Erratum for Hernandez et al., "Invasive Pneumococcal Disease and Influenza Activity in a Pediatric Population: Impact of PCV13 Vaccination in Epidemic and Nonepidemic Influenza Periods" [Errata]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Hernandez, S., Munoz-Almagro, C., Ciruela, P., Soldevila, N., Izquierdo, C., Codina, M. G., Diaz, A., Moraga-Llop, F., Garcia-Garcia, J. J., Dominguez, A., Working Group of Projects PI11/02081 and PI11/2345 Tags: Errata Source Type: research

The ASM Journals Committee Values the Contributions of Black Microbiologists [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Schloss, P. D., Junior, M., Alvania, R., Arias, C. A., Baumler, A., Casadevall, A., Detweiler, C., Drake, H., Gilbert, J., Imperiale, M. J., Lovett, S., Maloy, S., McAdam, A. J., Newton, I. L. G., Sadowsky, M. J., Sandri-Goldin, R. M., Silhavy, T. J., Ton Tags: Editorial Source Type: research

Development and Validation of the Elecsys Anti-SARS-CoV-2 Immunoassay as a Highly Specific Tool for Determining Past Exposure to SARS-CoV-2 [Virology]
The Elecsys Anti-SARS-CoV-2 immunoassay (Roche Diagnostics) was developed to provide accurate, reliable detection of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated sensitivity, specificity, cross-reactivity, and agreement with a vesicular stomatitis virus-based pseudoneutralization assay for the Elecsys Anti-SARS-CoV-2 immunoassay. Sensitivity and agreement between Elecsys Anti-SARS-CoV-2 immunoassay and pseudoneutralization assay measurements were evaluated using samples from patients with PCR-confirmed SARS-CoV-2 infection, a majority of whom were hospitalized. Specificity was ev...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Muench, P., Jochum, S., Wenderoth, V., Ofenloch-Haehnle, B., Hombach, M., Strobl, M., Sadlowski, H., Sachse, C., Torriani, G., Eckerle, I., Riedel, A. Tags: Virology Source Type: research

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection [Virology]
In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID50)/ml using inactivated virus and...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Pham, J., Meyer, S., Nguyen, C., Williams, A., Hunsicker, M., McHardy, I., Gendlina, I., Goldstein, D. Y., Fox, A. S., Hudson, A., Darby, P., Hovey, P., Morales, J., Mitchell, J., Harrington, K., Majlessi, M., Moberly, J., Shah, A., Worlock, A., Walcher, Tags: Virology Source Type: research

Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages [Virology]
As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve ...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Moreno-Contreras, J., Espinoza, M. A., Sandoval-Jaime, C., Cantu-Cuevas, M. A., Baron-Olivares, H., Ortiz-Orozco, O. D., Munoz-Rangel, A. V., Hernandez-de la Cruz, M., Eroza-Osorio, C. M., Arias, C. F., Lopez, S. Tags: Virology Source Type: research

Comparison of Extraction Methods and Thermocyclers for SARS-CoV-2 Molecular Detection Using Clinical Specimens [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Ransom, E. M., Potter, R. F., Wallace, M. A., Mitchell, K. F., Yarbrough, M. L., Burnham, C.-A. D., Anderson, N. W., Parikh, B. A. Tags: Letter To The Editor Source Type: research

A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay [Virology]
Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U ...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Artesi, M., Bontems, S., Göbbels, P., Franckh, M., Maes, P., Boreux, R., Meex, C., Melin, P., Hayette, M.-P., Bours, V., Durkin, K. Tags: Virology Source Type: research

Advances in Molecular Diagnosis of Tuberculosis [Minireviews]
Molecular tests for tuberculosis (TB) have the potential to help reach the three million people with TB who are undiagnosed or not reported each year and to improve the quality of care TB patients receive by providing accurate, quick results, including rapid drug-susceptibility testing. The World Health Organization (WHO) has recommended the use of molecular nucleic acid amplification tests (NAATs) tests for TB detection instead of smear microscopy, as they are able to detect TB more accurately, particularly in patients with paucibacillary disease and in people living with HIV. Importantly, some of these WHO-endorsed tests...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: MacLean, E., Kohli, M., Weber, S. F., Suresh, A., Schumacher, S. G., Denkinger, C. M., Pai, M. Tags: Minireviews Source Type: research

