Journal of Clinical Microbiology最新文献

The promising diagnostic performance of molecular testing for syphilis using saliva and urine samples has been reported; however, further evaluation of its possible application for diagnosis and molecular surveillance is required. In addition, the development of a rapid and easy-to-perform molecular test for syphilis is important for its use in the clinical setting. We comprehensively evaluated the diagnostic and surveillance performance of two novel loop-mediated isothermal amplification (LAMP) assays using saliva and urine samples. Saliva, urine, and whole blood were collected from patients who underwent serological testing for syphilis at outpatient clinics. Treponema pallidum DNA in specimens was detected using quantitative PCR (qPCR), nested PCR, and novel LAMP assays. T. pallidum genotyping was conducted by multi-locus sequence typing (MLST). Of the 163 patients recruited, 98 were diagnosed with syphilis (primary: n = 35; secondary: n = 40; latent: n = 23). qPCR showed the highest sensitivity among the molecular tests performed with a sensitivity of 54.1% and 30.3% for all syphilis patients using saliva and urine samples, respectively. A novel method of LAMP combined with dry reagents and crude DNA extraction (Dry-LAMP) showed a probit detection limit of 37.4 copies/reaction within 45 min. The agreement rate between Dry-LAMP and qPCR for saliva was 95.7% (κ coefficient 0.90). The T. pallidum genotype was identified in 48 patients by MLST using saliva samples. Molecular analysis of saliva could be used as a supplementary diagnostic test for syphilis and molecular surveillance of the T. pallidum genotype. Dry-LAMP is expected to be helpful in the clinical diagnosis of syphilis.

Rapid multiplex PCR kits have been used for rapid identification of blood culture isolates and prediction of antimicrobial resistance. We performed an evaluation of the QIAstat-Dx BCID GN and GPF research use only (RUO) kits on positive blood culture bottles using routine laboratory testing as the reference standard. Positive blood culture bottles between November 2023 and January 2024 were tested with QIAstat-Dx BCID GN and GPF kits based on initial Gram stain results and compared against routine identification and phenotypic susceptibility testing. A total of 174 monomicrobial blood cultures were included in the final analysis. The 174 monomicrobial blood cultures composed of 129 BCID GN tests and 45 BCID GPF tests. The majority of on-target Gram-negative organisms in monomicrobial cultures were identified. One Escherichia coli isolate was not identified as such, although the pan-Enterobacterales target was positive. All on-target Gram-positive organisms in monomicrobial cultures were identified. Overall sensitivity and specificity of tem/shv for detection of aminopenicillin resistance in E. coli was 94.7% (18/19) and 95.8% (23/24). The presence/absence of ctx-m and ampC had 100% sensitivity and specificity for identification of third-generation cephalosporin resistance in E. coli and Klebsiella pneumoniae. The combination of blaZ and mecA gene detection was fully predictive of phenotypic susceptibility results to penicillin and cloxacillin for Staphylococcus aureus. Overall, the QIAstat-Dx BCID GN and GPF kits were able to identify on-target pathogens. Detected resistance mechanisms were highly predictive of β-lactam resistance. Prediction of resistance for non-β-lactam antimicrobial was more variable.

Importance: This is one of the first evaluations of the QIAstat BCID kit and demonstrates high levels of correlation for both identification and antimicrobial resistance prediction.

