Journal of Clinical Microbiology最新文献

Streptococcus pneumoniae serotype 23B, a non-vaccine serotype, has shown an increasing prevalence and penicillin non-susceptibility among carriage and invasive pneumococcal disease (IPD) isolates. Recently, a novel penicillin non-susceptible genotype has emerged, named 23B1. In the framework of the Belgian pneumococcal carriage study, we studied the prevalence of 23B₀/23B1 among 586 23B strains (2016-2022) in 172 day care centers from 6- to 30-month-old children and among 130 pediatric 23B IPD isolates (2007-2021). Pneumococci were whole genome sequenced to determine the capsular polysaccharide genotype and sequence type (ST). Antimicrobial susceptibility testing determined penicillin and amoxicillin MICs, as well as resistance to co-trimoxazole and levofloxacin. 23B carriage was stable during 2016 ̶ 2022 except in the 2020-2021 winter season when it increased. The proportion of genotype 23B1 compared to 23B₀ decreased from 2016 ̶ to 2022 but remained consistently higher than 23B₀. In 2020-2021, an increase in the proportion of 23B1 was reflected in an overall increase in 23B carriage. All increases in 23B IPD cases were almost entirely driven by 23B1. The median penicillin MICs were significantly different for 23B₀ (0.03 mg/L) and 23B1 (0.25 mg/L). In 2021, increased intermediate levofloxacin susceptibility was noted in 23B. 23B1-associated ST2372 was the most prevalent ST in carriage and IPD during 2013-2022. We show that an increase in 23B carriage among children was paralleled in pediatric IPD in Belgium, reiterating the utility of pneumococcal surveillance in the day care population. Serotype 23B is reported worldwide as an important pediatric non-PCV13 serotype with reduced penicillin susceptibility, with 23B1 as the presumed driver for the increased prevalence.IMPORTANCEDuring the COVID-19 pandemic, the 23B serotype of Streptococcus pneumoniae has increased in prevalence in healthy carriage isolates from Belgian day care centers and pediatric (younger than 18 years of age) invasive pneumococcal disease (IPD) isolates. Additionally, an increase in penicillin non-susceptibility was also observed within this serotype. Recently, a genetic variant of 23B, named 23B1, was discovered, which is known to be related to decreased penicillin susceptibility. We showed that increases in 23B prevalence in healthy carriage and IPD cases always coincided with 23B1 expansions, leading to higher penicillin non-susceptibility rates. Increases in 23B in the day care population paralleled pediatric 23B IPD increases, indicating the vital role of day care monitoring of pneumococcal carriage. Countries should stay vigilant for prevalence increases in S. pneumoniae serotype 23B, given the decreased susceptibility to penicillin and co-trimoxazole of the 23B1 variant.

The COVID-19 pandemic highlighted the importance of laboratory preparedness. Regular monitoring of diagnostic tools via external quality assessments (EQAs) is key to maintaining robust public health response service. We hereby conducted a third SARS-CoV-2 EQA assessing the diagnostic capabilities of European expert public health laboratories. A 10 samples panel containing Alpha (used in previous EQA), BA.4, BA.5, and BQ.1.18 variants along with human seasonal coronaviruses and negative controls was produced and validated. Participants were invited by the European Centre for Disease Prevention and Control (ECDC) and asked to submit results and assay details via electronic forms. Thirty-eight laboratories from 31 European countries participated. Most (n = 32, 84%) identified all panel samples correctly and used in-house (11, 29%), commercial assays (22, 58%), or both (5, 13%). Compared to previous EQAs, correct detection of the SARS-CoV-2 samples in the panels increased: 8 (12%) in 2020, 45 (75%) in 2021, and 34 (90%) laboratories in 2023, respectively. The number of participants decreased to an average of one laboratory per country (range 1-3) compared to two (1-7) laboratories in both previous EQAs. The usage of commercial assays gradually increased in contrast to the usage of in-house or both approaches. The capacity for SARS-CoV-2 molecular diagnostics has markedly improved in Europe as evidenced by three consecutive EQAs carried out by expert public health laboratories. Routine monitoring of diagnostic and surveillance assays via EQAs remains key to maintaining rapid public health laboratory response systems.IMPORTANCEExternal quality assessments (EQAs) are crucial to ensure the reliability and consistency of diagnostic laboratories. They provide an objective framework for evaluating the performance of testing systems, enabling laboratories to identify weaknesses and implement improvements promptly. In the context of SARS-CoV-2, EQAs have become even more critical due to the high demand for accurate molecular diagnostics and the emergence of new variants. Accurate detection and typing of variants are especially essential for monitoring viral evolution. EQAs help standardize methodologies, ensuring that results across laboratories remain comparable and trustworthy. Moreover, they play a pivotal role in minimizing errors such as false positives or negatives. In this rapidly evolving landscape, regular EQAs are indispensable for maintaining high-quality standards in molecular diagnostics and variant surveillance. We demonstrate here that regular EQAs improve the molecular detection of SARS-CoV-2 in European laboratories.

