Kees Mourik, Igor Sidorov, Ellen C Carbo, David van der Meer, Arnoud Boot, Aloysius C M Kroes, Eric C J Claas, Stefan A Boers, Jutte J C de Vries
UNLABELLED: Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix...
May 17, 2024: Journal of Clinical Microbiology
Hannah P Moore, Philip J Palumbo, Kin Israel Notarte, Jessica M Fogel, Vanessa Cummings, Theresa Gamble, Carlos Del Rio, D Scott Batey, Kenneth H Mayer, Jason E Farley, Robert H Remien, Chris Beyrer, Sarah E Hudelson, Susan H Eshleman
HIV genotyping is used to assess HIV susceptibility to antiretroviral drugs. The Applied Biosystems HIV-1 Genotyping Kit with Integrase (AB kit, Thermo Fisher Scientific) detects resistance-associated mutations (RAMs) in HIV protease (PR), reverse transcriptase (RT), and integrase (IN). We compared results from the AB kit with results obtained previously with the ViroSeq HIV-1 Genotyping System. DNA amplicons from the AB kit were also analyzed using next-generation sequencing (NGS). HIV RNA was extracted using the MagNA Pure 24 instrument (Roche Diagnostics; 96 plasma samples, HIV subtype B, viral load range: 530-737,741 copies/mL)...
May 10, 2024: Journal of Clinical Microbiology
Aliaa Fouad, Patricia J Simner, David P Nicolau, Tomefa E Asempa
There are increasing reports of carbapenem-resistant Enterobacterales (CRE) that test as cefepime-susceptible (S) or susceptible-dose dependent (SDD). However, there are no data to compare the cefepime testing performance of BD Phoenix automated susceptibility system (BD Phoenix) and disk diffusion (DD) relative to reference broth microdilution (BMD) against carbapenemase-producing (CP bla KPC -CRE) and non-producing (non-CP CRE) isolates. Cefepime susceptibility results were interpreted according to CLSI M100Ed32...
May 7, 2024: Journal of Clinical Microbiology
Tyler Goshia, April Aralar, Nathan Wiederhold, Jeffrey D Jenks, Sanjay R Mehta, Aprajita Karmakar, Monish E S, Ankit Sharma, Haoxiang Sun, Refilwe Kebadireng, P Lewis White, Mridu Sinha, Martin Hoenigl, Stephanie I Fraley
UNLABELLED: Invasive mold infections (IMIs) are associated with high morbidity, particularly in immunocompromised patients, with mortality rates between 40% and 80%. Early initiation of appropriate antifungal therapy can substantially improve outcomes, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high-resolution melting (U-dHRM) analysis may enable rapid and robust diagnoses of IMI...
May 2, 2024: Journal of Clinical Microbiology
Lauren C Franco, Mahmoud Ahmed, Christopher G Kendra, R Matthew Sperling, Kayla Van Benten, John-Paul Lavik, Christopher L Emery, Ryan F Relich, Kenneth Gavina
UNLABELLED: Candida auris is a multidrug-resistant opportunistic fungal pathogen capable of causing serious infections and healthcare-associated outbreaks. Screening for colonization with C. auris has become routine and is recommended in many hospitals and healthcare facilities as an infection control and prevention strategy. Subsequently, and since there are currently no FDA-approved tests for this purpose, clinical microbiology laboratories have become responsible for developing protocols to detect C...
May 1, 2024: Journal of Clinical Microbiology
Arthur W Baker, Sophie E Nick, Fan Jia, Amanda M Graves, Bobby G Warren, Sofia Zavala, Jason E Stout, Mark J Lee, Barbara D Alexander, Rebecca M Davidson, Deverick J Anderson
We identified 23 cases of Mycobacterium immunogenum respiratory acquisition linked to a colonized plumbing system at a new hospital addition. We conducted a genomic and epidemiologic investigation to assess for clonal acquisition of M. immunogenum from hospital water sources and improve understanding of genetic distances between M. immunogenum isolates. We performed whole-genome sequencing on 28 M . immunogenum isolates obtained from August 2013 to July 2021 from patients and water sources on four intensive care and intermediate units at an academic hospital...