Evaluation of the SpeeDx MG parC (Beta) PCR Assay for Rapid Detection of Mycoplasma genitalium Quinolone Resistance-Associated Mutations [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Sweeney, E. L., Lowry, K., Ebeyan, S., Lundgren, M., Whiley, D. M. Tags: Letter To The Editor Source Type: research

Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies [Virology]
Coronavirus disease (COVID) serological tests are essential to determine the overall seroprevalence of a population and to facilitate exposure estimates within that population. We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Demographics, symptoms, comorbidities, treatment, and mortality of patients whose sera were used were also reviewed. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, an...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Charlton, C. L., Kanji, J. N., Johal, K., Bailey, A., Plitt, S. S., MacDonald, C., Kunst, A., Buss, E., Burnes, L. E., Fonseca, K., Berenger, B. M., Schnabl, K., Hu, J., Stokes, W., Zelyas, N., Tipples, G. Tags: Virology Source Type: research

Susceptibility of Clinical Isolates of Escherichia coli to Fosfomycin as Measured by Four In Vitro Testing Methods [Bacteriology]
Clinical isolates of Escherichia coli (n = 554) were tested against fosfomycin using agar dilution, disk diffusion, and Etest. Agar dilution (reference method) identified few isolates with fosfomycin MICs of 64 (n = 3), 128 (n = 4), and ≥256 μg/ml (n = 2). Applying CLSI (M100, 2020) and EUCAST (v. 10.0, 2020) breakpoints, 98.9% and 98.4% (agar dilution), 99.3% and 99.1% (disk diffusion), and 99.1% and 98.9% (Etest) of isolates were fosfomycin susceptible, respectively. Essential agreement (agar dilution versus Etest) was low (40.8%); 59.3% (131/221) of isolates with agar dilution MICs of 2 to 128 μg/ml tested 2 to...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Karlowsky, J. A., Lagace-Wiens, P. R. S., Laing, N. M., Baxter, M. R., Adam, H. J., Zhanel, G. G. Tags: Bacteriology Source Type: research

In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data [Bacteriology]
In conclusion, the addition of 38 ExPEC-associated genes and the associated alleles to the E. coli VirulenceFinder database allows for a more complete characterization of E. coli isolates based on WGS data, which has become increasingly important considering the plasticity of the E. coli genome. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Malberg Tetzschner, A. M., Johnson, J. R., Johnston, B. D., Lund, O., Scheutz, F. Tags: Bacteriology Source Type: research

Entamoeba histolytica DNA Detection in Serum from Patients with Suspected Amoebic Liver Abscess [Parasitology]
This study demonstrates that cell-free circulating E. histolytica DNA can be detected in serum in ALA. This may assist in both positive diagnoses and treatment efficacy follow-up. The origin of this circulating DNA remains to be investigated. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Ghelfenstein-Ferreira, T., Gits-Muselli, M., Delliere, S., Denis, B., Guigue, N., Hamane, S., Alanio, A., Bretagne, S. Tags: Parasitology Source Type: research

Performance of Four Fosfomycin Susceptibility Testing Methods against an International Collection of Clinical Pseudomonas aeruginosa Isolates [Bacteriology]
Fosfomycin has been shown to have a wide spectrum of activity against multidrug-resistant Gram-negative bacteria; however, breakpoints have been established only for Escherichia coli or Enterobacterales per the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST), respectively. A lack of additional organism breakpoints limits clinical use of this agent and has prompted extrapolation of these interpretive categories to other organisms like Pseudomonas aeruginosa without supporting evidence. Further complicating the utility of fosfomycin is the specifi...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Smith, E. C., Brigman, H. V., Anderson, J. C., Emery, C. L., Bias, T. E., Bergen, P. J., Landersdorfer, C. B., Hirsch, E. B. Tags: Bacteriology Source Type: research

Evaluation of MALDI Biotyper Interpretation Criteria for Accurate Identification of Nontuberculous Mycobacteria [Mycobacteriology and Aerobic Actinomycetes]
In conclusion, MALDI-TOF MS is a useful method for identifying a large diversity of NTM species. A score threshold of 1.60 proved useful for identifying almost all the isolates tested; only a few species required a higher score (≥2.00) to obtain a valid definitive identification. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Rodriguez-Temporal, D., Rodriguez-Sanchez, B., Alcaide, F. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

