Journal of Clinical Microbiology最新文献

Mosquito-borne viruses represent a large global health burden. With geographic expansion of competent vectors for chikungunya virus (CHIKV), dengue virus (DENV), and Zika virus (ZIKV) in Europe, it is anticipated that the number of autochthonous cases of these tropical viruses in Europe will increase. Therefore, regular assessment of diagnostic capabilities in Europe is important. Our aim was to evaluate the mosquito-borne virus molecular detection capability of expert European laboratories by conducting an external quality assessment in October 2023. Molecular panels included 12 plasma samples: one alphavirus (CHIKV), four orthoflaviviruses (ZIKV, yellow fever virus [YFV], DENV, and Japanese encephalitis virus [JEV]), and two negative control samples. Mosquito-borne virus detection was assessed among 36 laboratories in 24 European countries. Adequate capabilities were lacking for YFV and JEV. Many laboratories relied on a mix of laboratory-developed tests (some of which were pan-orthoflavivirus or pan-alphavirus in combination with sequencing) and commercial assays. 47.2% of laboratories characterized all external quality assessment (EQA) samples correctly. Correct result rates were 100% for CHIKV and ZIKV and >99% for DENV, but laboratories lacked capacity, specificity, and sensitivity for JEV and YFV. Three of the viruses in this panel emerged and transiently circulated in Europe: CHIKV, ZIKV, and DENV. Molecular detection was excellent for those viruses, but <50% is accurate for the remainder of the panel. With the possibility or continuation of imported cases and a growing global concern about climate change and vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended, as well as regular EQAs to monitor it.IMPORTANCEThe external quality assessment (EQA) focused on Aedes-borne viruses: chikungunya virus (CHIKV), dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV). Japanese encephalitis virus, an orthoflavivirus that is spread by mosquito species belonging to the genus Culex, was included in the quality assessment as well. CHIKV, DENV, and ZIKV have proven potential for transient and limited circulation in Europe upon introduction of viremic travelers returning to Aedes albopictus-endemic regions. Results of this EQA were excellent for those viruses, but <50% is accurate for the remainder of the panel (YFV and Japanese encephalitis virus). Considering imported cases and the threat of climate change and competent vector expansion, progress toward rapid, accurate mosquito-borne virus diagnostics in Europe is recommended.

Human strongyloidiasis is often underdiagnosed or misdiagnosed, which can relate to a lack of knowledge or recognition of the importance of particular developmental/larval stages of Strongyloides stercoralis in making an accurate diagnosis using parasitological methods (a morphological approach or morphological features/characters). Here, we report the identification of S. stercoralis autoinfective fourth-stage larvae (L4a) in naturally infected humans, encountered in two clinical cases in Australia. These larvae were identified in sputum (Case 1) and bronchoalveolar lavage (Case 2) specimens by direct wet-mount microscopy. The L4a of S. stercoralis can be morphologically differentiated from autoinfective third-stage larvae by its conical and pointed tail and a relatively mature genital primordium with an enlarged genital rudiment and the formation of a vulva within cuticle layers. This study emphasizes the need to consider these morphological features of the L4a stage for an accurate diagnosis of S. stercoralis infection. A detailed morphological description of this stage is given to guide laboratory practitioners and researchers in the identification and differentiation of this unique but neglected life-cycle stage of S. stercoralis.

The spread of carbapenemase-producing Enterobacterales (CPE) is emerging as a significant clinical concern in tertiary hospitals and, in particular, long-term care facilities with deficiencies in infection control. This study aims to evaluate an advanced matrix-assisted laser desorption/ionization (A-MALDI) mass spectrometry method for the identification of carbapenemases and further discrimination of their subtypes in clinical isolates. The A-MALDI method was employed to detect CPE target proteins. Enhancements were made to improve detectability and mass accuracy through the optimization of MALDI-TOF settings and internal mass calibration. A total of 581 clinical isolates were analyzed, including 469 CPE isolates (388 Klebsiella pneumoniae carbapenemases [KPC], 51 NDM, 40 OXA, and 2 GES) and 112 carbapenemase-negative isolates. Clinical evaluation of the A-MALDI demonstrated 100% accuracy and precision in identifying all the collected CPE isolates. Additionally, A-MALDI successfully discriminated individual carbapenemase subtypes (KPC-2 or KPC-3/KPC-4, OXA-48 or OXA-181 or OXA-232, GES-5 or GES-24) and also differentiated co-producing carbapenemase strains (KPC and NDM, KPC and OXA, KPC and GES, and NDM and OXA), attributed to its high mass accuracy and simultaneous detection capability. A-MALDI is considered a valuable diagnostic tool for accurately identifying CPE and carbapenemase's subtypes in clinical isolates. It may also aid in selecting appropriate antibiotics for each carbapenemase subtype. Ultimately, we expect that the A-MALDI method will contribute to preventing the spread of antibiotic resistance and improving human public health.

