article ; Online: Plasma Cell-Free DNA Metagenomic Sequencing: New Insights From the PICKUP Study.

Hanson, Kimberly E / Caliendo, Angela M

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2023 Volume 78, Issue 3, Page(s) 785–787

MeSH term(s)	Humans ; Prospective Studies ; Metagenomics ; Sequence Analysis, DNA ; Immunocompromised Host ; Pneumonia ; Cell-Free Nucleic Acids
Chemical Substances	Cell-Free Nucleic Acids
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciad600
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Article ; Online: Pathogen-agnostic immune biomarkers that predict infection after solid organ transplantation.

Imlay, Hannah / Seibert, Allan M / Hanson, Kimberly E

Transplant infectious disease : an official journal of the Transplantation Society

2023 Volume 25, Issue 2, Page(s) e14020

Abstract: Solid organ transplant recipients (SOTRs) remain at high risk for infection throughout their post-transplant course. Dosing of immunosuppressive medications, strategies that prevent infection, and choice of empiric antimicrobial treatment could be ... ...

Abstract	Solid organ transplant recipients (SOTRs) remain at high risk for infection throughout their post-transplant course. Dosing of immunosuppressive medications, strategies that prevent infection, and choice of empiric antimicrobial treatment could be optimized by a better understanding of an individual patient's risk for infectious complications. Diagnostic tests that qualitatively or quantitatively measure the function of the immune system and/or its response to infection may be useful for individualized management decisions. Numerous studies have identified an association between infectious outcomes after solid organ transplantation (SOT) and the results of a variety of non-pathogen-specific or "pathogen-agnostic" immune monitoring tests. These biomarkers include humoral immune markers, functional or quantitative assessments of cellular immunity, transcriptomic-based diagnostics, and replication of viruses within the human virome, which have been used to predict or diagnose a variety of different infectious diseases complicating SOT. In this narrative review, we discuss several host-derived immune biomarkers that show promise for either predicting or diagnosing infection among SOTRs. However, additional studies are needed to determine the optimal use of immune response testing. Whether immune biomarkers contribute added benefits to current standard clinical care has not yet been determined. Testing must be validated across a range of clinical scenarios, including surveillance to predict infection risk and diagnosis of active infection at various time points post transplant.
MeSH term(s)	Humans ; Organ Transplantation/adverse effects ; Organ Transplantation/methods ; Infections/etiology ; Transplant Recipients ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-01-27
Publishing country	Denmark
Document type	Journal Article ; Review
ZDB-ID	1476094-0
ISSN	1399-3062 ; 1398-2273
ISSN (online)	1399-3062
ISSN	1398-2273
DOI	10.1111/tid.14020
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Article ; Online: Performance of Non-nasopharyngeal Sample Types for Molecular Detection of SARS-CoV-2.

Kukull, Benjamin / Shakir, Salika M / Hanson, Kimberly E

Clinics in laboratory medicine

2022 Volume 42, Issue 2, Page(s) 249–259

Abstract: Nasopharyngeal swabs have historically been considered the preferred specimen type for the detection of respiratory viruses, including SARS-CoV-2. However, in response to a global pandemic with shortages of swabs and specimen transport media, limited ... ...

Abstract	Nasopharyngeal swabs have historically been considered the preferred specimen type for the detection of respiratory viruses, including SARS-CoV-2. However, in response to a global pandemic with shortages of swabs and specimen transport media, limited access to qualified health care personnel, and needs for large-scale testing in nonmedical settings, alternative sample types have been validated for COVID-19 diagnosis. The purpose of this review is to highlight the diagnostic accuracy and clinical utility of non-nasopharyngeal respiratory samples for SARS-CoV-2 molecular diagnostic testing.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Humans ; Molecular Diagnostic Techniques ; SARS-CoV-2
Language	English
Publishing date	2022-02-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	604580-7
ISSN	1557-9832 ; 0272-2712
ISSN (online)	1557-9832
ISSN	0272-2712
DOI	10.1016/j.cll.2022.02.002
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Article ; Online: Sequence-based diagnostics and precision medicine in bacterial and viral infections: from bench to bedside.

Pham, Jonathan / Su, LingHui David / Hanson, Kimberly E / Hogan, Catherine A

Current opinion in infectious diseases

2023 Volume 36, Issue 4, Page(s) 228–234

Abstract: ... for mixed samples, and has been used to detect resistance mutations in transplant-related viruses (e.g. CMV ...