May 1, 2024: Journal of Clinical Microbiology
Kaitlin M Hoyt, John R Barr, André O Hopkins, Janet K Dykes, Carolina Lúquez, Suzanne R Kalb
Botulism is a paralytic disease due to the inhibition of acetylcholine exocytosis at the neuromuscular junction, which can be lethal if left untreated. Botulinum neurotoxins (BoNTs) are produced by some spore-forming Clostridium bacteria. The current confirmatory assay to test for BoNTs in clinical specimens is the gold-standard mouse bioassay. However, an Endopep-MS assay method has been developed to detect BoNTs in clinical samples using benchtop mass spectrometric detection. This work demonstrates the validation of the Endopep-MS method for clinical specimens with the intent of method distribution in public health laboratories...
April 30, 2024: Journal of Clinical Microbiology
Katharine H D Crawford, Stacy Selke, Gregory Pepper, Erin Goecker, Aniela Sobel, Anna Wald, Christine Johnston, Alexander L Greninger
Herpes simplex virus (HSV) infections are one of the most common and stigmatized infections of humankind, affecting more than 4 billion people around the world and more than 100 million Americans. Yet, most people do not know their infection status, and antibody testing is not recommended, partly due to poor test performance. Here, we compared the test performance of the Roche Elecsys HSV-1 IgG and HSV-2 IgG, DiaSorin LIAISON HSV-1/2 IgG, and Bio-Rad BioPlex 2200 HSV-1 and HSV-2 IgG assays with the gold-standard HSV western blot in 1,994 persons, including 1,017 persons with PCR or culture-confirmed HSV-1 and/or HSV-2 infection...
April 30, 2024: Journal of Clinical Microbiology
Maria Stefania Latrofa, Marco Cereda, Viviane Noll Louzada-Flores, Filipe Dantas-Torres, Domenico Otranto
Leishmaniasis is a vector-borne disease caused by many Leishmania spp. which infect humans and other mammalian hosts. Leishmania infantum is the main agent of canine leishmaniasis (CanL) whose diagnosis is usually confirmed by serological and molecular tests. This study aimed to evaluate the clinical and analytical sensitivities of a lab-on-chip (LOC) real-time PCR applied on the portable Q3-Plus V2 platform (Q3 qPCR) in the detection of L. infantum . The Q3 qPCR performance was assessed by comparing the quantification cycle (Cq) values with those obtained using the qPCR run on a CFX96 Real-Time System (CFX96 qPCR)...
April 25, 2024: Journal of Clinical Microbiology
Flemming Scheutz, Camilla Hald Nielsen, Astrid von Mentzer
UNLABELLED: The identification of pathogens is essential for effective surveillance and outbreak detection, which lately has been facilitated by the decreasing cost of whole-genome sequencing (WGS). However, extracting relevant virulence genes from WGS data remains a challenge. In this study, we developed a web-based tool to predict virulence-associated genes in enterotoxigenic Escherichia coli (ETEC), which is a major concern for human and animal health. The database includes genes encoding the heat-labile toxin (LT) ( eltA and eltB ), heat-stable toxin (ST) ( est ), colonization factors CS1 through 30, F4, F5, F6, F17, F18, and F41, as well as toxigenic invasion and adherence loci ( tia , tibAC , etpBAC , eatA , yghJ , and tleA )...
April 24, 2024: Journal of Clinical Microbiology
Anjana Sasidharan, Christopher J Harrison, Rangaraj Selvarangan
Parechovirus A (PeV-A) infections have been detected with increasing frequency in US infants under 6 months of age, leading to a Centers for Disease Control and Prevention (CDC) health advisory in July 2022. Clinicians are advised to consider PeV-A laboratory testing of blood and cerebrospinal fluid when infants present with unexplained fever, sepsis-like illness, or neurological issues. Clinical laboratories are encouraged to offer in-house molecular testing for PeV-A to avoid diagnostic delays, unnecessary use of antibiotics, and prolonged hospitalization of infants presenting with sepsis-like illness...
