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Microbiology Time – January 2025

Microbiology Time

Here are the last 2024 papers that secured their place in our Microbiology Time:

  • In the first study, Dr. Chiereghin and colleagues evaluated self-sampling as an alternative to standard sampling for HPV primary screening in an Italian cervical cancer prevention program, focusing on acceptance, ease of use, and adherence to follow-up. The program offered self-sampling to nearly 20,000 women overdue for screening due to the COVID-19 pandemic and had irregular or no prior attendance. The study found that 11.5% of women opted for self-sampling – more than doubling the participation rate compared to clinician-sampling alone – thus demonstrating high acceptance. The return rate for self-samples was 79.5%, with only 1.1% deemed inadequate, indicating ease of use. HPV positivity and cervical cancer detection rates were higher in the self-sampling group compared to the regular screening population. In conclusion, self-sampling proved to be an easy-to-use and effective tool for reaching non-attenders who are at high risk of cancer.
  • The second study is a collaboration between the U.S. and Italy. In this research, the scientists examined the impact of a novel elite athlete-derived Lactobacillus probiotic on sleep quality, exercise recovery, and gut microbiome composition in both elite athletes and the general population. This large-scale study utilized a two-phase design, featuring an open-label trial and a controlled longitudinal study with a professional soccer team, to investigate the interactions among probiotics, the gut microbiome, and host health. During the placebo-controlled phase, significant enhancements were noted in self-reported sleep quality (69%), energy levels (31%), and bowel movements (37%) after probiotic intervention, compared to the placebo. These improvements aligned with reductions in oxidative stress and a higher free testosterone/cortisol ratio. Multi-omics analyses revealed specific changes in microbiome composition and function, hinting at the potential mechanisms underlying these effects. The study offers new insights into how Lactobacillus probiotics can enhance sleep, recovery, and microbiome health in athletes and the general population, highlighting the promise of tailored probiotics derived from fit individuals to boost health and performance.
  • Rapid DNA analysis methods can generate DNA profiles more quickly than traditional forensic workflows. These instruments have potential applications in decentralized settings without laboratory facilities. While effective for analyzing rich biological samples, these innovative methods typically consume the entire swab, which poses a challenge when working with limited samples. In the third study selected, French researchers developed a subsampling protocol to address this issue. By applying blood to FLOQSwabs and recovering portions of the biological material using a FLOQSwabs mini tip, they demonstrated that complete genetic profiles could be obtained from the mini swabs regardless of the initial blood volume, with improved profile intensity observed for larger volumes. This novel subsampling method offers a practical and adaptable strategy for forensic DNA analysis—especially in remote or decentralized environments—creating new opportunities for advancements in forensic genetics.

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Microbiology Time – December 2024

Microbiology Time

Here are the latest studies featured in 2024’s Microbiology Time:

  • In the first study, Dr. Cherkaoui and Prof. Schrenzel’s team addressed the need to reduce turn-around times and minimize costs for Group B Streptococcus (GBS) screening in pregnant patients by exploiting laboratory automation and AI. After comparing the performance of direct chromID™ Strepto B agar plating against LIM-broth enriched CA plating – finding nearly identical GBS detection rates – the Swiss researchers trained PhenoMATRIX™ with almost 9000 plate images, validating the results on other 800 pictures. With a sensitivity of 100%, specificity of 90.2%, and a negative predictive value of 100%, PhenoMATRIX™ showed the be a reliable tool for the automated release of GBS-negative results within 24 hours.
  • The single-molecule sequencing capabilities offered by the latest third-generation sequencing (TGS) techniques addressed the limitations of traditional NGS techniques. Still, its high error rate has hindered achieving accurate results. Three years ago, the high-accuracy sequencing Kit by Oxford Nanopore Technologies reported up to 99% accuracy. This month’s second study aimed to validate this kit for HLA genotyping in combination with a full-gene HLA PCR assay, comparing its performances with earlier flow cell models. The workflow was assessed for data throughput, sequence quality, accuracy, HLA genotyping resolution, flow cell stability, and barcode contamination. The findings underscore the advantages of ONT’s sequencing Kit flow cells for HLA genotyping and provide insights into their implementation in routine diagnostic HLA laboratories.
  • Rapid and accurate detection of SARS-CoV-2 in environmental settings had been essential for effective public health management during the COVID-19 pandemic. The third study by Professor Cristino evaluated the performance of RT-qPCR and Reverse Transcription loop-mediated isothermal amplification (RT-LAMP) in detecting SARS-CoV-2 from surface samples collected in healthcare environments. The reference method, RT-qPCR, identified 25% of the samples as positive, while RT-LAMP detected 27% as positive. RT-LAMP demonstrated a sensitivity of 32%, a specificity of 75%, a positive predictive value of 30%, and a negative predictive value of 77%, with an overall accuracy and concordance with RT-qPCR of 64%. RT-LAMP offered advantages in rapid screening and environmental surveillance, suggesting its potential as a valuable tool for the environmental monitoring of SARS-CoV-2, thereby aiding sanitation processes in both routine and emergency conditions.

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