Tuberculosis (TB) management in endemic regions often grapples with resource constraints, including the scarcity of Mycobacterium tuberculosis (M.tb) culture laboratories. The emergence of M.tb strains with complex drug resistance profiles necessitates rapid and comprehensive drug susceptibility testing (DST) to guide patient treatment. However, traditional phenotypic DST (pDST) for M.tb is costly and time-consuming. In this study, we retrospectively enrolled 829 participants from six specialized TB treatment hospitals in China from September 2022 to July 2023. The diagnostic performance of TBseq test, a targeted-nanopore sequencing assay, was compared head-to-head with M.tb culture, acid-fast bacillus smear, quantitative polymerase chain reaction, and Xpert MTB/RIF Ultra by using clinical diagnosis as the reference standard. Subsequently, pDST for seven anti-TB drugs (rifampicin, isoniazid, ethambutol, streptomycin, levofloxacin, amikacin, and capreomycin) was performed. The resistance predictions provided by the TBseq test were compared with pDST results, which were used as a reference standard. The performance estimates of TBseq test were quantified through sensitivity, specificity, positive predictive value, negative predictive value, and the area under the receiver operating characteristic curve (AUC), providing a comprehensive assessment of its diagnostic accuracy. We found that TBseq test demonstrated significantly superior diagnostic performance for TB compared to other methods, achieving a sensitivity of 90.9% (95% CI: 88.9%-93.0%), specificity of 93.0% (95% CI: 97.2%-99.5%), and an AUC of 0.92 (95% CI: 0.876-0.963). TBseq test also exhibited robust predictive capabilities for drug resistance to the seven anti-TB drugs, with sensitivity and specificity consistently above 90% for all drugs. The AUC values ranged from 0.919 to 0.998, indicative of high diagnostic accuracy in forecasting drug resistance.IMPORTANCEOur results show that TBseq test offers excellent identification performance for tuberculosis (TB), significantly outperforming Mycobacterium tuberculosis (M.tb) culture, acid-fast bacillus (AFB) smear, qPCR, and Xpert MTB/RIF. Its diagnostic accuracy for anti-TB drug resistance is also superior, with sensitivity and specificity above 90% for all drugs tested. This method can be integrated into routine clinical diagnostic workflows, enabling early diagnosis and reporting of drug resistance simultaneously.

Escherichia coli pathotypes are enteric pathogens detected in gastrointestinal multiplex polymerase chain reaction (mPCR), with controversial clinical relevance. Our study aimed to describe clinical features and therapeutic decisions associated with E. coli detections in gastrointestinal mPCR. Children with positive mPCR for enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), Shiga toxin-producing E. coli (STEC), and enteroinvasive E. coli (EIEC)/Shigella identified in two pediatric hospitals over 18 months (2020-2021) were included. We described the frequency of E. coli detection and subsequent modifications in antibiotic strategies. Among the 2,471 mPCRs performed, 338 (14%) tested positive for at least one E. coli pathotype. The patient's mean age was 4.2 years, with 95% experiencing gastrointestinal symptoms. Clinical presentation was generally comparable between E. coli pathotypes. A recent travel abroad was reported in 68/338 (20%) cases and was mainly observed in EIEC/Shigella infections. An E. coli was detected alone in 177/338 (52%) cases and with another virus, bacteria, or parasite in 161 (48%) cases. Multiple enteric pathogens were mainly detected with ETEC (n = 24/26, 92%) and EAEC (n = 82/121, 68%) detections. Antibiotic therapy was prescribed in 136/338 (40%) cases, with initiation based on mPCR results in 69/338 (20%). No antibiotic therapy was discontinued following positive mPCR results. Among the 69 initiations, 31 were deemed inappropriate after retrospective chart review. E. coli detection with mPCR tests may lead to inappropriate antibiotic initiation. Caution is advised when interpreting results from gastrointestinal mPCRs in children, as clinicians may be unaware of their often unclear or irrelevant clinical significance.IMPORTANCEEscherichia coli pathotypes are increasingly detected through the widely used syndromic gastrointestinal multiplex PCR panels. However, their clinical significance and impact on antibiotic therapy in children remain uncertain. This study describes the clinical and microbiological characteristics associated with E. coli detections, as well as the subsequent modifications in antibiotic strategies. It highlights the frequent detection of E. coli pathotypes, often in association with other enteric pathogens, and reveals that nearly half of the antibiotics prescribed following these results were deemed inappropriate. These results underscore the need to enhance clinicians' interpretation of E. coli-positive results and reassess treatment strategies to optimize patient care.

