Here are the three papers of this year’s last edition of the Microbiology Time:

• In the first paper, the Belgian researchers isolated a novel strain of Lactobacillus, named AMBV1719T, from a healthy participant’s vagina enrolled in the “Isala” female microbiome project. While its 16S rRNA gene resulted closely related to Lactobacillus taiwanensis, genome-wide comparison using Average Nucleotide Identity (ANI) revealed a distinct species with the highest ANI to Lactobacillus paragasseri. Moreover, AMBV1719T shows limited carbon source degradation compared to Lactobacillus gasseri, suggesting its adaptation to the host environment. The researchers finally suggested for this new strain, the name Lactobacillus isalae sp. nov.
  
• Campylobacter jejuni is a major cause of global bacterial gastroenteritis. While systemic C. jejuni infections are uncommon, osteomyelitis from the bacterium is extremely rare, with no previous reports of spinal bone biopsy cultivation. At Aalborg University Hospital, a 79-year-old male presented lower back pain, fever, and diarrhea. A FecalSwab obtained upon admission was PCR-positive for Campylobacter spp, and C. jejuni was cultured from an aerobic blood culture bottle. MRI revealed osteomyelitis at L1/L2 with an epidural abscess. Spinal surgery and targeted antibiotic treatment led to a swift recovery. The Danish clinicians indicate C. jejuni as a potential cause of vertebral osteomyelitis, especially with diarrheal symptoms. Susceptibility testing is vital due to emerging resistance, guiding effective treatment strategies.
• In this study, Elena Fontana et al. evaluated TDP-43 protein seeding activity and aggregate detection in the olfactory mucosa of individuals with frontotemporal lobar degeneration with TDP-43-immunoreactive pathology (FTLD-TDP). The Italian researchers optimized a novel TDP-43 seeding amplification assay with frontal cortex samples from 16 post-mortem cases. The assay exhibited 100% accuracy in discriminating cases with or without TDP-43 neuropathology. Olfactory mucosa samples from 17 FTLD-TDP patients and controls revealed detectable TDP-43 seeding activity in 82.4% of FTLD-TDP cases, suggesting the potential utility of TDP43-SAA in identifying and monitoring FTLD-TDP in living patients.

Read the full studies:

What if we replace an agar media glass bottle with a plastic shell?

This is the question we asked ourselves a few months ago, and now, we have the answer – introducing the new MediaBag™!

Our team at Newlab has designed this innovative product combining the ease of use of bottled media with many other advantages. First, the plastic bag used in MediaBag™ is much lighter than a glass bottle, which helps reduce shipment costs. Second, it is smaller and squeezable, optimizing storage space and reducing waste. Third, its processing is quick and safe and avoids hazardous touchpoints.

Ready-to-use and automation-friendly

MediaBag™ keeps unaltered the intrinsic advantages of a ready-to-use medium: no tedious preparation that involves hazardous touchpoints, easy adoption, and a shelf life of 6 months from 2 to 8°C.

Of course, all the MediaBag™ products are tested following ISO 11133 as a guideline and are fully compatible with Cyclone, Copan Newlab’s solution to automate your industry microbiological analysis workflow. By pairing it with MediaBag™, you truly make plate preparation an effortless task.

Availability

MediaBag™ is already in stock, prefilled with many agar media to fit your laboratory workflow; all the various media are available in 0.5 and 1 L formats.

Discover more on the dedicated brochure or by contacting our experts!

October was a fruitful month! Read here the best three papers we selected:

• The first study conducted in the US compared the performance of Colibrí™ with standard manual spotting for identifying bacteria in colonies grown from over 400 different samples, including urine, wound, respiratory, and positive blood cultures. The results showed that the two methods agreed 99.54% of the time, indicating that the use of Colibrí™ can help save time for technologists and ensure complete traceability from plating to organism identification.
• The vaginal microbiome plays a crucial role in maintaining reproductive and overall women’s health. In this paper, Sara Leeber and her colleagues analyzed the self-collected vaginal microbiome of 3,345 Belgian women performing 16S amplicon sequencing and conducting questionnaires. The researchers found that the microbiome composition was strongly associated with age, childbirth, and menstrual cycle, and Lactobacillus species were dominant in 78% of the vaginal samples. Moreover, a network correlation analysis revealed specific bacterial taxa that were linked to certain conditions such as estrogen levels, contraceptive use, menopause, and breastfeeding. This study provides a detailed map of the vaginal microbiome associated with various health, lifestyle, and dietary factors, which will help with follow-up clinical and mechanistic research.
• In the last years, full laboratory automation has transformed the field of clinical microbiology; today, deep learning architectures are fundamentally changing how computers can assist with challenging visual interpretation tasks in various domains. Here, the paper by Signoroni and colleagues introduces a system able to tackle a core task in clinical microbiology, the interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. The researchers achieved this by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture called DeepColony. By working with a large stream of clinical data and a complete set of 32 pathogens, the suggested system effectively aided plate interpretation with a surprising level of accuracy in the extensive and rigorous framework of urinary tract infections. In conclusion, thanks to the rich species-related information generated, DeepColony can be used to develop trustworthy clinical decision support services in laboratory automation ecosystems. Surprise: Deepcolony is at the base of what PhenoMATRIX currently is!

Read the full studies:

Here are the three papers we selected as the best ones in the last month:

• Getting infected by Tuberculosis is a concrete risk for healthcare professionals working with TB patients, collecting and handling sputum samples for TB diagnosis. This study evaluates the risk perceptions of an alternative, less dangerous method to diagnose TB, tongue swabbing, implemented during the COVID-19 pandemic. Eighteen South African Healthcare professionals with experience using tongue swabbing at the South African Tuberculosis Vaccine Initiative were interviewed and assessed by their attitude toward provider-collected and supervised self-collected tongue swabbing. Facilitators and barriers to the use of tongue swabbing were also evaluated. Perception, barriers, and motivators of the use of tongue swabbing varied by use case, highlighting specific educational resources to enhance the safety of and adherence to the self-collection method.
• HPV -DNA testing with self-collected samples showed extreme diagnostic accuracy and reliability. Nevertheless, to implement self-sampling in cervical screening programs, the standardization of the pre-analytical phase and the understanding of the acceptability of women are necessary in every country. In this second study, Illari Sechi and colleagues assessed the stability of self-collected vaginal samples, and the acceptability of self-collection in almost 200 women. Most of the women found it easy to use self-collection devices, and approximately half of the enrolled women declared preferring self-sampling to clinician-collected methods. This, paired with the high reliability and accuracy of HPV-DNA tests on self-collected samples, supports the adoption of self-collection in screening programs, even though HPV tests on self-samples must be standardized and optimized, and educational campaigns are needed to adequately inform and increase responsiveness in a target population.
• Covid-19 is mainly a respiratory syndrome that can affect multiple organ systems with various symptoms. Deficits in smell and taste are some of the most common COVID-19 symptoms, which may last for months after the infection and which mechanisms are not fully elucidated. To identify the determinants of olfactory symptom persistence, the Italian research group obtained olfactory mucosa from 21 subjects and grouped them by the severity/persistence of olfactory symptoms. By analyzing cells with transcriptome analyses, Lupi and colleagues discovered that the overall gene expression and micro-RNA expression profile are altered for a long time after infection. Patients with persistent olfactory deficits displayed increased expression levels of genes related to inflammation and zinc homeostasis, suggesting an association of this metal with the olfactory deficit.

Read the full studies:

Main 

Since the first use of DNA fingerprinting, forensic genetics has rapidly evolved. Today, scientists are implementing quicker, more specific, and more sensitive tools that could soon be applied to criminal cases and represent the future of genetic forensics investigation. That’s why now, more than ever, the importance of a neat evidence collection seems clear. 

Compliant with the latest standards 

To answer this need, we were the first swab manufacturer to obtain ISO 18385 compliance for its forensics (4N6) products, implementing a quality system that minimizes the risk of hDNA contamination during the manufacturing process, a mandatory requirement for the global forensic community. Today, our FLOQ technology enables forensic scientists to increase the amount of human DNA recovery from every sample, facilitating the processing and ensuring optimal sample integrity.  

Successful investigations begin with accurate evidence collection 

Even with the most advanced collection devices, the wide range of surfaces and materials from which the evidence can be collected could challenge investigators to choose the proper collection method case by case: which swab to use? Does it need to be moisturized? Which swab motion to use when collecting? 