April 22, 2024: Journal of Clinical Microbiology
Heba H Mostafa, Gavin Wall, Szu-Chi Su, Gerta Hysa, Lijie Gong, Urbain Charly Dadjeu, Helen Cheung, Andrew Pekosz, Delphine De Smet, Nikola Sklenovská, Lies Laenen, Laura Viñuela, Adolfo de Salazar, Ana Fuentes, Elizaveta Padalko, Federico Garcia
UNLABELLED: The mpox outbreak, caused by monkeypox virus (MPXV), accelerated the development of molecular diagnostics. In this study, we detail the evaluation of the Research Use Only (RUO) NeuMoDx MPXV assay by multiple European and US sites. The assay was designed and developed by Qiagen for the NeuMoDx Molecular Systems. Primers and probes were tested for specificity and inclusivity in silico . The analytical sensitivity of the assay was determined by testing dilutions of synthetic and genomic MPXV DNA...
April 19, 2024: Journal of Clinical Microbiology
Janessa D Lewis, Stephen J Salipante
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA...
April 17, 2024: Journal of Clinical Microbiology
Robert Hamilton-Seth, Vincent Streva, Natalie Gammel, Victoria L Campodónico, Patricia J Simner, Sean X Zhang, Karen C Carroll
No abstract text is available yet for this article.
April 17, 2024: Journal of Clinical Microbiology
Lucas J Osborn, John Fissel, Samantha Gomez, Javier Mestas, Jessica Flores-Vazquez, Jaehyeon Lee, Hesamedin Hakimjavadi, Cristina Costales, Jennifer Dien Bard
UNLABELLED: The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory...
April 16, 2024: Journal of Clinical Microbiology
Erik Munson
No abstract text is available yet for this article.
April 15, 2024: Journal of Clinical Microbiology
Michael Waters, Deepa Raju, Helen S Garmory, Michel R Popoff, Mahfuzur R Sarker
No abstract text is available yet for this article.
April 12, 2024: Journal of Clinical Microbiology
Michael Waters, Amanda Savoie, Helen S Garmory, Dawn Bueschel, Michel R Popoff, J Glenn Songer, Richard W Titball, Bruce A McClane, Mahfuzur R Sarker
No abstract text is available yet for this article.
April 12, 2024: Journal of Clinical Microbiology
Angel Moreno, Jordan Mah, Indre Budvytiene, Dora Y Ho, Hayden T Schwenk, Niaz Banaei
UNLABELLED: Aspergillus species and Mucorales agents are the primary etiologies of invasive fungal disease (IFD). Biomarkers that predict outcomes are needed to improve care. Patients diagnosed with invasive aspergillosis and mucormycosis using plasma cell-free DNA (cfDNA) PCR were retested weekly for 4 weeks. The primary outcome included all-cause mortality at 6 weeks and 6 months based on baseline cycle threshold (CT) values and results of follow-up cfDNA PCR testing. Forty-five patients with Aspergillus and 30 with invasive Mucorales infection were retested weekly for a total of 197 tests...
April 11, 2024: Journal of Clinical Microbiology
Marie L Landry, Sajjad Hassan, Bruce G Rottmann, Stacey J Pesak, Michael Ordazzo, Michael Skrzyniarz, Steven Deponte, David R Peaper
UNLABELLED: We compared the performance of a new modified two-tier testing (MTTT) platform, the Diasorin Liaison chemiluminescent immunoassay (CLIA), to the Zeus enzyme-linked immunoassay (ELISA) MTTT and to Zeus ELISA/Viramed immunoblot standard two-tier testing (STTT) algorithm. Of 537 samples included in this study, 91 (16.9%) were positive or equivocal by one or more screening tests. Among these 91 samples, only 57 samples were concordant positive by first-tier screening tests, and only 19 of 57 were concordant by the three second-tier methods...
April 10, 2024: Journal of Clinical Microbiology
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