Importance: A-MALDI clearly demonstrated excellent ability to identify CPEs such as KPC, NDM, OXA, and GES when carbapenemase is present in the strain (100% accuracy and precision). The method also successfully discriminated carbapenemase subtypes and simultaneous detection of co-producing multiple carbapenemases in a single strain. This is the first report for simultaneous and multiple detection of intact carbapenemases of KPC, NDM, OXA, and GES using matrix-assisted laser desorption/ionization mass spectrometry in a clinical isolate.

BluePoint MoldID can identify 43 fungal species through nucleic acid array hybridization and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) can identify 247 filamentous fungi through mass spectrometry. First, 43 standard isolates from the Bioresource Collection and Research Center, Taiwan, and the College of American Pathologists and 41 clinical Aspergillus species isolates confirmed by rDNA-ITS sequencing were analyzed using BluePoint MoldID and Bruker MALDI-TOF MS. BluePoint MoldID accurately identified 79% (34/43) of the standard isolates to the species level but failed to recognize nine isolates absent from its database; additionally, 87.8% (36/41) of the clinical isolates were identified at the species level, with 80.5% (33/41) accuracy. MALDI-TOF MS identified 86% (37/43) of the standard isolates, with 81.4% (35/43) accurately identified at the species level and two at the genus level, and identified all the clinical isolates, with 92.6% (38/41) accurately identified at the species level. Next, we analyzed 93 clinical Aspergillus species and compared the results by rDNA-ITS sequencing. BluePoint MoldID identified 87.1% (81/93) of the isolates at the species level, with 80.6% (75/93) accuracy. MALDI-TOF MS identified 97.8% (91/93) of the isolates, including some uncommon species, with 90.3% (84/93) accuracy at the species level. BluePoint MoldID and MALDI-TOF MS had turnaround times of 8 and 2 h, respectively, significantly reducing the time needed to identify filamentous fungi.

Importance: The BluePoint MoldID kit is an oligonucleotide array used for the identification of filamentous fungi, and it has not yet been mentioned in recent studies. We used a BluePoint MoldID kit to identify standard and clinical filamentous fungal isolates and compared its performance with that of Bruker MALDI-TOF MS. The former accurately identified 80.2% of the isolates (142/177), and the latter identified 92.6% of the isolates (164/177). The performance of the BluePoint MoldID kit was slightly inferior to that of Bruker MALDI-TOF MS because of the smaller database. However, the BluePoint MoldID kit can cover most clinically common opportunistic fungal infections; thus, it offers an alternative method for laboratories that lack MALDI-TOF MS equipment, as the device is less expensive.