Errors in collecting and handling biological evidence can result in their exclusion from the trial, highlighting the necessity of proper sample collection and storage. 

By gathering the most relevant peer-reviewed papers, a dense bibliography, and unpublished data obtained with close collaboration with forensics professionals, we conceived this guide to forensic sampling to help forensics professionals orient through the jungle of evidence collection methods, choose the appropriate one according to any situation, and ensure the success of their investigation.

UriSponge® is our beloved device for urine specimen collection, transport, and preservation from the sampling site to the testing laboratory.   

The good old UriSponge® 

Copan developed this innovative device with a sponge that rapidly, easily, and safely adsorbs the correct amount of urine, making the sample collection step and subsequential processing in the lab much simpler. This unique design avoids cumbersome urine transfer to other tubes and has helped hundreds of laboratories in the procedures for the cultivation of uropathogenic bacteria and yeasts. UriSponge® compact and leak-proof tube ensured a cost-effective shipment of samples to the laboratory, where they can either be loaded directly on the WASP® for automated streaking or manually centrifuged for manual processing of urine with standard culture procedures. All this in full compliance with M40-A2 and IVDR standards. 

But we could do better. 

Today, the time has come to unveil a new, updated version of UriSponge®, which still offers the same convenience and easiness of use but with an advanced preservative formula free of boric acid. The reasons behind this choice are obvious: no dangerous chemicals for humans or the environment mean increased sustainability; no handling and logistic issues related to boric acid mean no availability disruptions and faster delivery times. Additionally, the new UriSponge®’s formula outperforms other devices based on boric acid, as urine collected in UriSponge® can be stored at room temperature for up to 48 hours controlling the risk of overgrowth or overkill during transport. 

UriSponge® is immediately available to be ordered*. Contact us for more info. 

*Currently available for countries that require CE marking and apply IVD regulation. 

In 2020, the Italian headquarters of Mérieux NutriSciences hosted one of the first installations of the Copan Newlab Cyclone. This milestone project highlighted the cutting-edge capabilities of Cyclone’s automated workflow and pointed up the power of collaboration and knowledge exchange in shaping its evolution.

A Journey of Innovation and Cooperation

It all started when Mérieux NutriSciences, a global leader in food quality control, recognized the need for a quality control solution to address the dynamic demands of the modern food production industry. Thus, thanks to a solid collaboration with Copan, the company embarked on a journey to implement Cyclone in its workflow.

At the heart of this project was the spirit of cooperation. Mérieux NutriSciences and Copan teams worked hand in hand, merging their expertise and insights to seamlessly integrate the Cyclone system into the workflow of the Mérieux NutriSciences’s Italian headquarters. This close cooperation fostered an environment of mutual learning, enabling both teams to refine and tailor the system’s functionalities to the Mérieux NutriSciences’s specific needs:

Shaping the Present and Future of Food Industry Quality Control

The successful installation of Cyclone at Mérieux NutriSciences marked a profound turning point for the quality control workflow of the laboratory. The project’s success demonstrated how innovative solutions like Cyclone could be harnessed to streamline and enhance QA processes across the nation’s food producers. Implementing Copan’s Cyclone allowed Mérieux NutriSciences to take advantage of a reliable solution helping them manage large volumes of samples, even of different matrices.  Moreover, by reducing errors and enhancing standardization and reproducibility 24/7, Cyclone shortened Mérieux NutriSciences’ time-to-results, ensured workflow scalability during high-volume shifts, and empowered lab staff to focus on essential activities.

Unparalleled Quality Control Services Nationwide

As a direct result of this collaboration, Mérieux NutriSciences today boasts an unparalleled quality control service, made possible by the advanced capabilities of Cyclone: its implementation ensured not only the safety and compliance of products but also the optimization of production and QA processes.

This landmark case history showcases how a shared vision and dedicated teamwork can yield transformative outcomes, leaving an indelible mark on the quality control and food safety sector. The story of Mérieux NutriSciences and Copan’s Cyclone is about visionaries pushing boundaries, experts collaborating seamlessly, and two companies committed to excellence aiming at elevating quality control standards in the food industry.