This study evaluated thin-layer agar (TLA) as a faster alternative for both indirect minimum inhibitory concentration (MIC) determination of bedaquiline (BDQ) from culture isolates and direct drug-susceptibility testing (DST) from sputum samples. Indirect BDQ-MIC results from TLA were compared to the established 7H11 solid DST. Direct-TLA-DST performance was assessed using 143 baseline sputum samples from rifampicin-resistant TB cases. Direct-TLA tested susceptibility to rifampicin, isoniazid, levofloxacin, and BDQ, with results compared to Löwenstein-Jensen (LJ) and MGIT. For indirect BDQ-MIC determination, TLA accurately identified H37Rv MICs within the WHO control range (0.015-0.12μg/mL). Optimal results were obtained with standard incubation and day 7 reading of the plates. TLA correctly classified all wild-type clinical strains as BDQ-susceptible and detected 9 out of 10 BDQ-resistant strains with elevated MICs. Direct-TLA-DST detected MTB in 53.8% of samples, compared to 55.9% on LJ and 69.4% in MGIT. Uninterpretable results due to contamination or medium drying were low (4.9%). The median time to result was 15 days for smear-positive and 22 days for smear-negative samples, faster than WHO-endorsed methods. Sensitivity was 100% for rifampicin and 87.8% for isoniazid, with a specificity of 100% for all drugs except isoniazid (96.2%). No BDQ nor levofloxacin resistance was detected, thus direct TLA sensitivity could not be assessed. In conclusion, direct-TLA-DST offers a reliable and faster alternative to conventional DST methods for BDQ and other anti-TB drugs. Essentially, this technique can be operated at BioSafety Level 2, allowing decentralization of pDST for managing drug-resistant TB in settings with limited laboratory infrastructure.

Importance: This paper addresses the critical need for faster direct drug-susceptibility testing (DST) on sputum, especially for bedaquiline (BDQ), which is a key drug in treating drug-resistant TB. Currently, there is a lack of rapid, reliable methods for direct BDQ testing from sputum samples, limiting timely and accurate treatment decisions and monitoring. By demonstrating the potential of thin-layer agar (TLA) for direct BDQ-MIC determination, this study offers a promising solution that could significantly improve patient care.

Reduced susceptibility to antifungals is common among members of genera Scedosporium and Lomentospora, with optimal treatments still not fully defined. In vitro antifungal susceptibility results and clinical data do not comprehensively account for the advent of new Scedosporium species identified by molecular phylogenetics. Using Clinical and Laboratory Standards Institute (CLSI) methodology, we tested a total of 103 clinical isolates obtained from patients at the NIH Clinical Center. The most frequent species were Scedosporium apiospermum (63%) and Scedosporium boydii (11%), followed by Lomentospora prolificans (7%). The novel antifungal olorofim showed the lowest MICs against all Scedosporium spp. and L. prolificans, followed by micafungin. Among the triazoles, voriconazole showed lower MICs against Scedosporium spp. Amphotericin B and posaconazole demonstrated species-specific and inter-species variable activity. Itraconazole, isavuconazole, and terbinafine had higher MIC values against Scedosporium spp. and L. prolificans. Clinical data were retrospectively reviewed for 90 isolates, of which nine patients (28 isolates) had active disease/infection and received antifungal treatment that included voriconazole or posaconazole. Five of these patients (56%) died, while three patients (33%) with chronic granulomatous disease were cured following hematopoietic cell transplantation. In 24 patients (62 isolates), the presence of the fungus was considered airway colonization. In conclusion, our data support the existence of species-specific and inter-species differences in the antifungal susceptibility patterns among members of genera Scedosporium and L. prolificans. The novel investigational antifungal olorofim may be a promising therapy. Our clinical data suggest that host status and administration of antifungal therapy most effective for each Scedosporium species complex are important determinants of outcomes.IMPORTANCEUnderstanding the epidemiology and clinical spectrum of infections caused by Scedosporium species complex and Lomentospora prolificans is integral to improving outcomes, particularly in severely ill and immunocompromised patients. In vitro antifungal susceptibility testing can provide an estimate of antifungal activity against fungal pathogens. Our study showed that species-specific and inter-species differences exist in the distribution of antifungal susceptibility patterns between Scedosporium and L. prolificans. Our clinical data also highlight that host status, along with effective antifungal therapy, plays a crucial role in determining treatment outcomes.