Abstract	Purpose of review: Nucleic acid sequence-based organism identification plays an important role in the diagnosis and management of transplant and cancer-associated infectious diseases. Here, we provide a high-level overview of advanced sequencing technologies, discuss test performance, and highlight unmet research needs with a focus on immunocompromised hosts. Recent findings: Next-generation sequencing (NGS) technologies are powerful tools with a growing role in managing immunocompromised patients with suspected infection. Targeted NGS (tNGS) can identify pathogens directly from patient specimens, especially for mixed samples, and has been used to detect resistance mutations in transplant-related viruses (e.g. CMV). Whole-genome sequencing (WGS) is increasingly used for outbreak investigations and infection control. Metagenomic NGS (mNGS) is useful for hypothesis-free testing and can simultaneously assess pathogens and host response to infection. Summary: NGS testing increases diagnostic yield relative to standard culture and Sanger sequencing but may be limited by high cost, turnaround times, and detection of unexpected organisms or commensals of uncertain significance. Close collaboration with the clinical microbiology laboratory and infectious diseases is recommended when NGS testing is considered. Additional research is required to understand which immunocompromised patients are most likely to benefit from NGS testing, and when testing should ideally be performed.
MeSH term(s)	Humans ; Precision Medicine ; Virus Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; Clinical Laboratory Services ; Communicable Diseases
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	645085-4
ISSN	1473-6527 ; 1535-3877 ; 0951-7375 ; 1355-834X
ISSN (online)	1473-6527 ; 1535-3877
ISSN	0951-7375 ; 1355-834X
DOI	10.1097/QCO.0000000000000936
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Zs.A 2462: Show issues

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Article ; Online: The First Fully Automated Molecular Diagnostic Panel for Meningitis and Encephalitis: How Well Does It Perform, and When Should It Be Used?

Hanson, Kimberly E

Journal of clinical microbiology

2016 Volume 54, Issue 9, Page(s) 2222–2224

Abstract: Rapid and accurate molecular diagnostic tests for the most common causes of infectious meningitis and encephalitis have the potential for high clinical impact. In this issue of the Journal of Clinical Microbiology, Leber et al. (J Clin Microbiol 54:2251- ... ...

Abstract	Rapid and accurate molecular diagnostic tests for the most common causes of infectious meningitis and encephalitis have the potential for high clinical impact. In this issue of the Journal of Clinical Microbiology, Leber et al. (J Clin Microbiol 54:2251-2261, 2016, http://dx.doi.org/10.1128/JCM.00730-16) report results from a large clinical study designed to prospectively assess the performance of the FilmArray meningitis/encephalitis panel compared to conventional methods.
MeSH term(s)	Encephalitis ; Humans ; Meningitis ; Molecular Diagnostic Techniques ; Pathology, Molecular
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01255-16
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Article ; Online: Characterization of the Cytopathic Effects of Monkeypox Virus Isolated from Clinical Specimens and Differentiation from Common Viral Exanthems.

Ma, Angela / Langer, Janine / Hanson, Kimberly E / Bradley, Benjamin T

Journal of clinical microbiology

2022 , Page(s) e0133622

Abstract: While the practice of viral culture has largely been replaced by nucleic acid amplification tests, circumstances still exist in which the availability of viral culture will allow for the diagnosis of infections not included in a provider's differential ... ...

Abstract	While the practice of viral culture has largely been replaced by nucleic acid amplification tests, circumstances still exist in which the availability of viral culture will allow for the diagnosis of infections not included in a provider's differential diagnosis. Here, we examine the cytopathic effects (CPE) and clinical data associated with 18 cases of monkeypox virus (MPXV) isolated from 19 clinical samples submitted for viral culture. During the study period, a total of 3,468 viral cultures were performed with herpes simplex virus (HSV) most commonly isolated (646/3,468; 18.6%), followed by MPXV (19/3,468; 0.6%) and varicella-zoster virus (VZV) (12/3,468; 0.4%). Most MPXV-positive samples were obtained from males (14/19) and taken from genital (7/19) or rectal lesions (5/19). Cycle threshold values of tested samples ranged from 15.3 to 29.0. Growth of MPXV in cell culture was rapid, yielding detectable CPE at a median of 2 days (range: 1 to 4) often with >50% of the monolayer affected in RMK, BGM, A549, and MRC-5 cell lines. As clinical features of MPXV, HSV, and VZV lesions may overlap, CPE patterns were compared between viruses. HSV CPE developed in a similar time frame (median: 2 days, range: 1 to 7) but was more often negative in RMK cells relative to MPXV. VZV grew more slowly (median: 9 days, range: 5 to 11) and demonstrated CPE affecting ≤25% of cell monolayers when positive. Viral culture remains an important tool for the detection of rare or emerging viral pathogens, particularly when high viral load specimens are easily obtained.
Language	English
Publishing date	2022-11-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.01336-22
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Article ; Online: Candida auris: an Emerging Fungal Pathogen.

