This month, we dig into oropharyngeal cancer and HPV, microbiome and vaginitis, and microFLOQ in forensic DNA testing.

• In addition to cervical cancer, HPV is a significant factor in the development of oropharyngeal cancer, and its prompt detection is crucial for diagnosis and treatment planning. The first study from Italy investigates the effectiveness of two non-invasive sampling methods for detecting HPV DNA in patients with oral squamous cell carcinoma (OSCC). The study involved 26 patients, each providing two self-collected oral specimens, oral rinse and LolliSponge, which were analyzed using HPV genotyping techniques. Results showed that LolliSponge had higher specificity, sensitivity, and accuracy than the oral rinse method, with a significantly better diagnostic performance. The researchers conclude that oral sponge sampling is a valuable non-invasive option for detecting HPV in OSCC patients, particularly those with functional deficits due to the disease. Further research with larger cohorts is recommended to confirm these results and explore clinical integration.
• The second study addresses the limitations of current tools for vaginitis diagnosis, a common condition affecting women globally, with bacterial vaginosis (BV) being the most prevalent form. Traditional diagnostic methods rely on clinical criteria, microscopy, or limited microbial detection using qPCR. Still, many vaginal infections are linked to changes in the vaginal microbiome rather than a single causative agent. The US researchers introduce here a metagenomic sequencing test for the vaginal microbiome, providing a comprehensive analysis of all organisms present. This test demonstrates high accuracy, sensitivity, specificity, and BV predictive values and has been certified by regulatory bodies. So far, the test has been applied to over 7,000 vaginal samples, offering insights into the US population’s vaginal microbiome.
• The last study investigated the effectiveness of microFLOQ direct swabs in forensic DNA testing. It focused on their use in traditional polymerase chain reaction capillary electrophoresis (PCR-CE) and a new massively parallel sequencing (MPS) protocol. The study aimed to determine how well DNA profiles could be generated directly from small subsamples of blood, saliva, and semen without DNA extraction or quantitation. The researchers used cotton swabs and 4N6FLOQSwabs to collect both fresh and dried biological samples, which were then subsampled using microFLOQ swabs. The results indicated that subsamples from fresh bodily fluids produced more complete STR profiles than those from dried samples. Additionally, the custom MPS protocol successfully generated DNA profiles from diluted saliva, blood, and touch DNA collected from nonabsorbent surfaces. The study demonstrated that microFLOQ swabs are effective for direct amplification and producing high-quality DNA profiles suitable for forensic use.

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We are happy to repost here a news published by our Finnish partners at Mekalasi OY!

The clinical microbiology laboratory at the HUS Diagnostic Center in Helsinki, Finland, has been equipped with Copan’s lab automation since 2020. The lab currently automates its workflow with two WASPLab® culture automation lines, which include four Walk-Away Specimen Processor™ WASP® units, two connected incubators, and PhenoMATRIX® software that utilizes Artificial Intelligence for plate interpretation. Now, two Colibrí™ picking modules are being installed in connection with the automation line.

Colibrí™ is a device that automatically picks colonies on a culture plate – either selected by user input or by the AI PhenoMATRIX® TAG software – to perform MALDI-TOF identification or to prepare a suspension for Antibiotic Susceptibility Testing. Colibrí™ pipetting robot ensures precise colony selection, while the nephelometer checks the turbidity of the suspension. This further step toward lab automation improves even more HUS lab accuracy, standardization, and traceability while optimizing the laboratory workflow.

The HUS Diagnostics Center concentrates samples from satellite laboratories for the screening of UTIs and streptococci. The number of samples reaching the laboratory has increased significantly in recent years, and automation has helped handle growing sample volumes while maintaining quality.

Currently, more than 90 Colibrí™ have been installed worldwide – with 40 in Europe – but the two automation being installed at the HUS Diagnostic Center are the first in Finland and Scandinavia. Colibrí™ is conceived and produced by Copan, a family business founded in 1979 in Brescia, Italy. Copan manufactures and develops sample collection and transport devices and automation solutions for the needs of bacteriology, virology, and molecular biology. Noteworthy, Copan transports the equipment with its own trucks, and its in-house logistics is a part of its quality assurance and comprehensive care of the delivery process.

The Colibrí™ installation is carried out by Mekalasi’s maintenance staff and Copan experts. Mekalasi has its own Finnish-speaking service organization in Finland, with professional staff available for user and troubleshooting support if needed. After the installation, trained and certified personnel perform periodic maintenance following the equipment manufacturer’s maintenance program, ensuring full functionality and user safety.

The bacteriology automation system at the HUS Diagnostic Center is customized and optimized to meet the laboratory’s sample flows and workflow needs. The modular solution has been expanded since 2020. After the first WASP® installed, another two followed, and in 2022, WASPLab® was delivered. Last year, the second WASPLab® and the fourth WASP® were delivered. Now it’s the turn of the two Colibrí™. Who knows what’s next?

The original news can be found here!

Enjoy the studies we selected for you this month:

• Multi-drug resistant fungus Candida Auris is recognized as a critical issue by the WHO. Its permanence on human skin and surfaces makes hospital surveillance protocols essential to prevent nosocomial outbreaks. The study by Curtoni and colleagues aimed to apply Fourier transform infrared spectroscopy to examine the phylogenetic relationships among strains isolated from a C. auris outbreak in the ICU of a hospital in Turin, Italy. The results identified a dominant Alpha cluster and a minor Beta cluster. These findings were validated using an external C. auris strain and through Principal Component and Linear Discriminant Analyses. This study results highlight how FT-IR technology can provide valuable information on the phylogenetic relationships between microorganism strains and propose FT-IR as a cost-effective alternative to molecular methods for rapid and efficient typing of C. auris strains, with important clinical implications.
• The 2022 global spread of monkeypox led to the expansion of diagnostic testing worldwide. In the second study we selected, the Canadian researchers collected specimens from patients in Ontario to evaluate the performance characteristics of five RT-PCR assays in detecting Monkeypox during the 2022 outbreak. Swabs from various anatomical sites were collected, and all assays demonstrated excellent negative percent agreement, positive percent agreement, limit of detection, and precision. An amplicon-based whole-genome sequencing analysis identified six different monkeypox lineages. These results underline the need for performance monitoring to detect assay escape mutants and ensure the universal detection of evolving monkeypox strains.
• The third study investigated the culture of Mycobacterium tuberculosis from tongue swabs, either experimentally spiked after collection from healthy controls or directly sampled from patients with microscope-confirmed pulmonary tuberculosis. The performance of three culture processing methods was evaluated: NALC-NaOH/MGIT960 (MGIT), Kudoh-Ogawa (KO), and cetylpyridinium chloride-L¨owenstein-Jensen (CPC/LJ). Overall, the study concludes that MGIT is the optimal method for culturing Mycobacterium tuberculosis from tongue swabs. Anyhow

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