Diagnostic microbiology and infectious disease最新文献

Background: Efficient monitoring of HIV drug resistance (HIVDR) relies on standardized bioinformatics tools for accurate identification of drug resistance mutations (DRMs). Thus, we sought to compare the concordance of HIV-1 genotypic profiling from sequences analyzed with two commonly-used editing algorithms in low- and middle-income countries (LMICs).

Methods: A laboratory-based comparative study was conducted among treatment-experienced people living with HIV attending the Chantal BIYA International Reference Centre in Yaoundé-Cameroon from October-2022 through July-2023. For each individual, raw data of HIV-1 sequences were analyzed simultaneously using RECall (semi-automated) vs. Exatype (automated) algorithms. Outputs were compared for DRMs, polymorphisms and subtyping between the two algorithms, with significance at p<0.05.

Results: Overall, 221 participants were included (mean-age 32±15 years, 52.5% female). Validation of sequence quality was 70.1% (155/221) by RECall vs. 60.2% (133/221) by Exatype, Ka=0.78 (p<0.0001), indicating a good agreement between both algorithms. Importantly, a perfect concordance (100%) was found in HIV-1 clade inference (CRF02_AG [82/82], A1 [29/29], G [5/5], F2 [5/5] and others [12/12]). Similarly, high concordances were found for the identification of DRMs to protease-inhibitors (99.0%), nucleoside reverse-transcriptase inhibitors (98.0%), non-nucleoside reverse-transcriptase inhibitors (98.6%) and integrase-inhibitors (100.0%). The average turn-around-time was two-folds longer with RECall (5.5±1.7 min) vs. Exatype (2.5±1.1 min); giving a lower efficiency (i.e. validation rate/time) with RECall (12.7) vs. Exatype (24.1).

Conclusions: Semi-automated (RECall) and automated (Exatype) tools showed excellent agreement in detecting HIV-1 clades and DRMs, supporting their interoperability in clinical practice. Following efficiency, Exatype can be considered preferential, while RECall remains a quite suitable alternative for LMICs.

Intestinal diseases markedly impair quality of life, with irritable bowel syndrome (IBS), ulcerative colitis (UC), and Crohn's disease (CD) representing major functional and inflammatory gastrointestinal disorders. This study aimed to determine the prevalence of Dientamoeba fragilis and other intestinal parasites in these conditions and to compare the diagnostic performance of conventional and molecular methods. A total of 80 stool samples were analyzed, including 60 from patients with IBS, UC, or CD and 20 from healthy controls. Samples were examined using direct microscopy, concentration techniques, trichrome staining (TS), and real-time polymerase chain reaction (qPCR), which was applied specifically for the detection of D. fragilis. Overall, parasites were detected in 60% of patients and 15% of controls. Infection rates were 33.3% in CD, 68.8% in UC, and 58.5% in IBS patients. D. fragilis was identified in 18.8% of UC and 22.0% of IBS cases, with significant differences observed between microscopy, TS, and qPCR in detection rates. Blastocystis sp. was found in 21.7% of patients and 5% of controls, with the highest prevalence in UC patients (37.5%). Other detected parasites included Iodamoeba bütschlii, Endolimax nana, Entamoeba coli, Giardia intestinalis, Chilomastix mesnili, Entamoeba spp., and Cystoisospora belli. While direct microscopy showed limited sensitivity, TS improved detection moderately, and qPCR provided the highest sensitivity for D. fragilis. These findings highlight the predominance of D. fragilis in IBS and Blastocystis sp. in UC and underscore the importance of molecular methods for accurate parasitological diagnosis.

Background: Yeasts are one of the important fungi in food production. Some of them can be used as food. Pathogenic Candida is not known to be food for other organisms. This study aims to evaluate the use of pathogenic Candida as a supplement for dermatophyte growth.

Methods: Standard fungal media, Sabouraud's dextrose agar (SDA), were supplied with dead cells of three pathogenic Candida species, C. albicans, C. glabrata, and C. tropicalis, for culturing of 14 isolates of dermatophytes. Dry weight was measured to determine the biomass of growing dermatophytes.

Results: Candida-containing media significantly enhanced dermatophytic growth. C. tropicalis dead cells promoted the growth of Microsporum species, while Trichophyton species preferred growing on media of all Candida spp. with less variability among them. In contrast to C. tropicalis, media with C. albicans and C. glabrata were less effective at supporting Microsporum canis growth (0.150 g of biomass, 95% CI: 0.0482-0.252, and 0.165 g of biomass, 95% CI: 0.157-0.173, respectively).

Conclusions: Candida cells have a promotional impact on the growth of dermatophytes. Pathogenic Candida can be used by dermatophytes as an enhancement growth factor when they are in a dead state.

Introduction: Tuberculosis (TB) remains a major global health concern, particularly in low-income countries where the impact is greater. The lack of proper surveillance tools in these countries is a big impediment to effective TB control. Whole-genome sequencing (WGS) has successfully been integrated into routine TB programs in high-income countries and transformed disease surveillance by providing rapid, high-resolution transmission insights, drug resistance profiling, and outbreak detection. However, its uptake in resource-limited settings where TB burden is most prevalent remains limited.

Methods: This review examines how WGS is currently being utilised for TB surveillance and highlights the main obstacles to its adoption in limited-resource settings as well as the strategies that could improve its uptake. A literature search was conducted in PubMed, Google Scholar, and the World Health Organisation (WHO) databases with keywords "whole genome sequencing," "tuberculosis," "surveillance," "transmission," and "drug resistance." Studies published between 2015 and 2025 were prioritised, with a focus on applications in high-burden settings.

Results: Key challenges identified include infrastructural issues whereby 78% of high-burden countries lack adequate sequencing facilities according to WHO 2023 data; financial barriers, with recurring costs surpassing $150 per sample in low-resource settings as compared to $80 in high-income countries, and a shortage of trained personnel with only 2.3 bioinformaticians being available per African country. Other hurdles involve concerns over data sovereignty, weak regulatory frameworks, and ethical dilemmas surrounding privacy and equitable data usage, with only 31% of low-resource countries having genomic data policies. Nevertheless, promising innovations like portable sequencing devices which have a sensitivity of up to 92% and cloud-based platforms that reduce computational needs by 70% offer scalable opportunities for equitable integration. We also highlight partnership models that blend WHO technical guidance, Global Fund financing, and South-South collaborations that could enhance sustainability.

Conclusion: To realise the full potential of WGS in TB-endemic regions, a coordinated approach that combines technical advancements with policy changes, ethical data governance, and sustained investment is needed. Tackling these challenges is essential in achieving equitable, genomics-informed TB control that aligns with global TB elimination goals.