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

The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. 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

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

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

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)

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

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%

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) uses whole-genome sequencing (WGS) data for in silico characterization of E. coli isolates and enables researchers and clinical health personnel to quickly extract and interpret

Amoebic liver abscess (ALA) is regularly seen in travelers or immigrants from tropical countries. The diagnosis relies on liver imaging that is not specific and on the detection of anti-Entamoeba histolytica antibodies, which cannot distinguish an acute from a former infection. We tested whether E. histolytica DNA detection in serum can improve the diagnosis of ALA. We retrospectively tested available

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

Identification of mycobacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) requires not only a good protein extraction protocol but also an adequate cutoff score in order to provide reliable results. The aim of this study was to assess the cutoff scores proposed by the MALDI-TOF MS system for mycobacterial identification. A total of 693 clinical isolates

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

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

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

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

Interferon gamma (IFN-γ) 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-γ-induced protein 10 (IP-10) is an alternative biomarker with a 100-fold-higher expression level than IFN-γ, allowing for different analysis platforms

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

QuantiFERON-TB Gold Plus (QFT-Plus) is the most widely used interferon gamma release assay (IGRA) for the diagnosis of latent tuberculosis infection (LTBI). The aim of this study was to compare QFT-Plus results by enzyme-linked immunosorbent assay (ELISA) on the SkyLab system with those obtained with chemiluminescence immunoassay (CLIA) on the Liaison XL analyzer. Agreement between the two assays was

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

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

This study aimed to determine whether agar dilution, research-use-only disk diffusion (Mast Group Ltd., Bootle Merseyside, UK), Etest (bioMérieux, Inc., Durham, NC), and MIC test strip (MTS) (Liofilchem, Inc., Waltham, MA) methods yield equivalent results to those of broth microdilution (BMD) for imipenem-relebactam susceptibility testing using a collection of 297 Gram-negative bacilli, including members

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

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

Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate

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

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

To expand testing capacity during the SARS-CoV-2 pandemic, numerous molecular assays have been granted emergency use authorization (EUA) for testing individual patient samples but not for sample pooling.…

Infection by Trypanosoma cruzi or Chagas Disease (ChD) affects around 7 million people in the Americas, most of which are unaware of their status due to lack of clinical manifestations and poor access to diagnosis. Rapid diagnostic tests (RDTs) are widely used for screening different infections (HIV, Hepatitis B, Syphilis), and their application for ChD would facilitate access to diagnosis, especially

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) based species identification has found its place in many clinical routine diagnostic laboratories over the past years allowing significantly reduced turnaround times and high-precision results. With regard to MALDI-TOF MS for filamentous fungi, here we discuss different approaches of sample processing and growth

Background: Cefiderocol antimicrobial susceptibility testing (AST) poses challenges because of its unique mechanism of action (i.e., requiring an iron depleted state) and due to differences in interpretative criteria by the Clinical and Laboratory Standards Institute (CLSI), U.S. Food and Drug Administration (FDA), and European Committee of Antimicrobial Susceptibility Testing (EUCAST). Our objective

Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid submitted to a reference laboratory from December 2017 through December 2019. Of

Quantitative polymerase chain reaction (qPCR) is the gold standard for diagnosis of Pneumocystis (P.) jirovecii pneumonia (PCP). However, it is laborious and requires skilled personnel. Therefore, execution outside regular working hours of the molecular biology laboratory is limited. The eazyplex®-P. jirovecii assay (eazyplex®-PJA) uses loop-mediated isothermal amplification for detection of P. jirovecii

Johne's disease (JD) is an economically important infectious disease in livestock farming caused by Mycobacterium avium subsp. paratuberculosis (MAP). As an alternative to serological tests, which are mainly used for the screening of whole herds, we developed a novel ResoLight-based real-time PCR (RL-PCR) assay with pooled faecal samples for the detection of faecal shedders in cattle herds. The RL-PCR

Neisseria meningitidis (Nm) is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens such as cerebrospinal fluid (CSF), blood, or urine. However, genome sequencing of specimens

Background: M. abscessus (Mab) is a highly antibiotic resistant opportunistic pathogen causing clinically challenging infections in patients with preexisting lung diseases or under immunosuppression. Hence, reliable antibiotic susceptibility data is required for effective treatment. Aims of this study were to investigate (i) the congruence of genotypic and phenotypic antimicrobial susceptibility testing

Various Gram staining automated systems are available to accelerate and standardize the staining process but a systematic comparison of different systems is largely lacking. The objective of this study was to evaluate two devices in comparison to manual Gram staining.

Domestic arthropod-borne viruses (arboviruses) are single stranded RNA viruses, the most common of which include the mosquito-borne West Nile virus, St. Louis Encephalitis virus, La Crosse virus, Jamestown Canyon virus, and Eastern Equine Encephalitis virus, as well as the tick-borne Powassan virus. Previously considered to be rare infections, they have been detected with increasing frequency over

The development of neutralizing antibodies (nAb) against SARS-CoV-2, following infection or vaccination, is likely to be critical for the development of sufficient population immunity to drive cessation of the COVID19 pandemic. A large number of serologic tests, platforms and methodologies are being employed to determine seroprevalence in populations to select convalescent plasmas for therapeutic trials

Aspergillus fumigatus has widely evolved resistance to the most commonly used class of antifungal chemicals, the azoles. Current methods for identifying azole resistance are time-consuming and depend on specialized laboratories. There is an urgent need for rapid detection of these emerging pathogens at point-of-care to provide the appropriate treatment in the clinic and to improve management of environmental