A Diagnostic Stewardship Intervention To Improve Blood Culture Use among Adult Nonneutropenic Inpatients: the DISTRIBUTE Study [Bacteriology]
Interventions to optimize blood culture (BCx) practices in adult inpatients are limited. We conducted a before-after study evaluating the impact of a diagnostic stewardship program that aimed to optimize BCx use in a medical intensive care unit (MICU) and five medicine units at a large academic center. The program included implementation of an evidence-based algorithm detailing indications for BCx use and education and feedback to providers about BCx rates and indication inappropriateness. Neutropenic patients were excluded. BCx rates from contemporary control units were obtained for comparison. The primary outcome was the...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Fabre, V., Klein, E., Salinas, A. B., Jones, G., Carroll, K. C., Milstone, A. M., Amoah, J., Hsu, Y.-J., Gadala, A., Desai, S., Goyal, A., Furfaro, D., Zimmerman, J., Lin, S., Cosgrove, S. E. Tags: Bacteriology Source Type: research

Performance Evaluation of the Novodiag Bacterial GE+ Multiplex PCR Assay [Bacteriology]
The bacteriological diagnosis of intestinal bacterial infections has historically been based on culture on agar plates. However, culture may lack sensitivity, and some enteropathogens, such as pathovars of Escherichia coli, may escape routine diagnosis. Our goal was to evaluate the analytical performance of the Novodiag Bacterial GE+ kit for the detection of enteropathogenic bacteria in acute community diarrhea. We included 251 stools in this study (198 retrospective and 53 prospective). The analytical performance was calculated using a composite reference standard (CRS) in the absence of a perfect gold standard (lack of s...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Roy, C., Robert, D., Benejat, L., Buissonniere, A., Ducournau, A., Megraud, F., Bessede, E., Boraud, D., Lehours, P. Tags: Bacteriology Source Type: research

An Optimal Diagnostic Strategy for Tuberculosis in Hospitalized HIV-Infected Patients Using GeneXpert MTB/RIF and Alere Determine TB LAM Ag [Mycobacteriology and Aerobic Actinomycetes]
The diagnosis of tuberculosis (TB) in HIV-infected patients is challenging. Both a urinary lipoarabinomannan (LAM) test (Alere TB LAM) and GeneXpert-MTB/RIF (Xpert) are useful for the diagnosis of TB. However, how to optimally integrate Xpert and LAM tests into clinical practice algorithms remain unclear. We performed a post hoc analysis of 561 HIV-infected sputum-expectorating patients (median CD4 count of 130 cells/ml) from a previously published randomized controlled trial evaluating the LAM test in hospitalized HIV-infected patients with suspected TB. We evaluated 5 different diagnostic strategies using sputum culture ...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Esmail, A., Pooran, A., Sabur, N. F., Fadul, M., Brar, M. S., Oelofse, S., Tomasicchio, M., Dheda, K. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Improved Early Detection of Focal Brucellosis Complications with Anti-Brucella IgG [Bacteriology]
To evaluate the associations of inflammatory factors and serological test results with complicated brucellosis, we recruited 285 patients with a diagnosis of brucellosis between May 2016 and September 2019. The patients were subsequently classified into two groups according to the presence of complications. We collected demographic and clinical information and routine laboratory test results in addition to anti-Brucella IgG and IgM levels. Anti-Brucella IgG and IgM were uniformly tested using enzyme-linked immunosorbent assays (ELISAs) in this study. Among the 285 patients with brucellosis, 111 (38.95%) had complicated bru...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Xu, N., Dong, X., Yao, Y., Guan, Y., Chen, F., Zheng, F., Wang, G. Tags: Bacteriology Source Type: research