Spivak, Emily S / Hanson, Kimberly E

Journal of clinical microbiology

2018 Volume 56, Issue 2

Abstract: ... Candida ... ...

Abstract	Candida auris
MeSH term(s)	Antifungal Agents/administration & dosage ; Antifungal Agents/pharmacology ; Antimicrobial Stewardship ; Candida/drug effects ; Candida/isolation & purification ; Candida/pathogenicity ; Candida/physiology ; Candidiasis/drug therapy ; Candidiasis/epidemiology ; Candidiasis/microbiology ; Candidiasis/prevention & control ; Clinical Laboratory Techniques ; Cross Infection/epidemiology ; Cross Infection/prevention & control ; Drug Resistance, Fungal/genetics ; Humans ; Skin/microbiology ; Virulence Factors
Chemical Substances	Antifungal Agents ; Virulence Factors
Language	English
Publishing date	2018-01-24
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.01588-17
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Article ; Online: Prediction of Infection After Solid Organ Transplantation: Is Measuring Cell-Mediated Immunity the Answer?

Hanson, Kimberly E / Limaye, Ajit P

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2017 Volume 66, Issue 9, Page(s) 1398–1399

MeSH term(s)	Humans ; Immunity, Cellular ; Organ Transplantation ; Transplant Recipients
Language	English
Publishing date	2017-12-23
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/cix1009
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Article ; Online: Development and validation of a next-generation sequencing assay with open-access analysis software for detecting resistance-associated mutations in CMV.

Mallory, Melanie A / Hymas, Weston C / Simmon, Keith E / Pyne, Michael T / Stevenson, Jeffery B / Barker, Adam P / Hillyard, David R / Hanson, Kimberly E

Journal of clinical microbiology

2023 Volume 61, Issue 12, Page(s) e0082923

Abstract: Cytomegalovirus (CMV) resistance testing by targeted next-generation sequencing (NGS) allows for the simultaneous analysis of multiple genes. We developed and validated an amplicon-based Ion Torrent NGS assay to detect CMV resistance mutations in UL27, ... ...

Abstract	Cytomegalovirus (CMV) resistance testing by targeted next-generation sequencing (NGS) allows for the simultaneous analysis of multiple genes. We developed and validated an amplicon-based Ion Torrent NGS assay to detect CMV resistance mutations in UL27, UL54, UL56, and UL97 and compared the results to standard Sanger sequencing. NGS primers were designed to generate 83 overlapping amplicons of four CMV genes (~10 kb encompassing 138 mutation sites). An open-access software plugin was developed to perform read alignment, call variants, and interpret drug resistance. Plasmids were tested to determine NGS error rate and minor variant limit of detection. NGS limit of detection was determined using the CMV WHO International Standard and quantified clinical specimens. Reproducibility was also assessed. After establishing quality control metrics, 185 patient specimens previously tested using Sanger were reanalyzed by NGS. The NGS assay had a low error rate (<0.05%) and high accuracy (95%) for detecting CMV-associated resistance mutations present at ≥5% in contrived mixed populations. Mutation sites were reproducibly sequenced with 40× coverage when plasma viral loads were ≥2.6 log IU/mL. NGS detected the same resistance-associated mutations identified by Sanger in 68/69 (98.6%) specimens. In 16 specimens, NGS detected 18 resistance mutations that Sanger failed to detect; 14 were low-frequency variants (<20%), and six would have changed the drug resistance interpretation. The NGS assay showed excellent agreement with Sanger and generated high-quality sequence from low viral load specimens. Additionally, the higher resolution and analytic sensitivity of NGS potentially enables earlier detection of antiviral resistance.
MeSH term(s)	Humans ; Cytomegalovirus/genetics ; Reproducibility of Results ; Mutation ; Cytomegalovirus Infections/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Drug Resistance, Viral/genetics
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.00829-23
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