Fungal keratitis (FK) is a serious suppurative and ulcerative corneal infection leading to blindness and vision loss. Rapid diagnosis of FK can contribute to prompt clinical management with early recovery. The study aimed to standardize the detection of (1,3)-β-D-glucan (BDG) and establish the diagnostic cut-off concentration in tears of suspected FK patients along with non-infected controls. This prospective multicentric study was conducted between the period of August 2022 and April 2024. Samples were collected from three tertiary eye-care facilities across India. All suspected FK patients were enrolled in the study. Prior to tear collection, the eye and eyelid were gently cleansed using sterile normal saline (NS) and lint-free tissue paper. Subsequently, 50 µL of sterile NS was instilled into the eye, followed by tear sample collection after 60 s using sterile fine microtips. Tear samples were collected from the contralateral eyes of the FK patients, and those from healthy volunteers served as controls. The concentration of BDG in tears in varying dilutions was quantitatively measured using the Fungitell Assay Kit (Associates of Cape Cod, East Falmouth, Massachusetts). A total of 53 tear samples were analyzed at 1:10 and 1:20 dilutions. The receiver operating curve revealed an area under the curve (AUC) of 0.919 for the 1:10 dilution, with a cut-off value of 123 pg/mL, yielding a sensitivity of 100% and specificity of 84.85%. The corresponding Youden Index was 0.798. At the 1:20 dilution, the AUC was 0.898 with a cut-off of 84 pg/mL, achieving a sensitivity of 70% and specificity of 96.88% with a Youden Index of 0.670. Given the higher specificity at the 1:20 dilution, it was further validated in 145 tear samples. The validation cohort demonstrated a sensitivity of 95.56%, specificity of 83%, positive predictive value (PPV) of 71.67%, negative predictive value (NPV) of 97.65%, and diagnostic odds ratio of 112.4. Notably, a significantly higher BDG concentration (P < 0.0001) was observed in infected tear samples compared to controls (270.6 ± 128.5 vs 37.31 ± 31.32). Detection of BDG in tear samples is a new, non-invasive, and rapid technique showing excellent performance and can be effectively implemented for diagnosing FK in laboratories.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its largely aseasonal spread with millions of cases per year. Highly sensitive, point-of-care testing is critical for rapid detection of coronavirus disease 2019 (COVID-19) cases and initiation of antiviral therapy to avert adverse health outcomes and reduce onward transmission of the virus. While hundreds of COVID-19 diagnostics received emergency use authorization from the FDA during the pandemic, significantly fewer have navigated the course to FDA clearance or approval. Here, we determined the clinical performance of the Cepheid Xpert Xpress CoV-2 plus for detection of SARS-CoV-2 in 3,750 anterior nasal swab (NS) specimens and nasopharyngeal swab (NPS) from 32 sites in comparison to the FDA-authorized BioFire Respiratory Panel 2.1. Three-quarters of specimens collected were tested on the Xpert Xpress CoV-2 plus in the point-of-care setting. Overall positive percent agreement (PPA) was 98.1% (95% CI: 96.7%-98.9%) and negative percent agreement (NPA) was 98.3% (97.7%-98.7%). Performance of the Xpert Xpress CoV-2 plus was slightly improved in NS compared to NPS specimens, with PPA of 99.3% versus 97.0% (Fisher's exact test, P = 0.06) and NPA of 98.3% versus 98.2% (P = 0.89), respectively. Assay PPA was similar between untrained and trained users (98.7% vs 97.3%, P = 0.75), while NPA was slightly improved for untrained users (99.0% vs 97.6%, P = 0.0003). This study showed that Cepheid Xpert Xpress COV-2 plus is highly sensitive and specific/has high PPA and NPA for detection of SARS-CoV-2 from both NS and NPS specimens.

Importance: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause millions of infections and tens of thousands of deaths per year in the United States. While the FDA authorized hundreds of SARS-CoV-2 tests during the public health emergency, significantly fewer have made the transition to being cleared or approved. There continues to be a need for FDA-authorized point-of-care SARS-CoV-2 testing that can be performed by untrained users. We conducted a large prospective study of the Cepheid Xpert Xpress CoV-2 plus test for detection of SARS-CoV-2 in both nasal and nasopharyngeal swabs by trained and untrained users. The assay demonstrated excellent clinical performance characteristics and, as a result of this study, was cleared by the FDA.

Invasive aspergillosis (IA) is a life-threatening infection. Early and specific diagnosis is pivotal to ensure adequate therapy. Antigen testing from blood is a widespread and convenient diagnostic approach. Various tests for the detection of Aspergillus antigen as well as for the panfungal antigen β-1,3-D-glucan (BDG) are available, for which comprehensive comparisons are still lacking. Blood samples of 82 proven/probable (11/71) IA patients and 52 controls were tested using two enzyme-linked immunosorbent assays (ELISAs) (Bio-Rad and Euroimmun), one chemiluminescent immunoassay (CLIA) (Vircell), one BDG assay (Fujifilm Wako), and two point of care (PoC) assays (Immy sōna and OLM). PoC assays were evaluated visually and used automated read out systems. Of the 82 IA patients, 37 had received solid organ transplantation (SOT) and 25 hematopoietic stem cell transplant (HSCT). Sensitivities and specificities for the eight test systems ranged from 27% to 71% and from 64% to 100%. Estimating a 10% prevalence of IA, test performance would have resulted in positive and negative predictive values of 14%-100% and 91%-95%. Areas under the curve (AUCs) for all tests except GM were below 0.7. When the cut-off values for quantitative tests were normalized to a specificity close to 95%, sensitivities ranged from 14% to 40%. The use of automated read out systems for the PoC assays had a significant impact. Combining different tests did not result in better test strategies. Sensitivity of Aspergillus antigen testing from single serum samples is low. Due to specificity issues, the majority of tests is not suited for screening purposes. The different assays can meet different needs in different diagnostic settings.

Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the International Journal of Systematic and Evolutionary Microbiology during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to Aerococcus spp., several Corynebacterium spp., Exercitatus varius gen. nov., sp. nov., and Mycoplasma phocimorsus sp. nov. With respect to nomenclature revision, the Bacillus and Clostridium genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera Hallella, Hoylesella, Leyella, Segatella, and Xylanibacter impacted several Bacteroides spp. and Prevotella spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.

With the proliferation of abundant bacterial genomic data comes the recognition of new organisms as well as a better understanding of the relatedness of known bacteria. Recognizing the associated taxonomic changes enhances communication and understanding about the significance of novel organisms and deeper understanding of known pathogens. This review addresses the addition of multiple gastrointestinal bacteria that form the normal microbiota in a variety of animals including honeybees as well as novel bacteria from domestic animals including an alpha-hemolytic Streptococcus species from guinea pigs, two Moraxella spp. from cows and goats, a new Capnocytophaga species from cats, a thermophilic Campylobacter species from pigs, and the new Exercitatus genus in Family Pasteurellaceae. Several revisions to the nomenclature also appeared in 2023 including the change of Clostridium spiroforme, which causes anorexia and diarrhea in domestic rabbits, to Thomasclavelia spiroformis comb. nov. and Mannheimia ovis to Mannheimia pernigra.

Rapid antimicrobial susceptibility testing (rAST) performed directly from blood cultures is essential to influencing the selection of appropriate antibiotics, preferably targeted therapy, for the treatment of bloodstream infections. Affinity Biosensors has developed the LifeScale, a phenotypic rAST system based on microfluidic sensors with a mechanical resonator that measures the mass of individual microbes. The combination of replication, biomass, and population profiling of individual microbes is analyzed to produce rAST results. The performance of the LifeScale was evaluated and compared to our current standard of care (SOC) antimicrobial susceptibility testing (AST) system under clinical conditions. The results indicated that the LifeScale is easy to use and provides rapid, reliable, and accurate AST results in less than 5 h directly from from positive blood cultures containing Gram-negative organisms listed in the current database. For all organism-antibiotic combinations involving polymicrobial cultures, LifeScale showed a resistant result when either mixed isolate was resistant. If these results prove to be robust on further testing, this may justify the reporting of rapid LifeScale results without the need for additional confirmatory testing.

Importance: This is the first clinical-based study of a unique technology using microfluidic sensors to generate rapid antimicrobial susceptibility test results directly from blood cultures containing Gram-negative rods. The issue of polymicrobial cultures was also addressed in this study, which, to our knowledge, has not been addressed in publications of other rapid phenotypic AST systems. Overall, LifeScale results compared favorably with the SOC in terms of overall agreement, especially categorical agreement.

Shiga toxin-producing Escherichia coli (STEC) are the main etiological agents of hemolytic uremic syndrome (HUS). Good clinical management of STEC infections and HUS depends on early, rapid, and accurate diagnosis. Here, we have developed and evaluated the first multiplex and glycoprotein-based immunochromatographic test for the detection of IgM antibodies against the O-polysaccharide of the lipopolysaccharide of E. coli O157 and O145 in human serum samples. A retrospective study was carried out resulting in a diagnostic sensitivity of the E. coli O157/O145 LFIA (lateral flow immunoassay) of 97.1% and 98.9% for O157 and O145, respectively, and 97.9% for both serogroups. The diagnostic specificity was 98.7% for O157 and O145, and the overall specificity 97.4%. In samples obtained before 3 days after the onset of diarrhea, the detection percentage was 83%, increasing to 100% from 3 days onward. Finally, the association of bloody diarrhea (BD) or HUS cases to an STEC infection increased from 22.8% to 77.2% when stool culture and stx/Stx detection were combined with serology by LFIA. Our results demonstrate that the E. coli O157/O145 LFIA is a highly accurate and serospecific test for the early and rapid diagnosis of E. coli O157 and O145 infections in BD or HUS cases. This test allows the detection of specific IgM antibodies very early in the course of the infection, making it an ideal diagnostic tool to be implemented in pediatric emergencies and, thus, avoid delays in the application of the correct supportive or specific treatment and prevent complications associated with HUS.