Diagnostic Accuracy of Interferon Gamma-Induced Protein 10 mRNA Release Assay for Tuberculosis [Mycobacteriology and Aerobic Actinomycetes]
Interferon gamma (IFN-) release assays (IGRAs) are increasingly used to test for latent tuberculosis (TB) infection. Although highly specific, IGRAs have a relatively high false-negative rate in active TB patients. A more sensitive assay is needed. IFN--induced protein 10 (IP-10) is an alternative biomarker with a 100-fold-higher expression level than IFN-, allowing for different analysis platforms, including molecular detection. The PCR technique is already an integrated tool in most TB laboratories and, thus, an obvious platform to turn to. In this case-control study, we investigated the diagnostic sensitivity and specif...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Blauenfeldt, T., Villar-Hernandez, R., Garcia-Garcia, E., Latorre, I., Holm, L. L., Muriel-Moreno, B., De Souza-Galvao, M. L., Millet, J. P., Sabria, F., Sanchez-Montalva, A., Ruiz-Manzano, J., Pilarte, J., Jimenez, M. A., Centeno, C., Torres, C., Molina- Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Persistent Challenges of Interassay Variability in Transplant Viral Load Testing [Minireviews]
While quantification of viruses that cause important infections in transplant recipients has been the standard of care for years, important challenges related to standardization remain. The issues are wide ranging, and until they are adequately addressed, the full impact of viral load testing regarding clinical management decisions will not be realized. This review focuses on a broad array of problems, including the lack of available FDA-approved/cleared tests, limited uptake of international standards, accurate quantification of secondary standards, specific assay characteristics, and commutability. Though some of these t...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Hayden, R. T., Caliendo, A. M. Tags: Minireviews Source Type: research

QuantiFERON-TB Gold Plus with Chemiluminescence Immunoassay: Do We Need a Higher Cutoff? [Mycobacteriology and Aerobic Actinomycetes]
In conclusion, automated QFT-Plus with CLIA is comparable to QFT-Plus performed by ELISA. Within the linearity range of the test, CLIA detects higher quantitative values than ELISA, resulting in a higher number of determinate results and the conversion of samples that were close to the cutoff into positive borderline results. A higher cutoff for QFT-CLIA needs to be defined based on clinical diagnostic criteria. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Bisognin, F., Lombardi, G., Re, M. C., Dal Monte, P. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies [Epidemiology]
Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016–2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequenc...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Joseph, L. A., Francois Watkins, L. K., Chen, J., Tagg, K. A., Bennett, C., Caidi, H., Folster, J. P., Laughlin, M. E., Koski, L., Silver, R., Stevenson, L., Robertson, S., Pruckler, J., Nichols, M., Pouseele, H., Carleton, H. A., Basler, C., Friedman, C. Tags: Epidemiology Source Type: research

Molecular Characterization of Mycoplasma pneumoniae Isolates in the United States from 2012 to 2018 [Epidemiology]
Mycoplasma pneumoniae is a major cause of community-acquired pneumonia. There are limited data in the United States on the molecular epidemiological characteristics of M. pneumoniae. We collected 446 M. pneumoniae-positive specimens from 9 states between August 2012 and October 2018. Culture, antimicrobial susceptibility testing, P1 subtyping, and multilocus VNTR (variable-number tandem repeats) analysis (MLVA) were performed to characterize the isolates. Macrolide-resistant M. pneumoniae (MRMp) was detected in 37 (8.3%) specimens. P1 subtype 2 (P1-2) was the predominant P1 subtype (59.8%). P1 subtype distribution did not ...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Xiao, L., Ratliff, A. E., Crabb, D. M., Mixon, E., Qin, X., Selvarangan, R., Tang, Y.- W., Zheng, X., Dien Bard, J., Hong, T., Prichard, M., Brooks, E., Dallas, S., Duffy, L. B., Fowler, K. B., Atkinson, T. P., Waites, K. B. Tags: Epidemiology Source Type: research

Imipenem-Relebactam Susceptibility Testing of Gram-Negative Bacilli by Agar Dilution, Disk Diffusion, and Gradient Strip Methods Compared with Broth Microdilution [Bacteriology]
In conclusion, agar dilution and Etest yielded comparable results to BMD for imipenem-relebactam. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Hakvoort, H., Bovenkamp, E., Greenwood-Quaintance, K. E., Schmidt-Malan, S. M., Mandrekar, J. N., Schuetz, A. N., Patel, R. Tags: Bacteriology Source Type: research

DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples [Mycobacteriology and Aerobic Actinomycetes]
Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0.05 M HEPES buffer, pH 7.5, 0.1% dithiothreitol [DTT]). The buffer emulated intrace...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: George, S., Xu, Y., Rodger, G., Morgan, M., Sanderson, N. D., Hoosdally, S. J., Thulborn, S., Robinson, E., Rathod, P., Walker, A. S., Peto, T. E. A., Crook, D. W., Dingle, K. E. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

Detection and Characterization of Diphtheria Toxin Gene-Bearing Corynebacterium Species through a New Real-Time PCR Assay [Bacteriology]
Respiratory diphtheria, characterized by a firmly adherent pseudomembrane, is caused by toxin-producing strains of Corynebacterium diphtheriae, with similar illness produced occasionally by toxigenic Corynebacterium ulcerans or, rarely, Corynebacterium pseudotuberculosis. While diphtheria laboratory confirmation requires culture methods to determine toxigenicity, real-time PCR (RT-PCR) provides a faster method to detect the toxin gene (tox). Nontoxigenic tox-bearing (NTTB) Corynebacterium isolates have been described, but impact of these isolates on the accuracy of molecular diagnostics is not well characterized. Here, we ...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Williams, M. M., Waller, J. L., Aneke, J. S., Weigand, M. R., Diaz, M. H., Bowden, K. E., Simon, A. K., Peng, Y., Xiaoli, L., Cassiday, P. K., Winchell, J., Tondella, M. L. Tags: Bacteriology Source Type: research

Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples [Mycobacteriology and Aerobic Actinomycetes]
In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION’s portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Cabibbe, A. M., Spitaleri, A., Battaglia, S., Colman, R. E., Suresh, A., Uplekar, S., Rodwell, T. C., Cirillo, D. M. Tags: Mycobacteriology and Aerobic Actinomycetes Source Type: research

A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings [Virology]
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing. This method overcomes several major technical challenges that ha...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Bonsall, D., Golubchik, T., de Cesare, M., Limbada, M., Kosloff, B., MacIntyre-Cockett, G., Hall, M., Wymant, C., Ansari, M. A., Abeler-Dörner, L., Schaap, A., Brown, A., Barnes, E., Piwowar-Manning, E., Eshleman, S., Wilson, E., Emel, L., Hayes, Tags: Virology Source Type: research

Rapid Salivary IgG Antibody Screening for Hepatitis A [Immunoassays]
Hepatitis A virus (HAV) is a common infection that is transmitted through the fecal-oral route, shed in the stool of infected individuals, and spread either by direct contact or by ingesting contaminated food or water. Each year, approximately 1.4 million acute cases are reported globally with a major risk factor for exposure being low household socioeconomic status. Recent trends show a decrease in anti-HAV antibodies in the general population, with concomitant increases in the numbers of HAV outbreaks. In line with a recreational water study, this effort aims to assess the prevalence of salivary IgG antibodies against HA...
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Augustine, S. A. J., Eason, T. N., Simmons, K. J., Griffin, S. M., Curioso, C. L., Ramudit, M. K. D., Sams, E. A., Oshima, K. H., Dufour, A., Wade, T. J. Tags: Immunoassays Source Type: research

Closing the Brief Case: What a Fluke! A Case of Fascioliasis with Pulmonary Involvement in a Peace Corps Volunteer [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Castillo Almeida, N. E., Gurram, P., Kolluri, N., Pritt, B., Enzler, M., Suh, G. A. Tags: The Brief Case Source Type: research

The Brief Case: What a Fluke! A Case of Fascioliasis with Pulmonary Involvement in a Peace Corps Volunteer [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Castillo Almeida, N. E., Gurram, P., Kolluri, N., Pritt, B., Enzler, M., Suh, G. A. Tags: The Brief Case Source Type: research

Answer to October 2020 Photo Quiz [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Yan, M., Nakfoor, R., Sigel, J., Rhoads, D. Tags: Photo Quiz Source Type: research

Photo Quiz: Dry Gangrenous Necrosis of the Foot of a Septuagenarian [Photo Quiz]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Authors: Yan, M., Nakfoor, R., Sigel, J., Rhoads, D. Tags: Photo Quiz Source Type: research

Editorial Board [Masthead]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - September 21, 2020 Category: Microbiology Tags: Masthead Source Type: research

