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.

Read the full studies below:

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Here are the three studies selected for this month’s Microbiology Time:

• In the first paper, the Spanish researchers investigated persistent biomarkers in the nasopharyngeal tract of fully asymptomatic patients two years post-SARS-CoV-2 infection, considering the initial severity of their illness. This study aims to shed light on SARS-CoV-2’s wide range of symptoms that span from mild to severe cases requiring intensive care. The study found 371 proteins and their related pathways that reflect different adverse effects of the infection, demonstrating that biomarkers can persist long-term and indicate the severity of the initial infection. While significant efforts have been made to identify severity-linked biomarkers and those connected with long-COVID, this provides the first evidence of biomarkers persisting years after recovery.
• For the second study, we move to Denmark. This Chronic Wound Characterisation (CWC) study aims to investigate chronic wounds, focusing on bacterial communities and biofilm, inflammation, and their effects on wound healing. The study comprised two cohorts: the predictive cohort involving patients with chronic wounds undergoing mechanical debridement and the in-depth cohort following patients receiving split-thickness skin grafts. The samples from the two cohorts were then analyzed using culturing and next-generation sequencing, laying the foundation to identify human genes and microbes related to infection and healing. Moreover, the researchers established a biobank of clinical samples and data that will also help explore the influence of bacteria on wound progression and healing.
• In the last paper, R. Traynor and colleagues investigated a PVL-producing methicillin-resistant Staphylococcus Aureus outbreak in the Irish National Burns Unit in 2022, involving seven patients, two staff members, and two positive environmental samples. Staff and environmental screening, along with enhanced cleaning protocols, were crucial for effectively managing this outbreak. The application of real-time whole genome sequencing (WGS) facilitated the quick identification of related cases and enabled a swift response to the outbreak, making the management of this infection an example of effective outbreak management.