The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analysed all mutations in candidate genomic regions associated

This is the first case of Spiromastigoides asexualis human infection and notably gave a false-positive Blastomyces DNA probe laboratory result. We further investigated other Spiromastigoides isolates as a cause of false-positive testing results, their phylogenetic relationship, and their susceptibility profiles to clinically available antifungal agents. Other S. asexualis isolates also resulted in

Nontyphoidal Salmonella (NTS) are among the most common aetiological agents of diarrhoeal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalised with diarrhoea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical

Human papillomavirus (HPV) epidemiological and vaccine studies require highly sensitive HPV detection systems. The widely used broad-spectrum SPF10-DEIA-LiPA25 (SPF10 method) has reduced sensitivity towards HPV-45 and -59. Therefore, anogenital samples from the PASSYON study were retrospectively analyzed with type-specific (TS) HPV-45 and -59 qPCR assays. The SPF10 method missed 51.1% of HPV-45 and

Background: The ongoing COVID-19 pandemic has resulted in shortages in nasopharyngeal swabs (NPS) and viral transport media, necessitating the search for alternate diagnostic specimens, such as saliva. We directly compared matched saliva and NPS specimens from symptomatic patients suspected of having COVID-19.

Tickborne diseases, due to a diversity of bacterial pathogens, represent a significant and increasing public health threat throughout the northern hemisphere. A high-throughput 16S V1-V2 rDNA-based metagenomics assay was developed and evaluated using >13,000 residual samples from patients suspected of tickborne illness and >1000 controls. Taxonomic predictions for tickborne bacteria were exceptionally

Objectives: The objective of this study was to evaluate the MICRONAUT-S Carbapenemases Detection microtiter plate assay for detection of carbapenemases and Ambler class determination.

The worldwide emergence and spread of antimicrobial resistance in Gram-negative bacteria is severely limiting therapeutic options, and thus constitutes a major public health threat. The timely accurate detection of carbapenemase producers and the determination of carbapenemase class according to the Ambler classification can guide antimicrobial therapy and facilitate infection control measures. A modified

Identification (ID) and antimicrobial susceptibility testing (AST) of respiratory pathogens are critical to the management of patients with pneumonia to facilitate optimal antibiotic therapy selection. Few studies have examined the time to results (TTR) for this critical specimen, and such data can be valuable for benchmarking the current paradigm of diagnostic approaches. TTR for bronchoalveolar lavage

Along with the implementation of the measles case-based surveillance, measles vaccine-associated rash illness (VARI) cases were detected in China. To better understand the characteristics of VARI, 101 VARI cases confirmed by measles virus genotyping in 2011-2018 were analyzed in this study. With the decrease in measles incidence, the detection rate of VARI cases increased among the cases confirmed

Diagnosis of Mycoplasma pneumoniae (Mp) infection with community-acquired pneumonia (CAP) is challenging (1).…

Influenza A viruses (IAVs) infect humans and a variety of other animal species. Infections with some subtypes of IAV were also reported in domestic cats and dogs. Besides animal health implications, close contact between companion animals and humans also poses a potential risk of zoonotic IAV infections. In this study, serum samples from different cat and dog cohorts were analyzed for IAV antibodies

Ancestral genetic exchange between members of many important bacterial pathogen groups has resulted in phylogenetic relationships better described as networks than as bifurcating trees. In certain cases, these reticulated phylogenies have resulted in phenotypic and molecular overlap that challenges the construction of practical approaches for species identification in the clinical microbiology laboratory

Tickborne disease pathogen identification remains a diagnostic challenge due to the multiple tests necessary for diagnosis. Targeted metagenomic sequencing is an evolving method to detect multiple different pathogens with a single test. In this issue of the Journal of Clinical Microbiology, L. Kingry, S. Sheldon, S. Oatman, B. Pritt, et al. (J Clin Microbiol 58:e00147-20, 2020, https://doi.org/10.1128/JCM

Background Entamoeba histolytica infection is an increasingly common sexually transmitted infection in Japan. Currently, stool ova and parasite examination (O&P) is the only approved diagnostic method. Herein, we assessed the utility of the commercially available rapid antigen detection test (QUIK CHEK) for E. histolytica.

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has caused a global pandemic of COVID-19 resulting in cases of mild to severe respiratory distress and significant mortality. The global outbreak of this novel coronavirus has now infected >20 million people worldwide with >5 million cases in the US (August 11th, 2020). The development of diagnostic and research tools to determine infection

Visceral leishmaniasis (VL) is a threat in many developing countries. Plenty of efforts have been put to eliminate this disease, for which serodiagnosis remains the mainstay for VL control programs. New and improved antigens as diagnostic candidates are required since available antigens fail to demonstrate optimum performance in endemic areas equally. Moreover, the diagnosis is dependent on invasive

Coronavirus disease 19 (COVID-19), caused by SARS-CoV-2 is a major pandemic (2).…

Objectives In the early 2000s, a binary toxin (CDT)-producing strain of Clostridium difficile, ribotype (RT) 027, caused extensive outbreaks of diarrhoeal disease in North America and Europe. This strain has not established in Australia and there is a markedly different repertoire of circulating strains compared to other regions of the world. The C. difficile Antimicrobial Resistance Surveillance (CDARS)

Background: Cryptococcal epidemiology is shifting towards HIV-negative populations who have diverse presentations. Cryptococcal antigen testing (CrAg) is als