Fourth-Generation QuantiFERON-TB Gold Plus: What Is the Evidence? [Minireviews]
QuantiFERON-TB Gold Plus (QFT-Plus) is the latest generation of interferon gamma release assays (IGRAs) to receive approval from the U.S. FDA, replacing its predecessor, QuantiFERON-TB Gold In-Tube (QFT-GIT). The novelty of QFT-Plus is that it elicits a response from CD8 T cells, in addition to CD4 T cells, thus collecting a broader response from T-cell subsets than QFT-GIT. It was developed with the aim to improve the detection of latent tuberculosis infection (LTBI), especially among recently exposed contacts, immunocompromised hosts, and young children. In this minireview, we summarize the performance of QFT-Plus compar...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Shafeque, A., Bigio, J., Hogan, C. A., Pai, M., Banaei, N. Tags: Minireviews Source Type: research

Closing the Brief Case: Secondary Measles and the Pitfalls of Diagnostic Testing [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Azar, M. M., Canterino, J., Landry, M. L. Tags: The Brief Case Source Type: research

The Brief Case: Secondary Measles and the Pitfalls of Diagnostic Testing [The Brief Case]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Azar, M. M., Canterino, J., Landry, M. L. Tags: The Brief Case Source Type: research

Performance of PCR/Electrospray Ionization-Mass Spectrometry on Whole Blood for Detection of Bloodstream Microorganisms in Patients with Suspected Sepsis [Bacteriology]
Blood culture (BC) often fails to detect bloodstream microorganisms in sepsis. However, molecular diagnostics hold great potential. The molecular method PCR/electrospray ionization-mass spectrometry (PCR/ESI-MS) can detect DNA from hundreds of different microorganisms in whole blood. The aim of the present study was to evaluate the performance of this method in a multicenter study including 16 teaching hospitals in the United States (n = 13) and Europe (n = 3). First, on testing of 2,754 contrived whole blood samples, with or without spiked microorganisms, PCR/ESI-MS produced 99.1% true-positive and 97.2% true-negative res...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Stralin, K., Rothman, R. E., Özenci, V., Barkataki, K., Brealey, D., Dhiman, N., Poling, L., Kurz, M. C., Limaye, A. P., LoVecchio, F., Lowery, K., Miller, L. G., Moran, G. J., Overcash, J. S., Parekh, A., Peacock, W. F., Rivers, E. P., Sims, M., Tags: Bacteriology Source Type: research

The Addition of Anaerobic Blood Cultures for Pediatric Patients with Concerns for Bloodstream Infections: Prevalence and Time to Positive Cultures [Bacteriology]
Anaerobes are an important but uncommon cause of bloodstream infections (BSIs). For pediatric patients, routine inclusion of an anaerobic blood culture alongside the aerobic remains controversial. We implemented automatic anaerobic blood culture alongside aerobic blood cultures in a pediatric emergency department (ED) and sought to determine changes in recovery of obligate and facultative anaerobes. This was a cohort study in a pediatric ED (August 2015 to July 2018) that began in February 2017. Blood culture positivity results for true pathogens and contaminants were assessed, along with a secondary outcome of time to pos...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Dien Bard, J., Chang, T. P., Yee, R., Manshadi, K., Lichtenfeld, N., Choi, H. J., Festekjian, A. Tags: Bacteriology Source Type: research

Optimization and Evaluation of a Multiplex Quantitative PCR Assay for Detection of Nucleic Acids in Human Blood Samples from Patients with Spotted Fever Rickettsiosis, Typhus Rickettsiosis, Scrub Typhus, Monocytic Ehrlichiosis, and Granulocytic Anaplasmosis [Chlamydiology and Rickettsiology]
Spotted fever group rickettsioses (SFGR), typhus group rickettsioses (TGR), scrub typhus (caused by Orientia tsutsugamushi), ehrlichiosis, and anaplasmosis often present as undifferentiated fever but are not treated by agents (penicillins and cephalosporins) typically used for acute febrile illness. Inability to diagnose these infections when the patient is acutely ill leads to excess morbidity and mortality. Failure to confirm these infections retrospectively if a convalescent blood sample is not obtained also impairs epidemiologic and clinical research. We designed a multiplex real-time quantitative PCR (qPCR) assay to d...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Reller, M. E., Dumler, J. S. Tags: Chlamydiology and Rickettsiology Source Type: research

