Microbiology Spectrum

The use of carbapenem antibiotics is threatened by the global spread of carbapenemase-producing Enterobacterales (CPE), bacterial pathogens which hydrolyze these last-resort antimicrobials. Rapid detection of CPE is vital to ensure timely administration of antimicrobial therapy to infected patients, as well as the implementation of infection control measures to prevent outbreaks in healthcare settings. In this study, we report the development of resaCPE, a rapid, low-cost CPE detection method th...

In this report, we describe the development and initial validation of novel SARS-COV-2 Omicron-specific reactions that enable the identification of Omicron (BA.1) and BA.2 variants. Mutations that are either shared by both BA.1 and BA.2, or are exclusive for BA.1 or for BA.2 were identified by bioinformatic analysis, and corresponding probe-based quantitative PCR reactions were developed to identify them. We show that multiplex combinations of these reactions provide a single-reaction identifica...

BackgroundPatients have been shown to shed SARS-CoV-2 viral RNA in nasopharyngeal (NP) specimens for over 100 days after resolution of clinical disease (1, 2). How this relates to anterior nares and oral fluid specimens has not previously been investigated. MethodsWe prospectively collected oral fluid, anterior nares, NP swab and serum specimens from 1,326 individuals at 2 "drive-through" testing locations. The Curative SARS-CoV-2 Assay (Curative Assay)(3) on oral fluid and anterior nares speci...

Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the viruss transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LD...

Ziehl-Neelsen (ZN) smear microscopy remains central to tuberculosis (TB) diagnosis and treatment monitoring, yet its sensitivity is limited by incomplete recovery of Mycobacterium tuberculosis during pre-analytical processing. This study evaluated whether modifying centrifugation force and duration improves bacillary recovery and ZN smear performance. Laboratory experiments were conducted using M. tuberculosis H37Rv and pulmonary TB sputum samples. Following NALC-NaOH decontamination, samples we...

Given the unprecedented demand for SARS-CoV-2 testing during the COVID-19 pandemic, the benefits of specimen pooling have recently been explored. As previous studies were limited to mathematical modeling or testing on low throughput PCR instruments, this study aimed to assess pooling on high throughput analyzers. To assess the impact of pooling, SARS-CoV-2 dilutions were performed at varying pool depths (i.e. 1:2, 1:4, and 1:8) into test-negative nasopharyngeal or oropharynx/anterior nares swabs...

Oral swabs are emerging as a non-invasive sample type for diagnosing infectious diseases including Ebola, tuberculosis (TB), and COVID-19. To assure proper sample collection, sample adequacy controls (SACs) are needed that detect substances indicative of samples collected within the oral cavity. This study evaluated two candidate SACs for this purpose. One detected representative oral microbiota (Streptococcus species DNA) and the other, human cells (human mitochondrial DNA, mtDNA). Quantitative...

BackgroundMetagenomics has the potential to revolutionise infectious diseases diagnostics, from rapid species and antimicrobial resistance prediction, to finding unrecognised and sometimes untreated infections. Our aim was to summarise all literature on culture-independent metagenomic sequencing to describe the accuracy of species and antimicrobial resistance prediction and, describe the challenges and progress in the field. MethodsWe conducted a systematic review with meta-analysis from eligib...

We had developed a MALDI-TOF mass spectrometry method for detection of SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conference and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR dependent rapid affordable SARS-CoV-2 infection screening tests, which als...

A quantitative biophotonic assay for IgG antibodies for the SARS-CoV-2 spike protein has been standardised against the NISTmAb antibody. Serum from patients recovering from infection, a sterilising serum, and post-vaccination, are used to profile anti-spike protein IgG responses. The vaccine response distributions were used to quantify live-challenge protective thresholds: the 31st percentile of the AstraZeneca ChAdOx1-S (AZ, n =35 patients) distribution (2.90 {+/-} 1.10 mg/L) and the 7th percen...

The Omicron variant is characterised by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined. We evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants. The positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI:...

The immunochromatographic assay RESIST ACINETO (Coris BioConcept) was evaluated on a collection of 121 Acinetobacter spp. clinical isolates, including 104 carbapenemase producers. The strains producing carbapenemases OXA-23, -40, -58, or/and NDM were accurately detected from bacterial cultures and directly from blood cultures, with the exception of an OXA-23/NDM-1-positive A. radioresistens isolate (only detected through standard culture). The performance of the RESIST ACINETO test was excellent...

Antigen-detection rapid diagnostic tests (Ag-RDTs) have become a central pillar for the management of COVID-19 worldwide due to their speed and ease of use, and are now being developed for use in other emerging outbreaks. Like other viruses, SARS-CoV-2 is subject to rapid mutation as it spreads, and new Variants of Concern (VOCs) emerge frequently, posing a significant challenge for the reliability of Ag-RDTs designed against the original strain to detect newer, highly mutated variants. It is th...

BackgroundThe exponential growth of COVID-19 cases and testing has created supply shortages at various points in the testing workflow. As of April 15, 2020 FDA recommendations only allowed for the use of nasopharyngeal, flocked mid turbinate, or foam nasal swabs, all of which are in very low supply. Polyester swabs are more readily available and mass producible. We compare the performance of polyester and foam swabs stored in different transport media. MethodsBoth polyester and foam nasal swabs...

Tongue dorsum swabbing is a potential alternative to sputum collection for tuberculosis (TB) testing. Previous studies showed that Cepheid Xpert(R) MTB/RIF Ultra (Xpert Ultra) can detect Mycobacterium tuberculosis (MTB) DNA in tongue swabs stored in buffer, with 72% sensitivity and 100% specificity relative to a sputum microbiological reference standard (sputum MRS). The present study evaluated a more convenient sample collection protocol (dry swab storage), combined with streamlined sample proc...

BackgroundSputum-based testing has long been the cornerstone of tuberculosis (TB) diagnosis, but emerging specimen types like tongue swabs (TS) offer additional approaches for detecting Mycobacterium tuberculosis complex (MTBC). This two-phase study evaluated the impact of storage and transport conditions, along with laboratory processing modifications, to improve MTBC detection using TS tested on quantitative PCR (qPCR) and Xpert MTB/RIF Ultra (Ultra). MethodsParticipants with positive Ultra s...

We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, ...

ObjectivesAntigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the Covid-19 pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend molecular confirmation of positive Ag-RDT results. This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular method for SA...

ObjectiveThe rapid availability of phenotypic antimicrobial susceptibility results is crucial for the timely detection of multidrug-resistant Gram-negative organisms and for guiding optimized treatment strategies. Recently, novel methods have been introduced that enable direct antimicrobial susceptibility testing (AST) from positive blood cultures. However, their performance has not yet been systematically compared in head-to-head evaluations. This study aimed to assess the analytical performanc...

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 6.8 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The primary goal of this study was to assess the prevalence of bacterial co-infections and to describe any trends observed during the height of the COVID-19 pandemic. To do this, we investigated SARS-CoV-2 and...