Accurate identification of non-tuberculous mycobacterial (NTM) species is crucial for the diagnosis and appropriate management of NTM infections. This study aimed to evaluate the performance of two assays, FluoroType Mycobacteria VER 1.0 and Maldi BioTyper (MBT) Mycobacteria. The two assays were evaluated using 119 NTM, including 85 slow-growing mycobacteria and 34 rapid-growing mycobacteria, representing a total of 33 species isolated in three French clinical laboratories. We used the GenoType assays as reference method for species identification, followed by 16S rRNA gene sequencing if the GenoType kits returned Mycobacterium sp. Compared to the reference method, the FluoroType Mycobacteria assay provided correct species identification in 89.9% of cases (107/119). Among the most frequently encountered species in clinical settings, low concordance was obtained for Mycobacterium intracellulare (82.4%, 14/17), Mycobacterium gordonae (66.7%, 6/9), and Mycobacterium xenopi (75%, 6/8). Misidentification was obtained in two cases (Mycobacterium smegmatis instead of Mycobacterium mageritense, and Mycobacterium mucogenicum instead of Mycobacterium phocaicum). Using the MBT Mycobacteria assay, 78.1% (93/119) of NTM isolates were correctly identified at the species level. One Mycobacterium europaeum isolate was misidentified as M. intracellulare/Mycobacterium chimaera. In five cases, the assay provided more accurate NTM identification compared to GenoType assays, in which closely related species are identified as a group. The FluoroType Mycobacteria VER 1.0 and the MBT Mycobacteria assays are useful tools for NTM identification from positive cultures, reducing handling time compared to GenoType assays. Their routine use in laboratories must take into consideration their performance and limitations in clinical settings.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with a high mortality rate that is often underdiagnosed due to the limitations of current laboratory testing. Timely diagnosis and early identification of severe cases are crucial to improving patient outcomes and overall survival rates. This study aimed to evaluate the efficacy of two transcripts, IFI44L and PI3, in the early differentiation between SFTS virus (SFTSV) infection and bacterial sepsis, as well as in the prompt identification of severe cases during epidemic seasons. In a prospective study conducted between 1 May 2021 and 30 September 2022, we enrolled 225 patients who presented with acute fever and thrombocytopenia at four hospitals in Shandong Province, China. The two-transcript signature provided a clear distinction between SFTS and bacterial infection, achieving an area under the receiver operating characteristic curve of 0.961 (95% confidence interval [95% CI] 0.916-0.986), outperforming C-reactive protein (0.810 [95% CI 0.738-0.870]) and procalcitonin (0.764 [95% CI 0.687-0.830]). Importantly, the relative expression of the IFI44L gene was significantly elevated in fatal SFTS cases, with an area under the curve (AUC) of 0.820 (95% CI 0.727-0.914), indicating its potential as an early prognostic marker. Additionally, IFI44L and PI3 were identified as potential biomarkers for distinguishing SFTS patients with and without invasive pulmonary aspergillosis, with AUC values of 0.817 and 0.753, respectively. Our findings demonstrate that the two-transcript signature effectively distinguishes SFTSV infection from bacterial sepsis and helps identify high-risk individuals, guiding appropriate treatment during SFTS outbreak.

The laboratory diagnosis of Clostridioides difficile infection (CDI) is controversial. Nucleic acid amplification tests (NAAT) and toxin enzyme immunoassays (EIA) are most widely used, often in combination. However, the interpretation of a positive NAAT and negative toxin immunoassay (NAAT+/EIA-) is uncertain. PubMed and EMBASE were searched for studies reporting clinical outcomes in NAAT+/EIA- versus NAAT+/EIA+ patients. Forty-six studies comprising 33,959 patients were included in this meta-analysis. All-cause mortality (RR 0.96, 95% CI 0.80-1.15), attributable mortality (RR 0.61, 95% CI 0.20-1.91), fulminant CDI (RR 0.83, 95% CI 0.57-1.20), radiographic evidence of CDI (RR 0.87, 95% CI 0.65-1.16), total CDI complications (RR 0.95, 95% CI 0.59-1.53), colectomies (RR 0.78, 95% CI 0.34-1.79), and ICU admission (RR 1.04, 95% CI 0.84-1.30) did not significantly differ between NAAT+/EIA- and NAAT+/EIA+ patients. However, rates of recurrent (RR 0.62, 95% CI 0.50-0.77) or severe (RR 0.74, 95% CI 0.63-0.88) CDI were significantly lower in NAAT+/EIA- patients than in NAAT+/EIA+ patients. The pooled prevalence of NAAT+/EIA- patients who were treated with antibiotics for CDI was 73.4% (pooled proportion 0.72, 95% CI 0.52-0.88). NAAT+/EIA- patients have lower rates of recurrence and are at reduced risk for severe CDI compared with NAAT+/EIA+ patients but have a risk of CDI-related complications and mortality comparable to that of NAAT+/EIA+ patients. Toxin results cannot rule in or rule out CDI, and the decision whether to treat symptomatic NAAT+/EIA- patients for CDI should be based on clinical presentation and not on the toxin result.IMPORTANCEClostridioides difficile infection (CDI) is a common cause of healthcare-associated infections and the leading cause of antibiotic-associated diarrhea. However, the laboratory diagnosis of CDI, primarily done by nucleic acid amplification test (NAAT) and enzyme immunoassay (EIA), is controversial, especially in patients who test positive by NAAT but negative by EIA. In this systematic review, we compared the clinical outcomes of NAAT+/EIA- versus NAAT+/EIA+ patients and found that the two groups have similar risk of mortality and CDI-related complications. However, NAAT+/EIA- patients had significantly lower rates of recurrence and severe CDI than NAAT+/EIA+ patients, and most NAAT+/EIA- patients received CDI therapy. Toxin testing can help to predict the likelihood of CDI recurrence or severe infection, but the toxin result should not be a determining factor in the administration of CDI therapy. The decision on whether to treat NAAT+/EIA- patients should be based on clinical assessment.