Is This a Critical Result? A Micro-Comic Strip [Editorial]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: McAdam, A. J. Tags: Editorial Source Type: research

Direct Comparison of SARS-CoV-2 Analytical Limits of Detection across Seven Molecular Assays [Virology]
Analytical sensitivity for SARS-CoV-2 detection is a key performance metric for the evaluation of viral detection assays. We determined analytical limits of detection for seven SARS-CoV-2 assays using serial dilutions of pooled patient material quantified with droplet digital PCR. Limits of detection ranged from ≤10 to 74 copies/ml for commercial high-throughput laboratory analyzers (Roche Cobas, Abbott m2000, and Hologic Panther Fusion) and 167 to 511 copies/ml for sample-to-answer (DiaSorin Simplexa, GenMark ePlex) and point-of-care instruments (Abbott ID NOW). The CDC assay yielded limits of detection ranging from 85...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Fung, B., Gopez, A., Servellita, V., Arevalo, S., Ho, C., Deucher, A., Thornborrow, E., Chiu, C., Miller, S. Tags: Virology Source Type: research

Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription-Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 [Virology]
The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcr...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Nagura-Ikeda, M., Imai, K., Tabata, S., Miyoshi, K., Murahara, N., Mizuno, T., Horiuchi, M., Kato, K., Imoto, Y., Iwata, M., Mimura, S., Ito, T., Tamura, K., Kato, Y. Tags: Virology Source Type: research

QuantiFERON-TB Gold Plus: High Qualitative and Quantitative Agreement between Enzyme-Linked Immunosorbent Assay (ELISA) and Chemiluminescence Immunoassay (CLIA) [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Villalta, D., Martelli, P., Moratto, A., Ligato, E., Giacomello, R., El Idrissi El Hachimi, S. Tags: Letter To The Editor Source Type: research

Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms [Virology]
The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either ...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Szymczak, W. A., Goldstein, D. Y., Orner, E. P., Fecher, R. A., Yokoda, R. T., Skalina, K. A., Narlieva, M., Gendlina, I., Fox, A. S. Tags: Virology Source Type: research

Reporting Considerations for Cefepime-Susceptible and -Susceptible-Dose Dependent Results for Carbapenemase-Producing Enterobacterales [Letter To The Editor]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Fissel, J. A., Yarbrough, M. L., Tekle, T., Burnham, C.- A. D., Simner, P. J. Tags: Letter To The Editor Source Type: research

Biographical Feature: Robin Patel, M.D.(C.M.), D(ABMM), F(AAM), FIDSA, FACP [Biographical Feature]
(Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Munson, E. Tags: Biographical Feature Source Type: research

Clinical and Analytical Performance of an Automated Serological Test That Identifies S1/S2-Neutralizing IgG in COVID-19 Patients Semiquantitatively [Immunoassays]
In the coronavirus (CoV) disease 2019 (COVID-19) pandemic, highly selective serological testing is essential to define exposure to severe acute respiratory syndrome CoV 2 (SARS-CoV-2). Many tests have been developed, yet with variable speeds to first results, and are of unknown quality, particularly when considering the prediction of neutralizing capacity. The LIAISON SARS-CoV-2 S1/S2 IgG assay was designed to measure antibodies against the SARS-CoV-2 native S1/S2 proteins in a standardized automated chemiluminescence assay. The clinical and analytical performances of the test were validated in an observational study using...
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Bonelli, F., Sarasini, A., Zierold, C., Calleri, M., Bonetti, A., Vismara, C., Blocki, F. A., Pallavicini, L., Chinali, A., Campisi, D., Percivalle, E., DiNapoli, A. P., Perno, C. F., Baldanti, F. Tags: Immunoassays Source Type: research

Mild or Malign: Clinical Characteristics and Outcomes of Clostridium difficile Infection in Thailand [Bacteriology]
In conclusion, CDI in Thailand was relatively mild, and metronidazole remained an effective treatment option for these mild infections. (Source: Journal of Clinical Microbiology)
Source: Journal of Clinical Microbiology - August 23, 2020 Category: Microbiology Authors: Imwattana, K., Putsathit, P., Leepattarakit, T., Kiratisin, P., Riley, T. V. Tags: Bacteriology Source Type: research