This month we selected three papers from Italian research teams. The first two explored the link between microbiome and cancer, while the third assessed bacterial water contamination in a dental clinic setting.

• In the first paper, M. G. Clavenna and colleagues analyzed the microbiome and its metabolome directly collected from the colon polyps’ surface to offer a new perspective on the link between the microbiome and colorectal cancer. Their research showed different bacterial and metabolite signatures that discriminate between patients with low- and high-grade dysplastic polyps. Moreover, they revealed that different bacterial compositions were associated with the tumor stage. For example, some of these bacteria are enriched in the early stages of tumor development and may act as drivers of carcinogenesis. All this can be extremely useful in understanding specific bacteria’s role in cancer development and designing targeted therapies.

• Again the gut microbiome, this time analyzed because of its possible association with HR+/HER2- metastatic breast cancer and its therapy. In this study, the researchers assessed the potential link between fecal microbiota and the therapeutic efficacy of CDK4/6-inhibitors by collecting stool samples from responder or non-responder patients. With machine-learning algorithms, they evidenced four bacterial species as a discriminant for responder and non-responder patients, and cross-correlations among several patients’ circulating immune cells/biomarkers and bacterial species’ relative abundances showed associations with potential prognostic implications. Thus, microbiota manipulation strategies might be hypothesized to improve response to CDK4/6-inhibitors.
• The last study aimed at developing a water safety plan for a dental unit waterline – which usually represents an environment able to promote microbial contamination – with the main goal of preserving the health of dentists, staff, and patients. With a new sampling strategy, the researchers assessed Legionella and Pseudomonas aeruginosa contamination in three different water systems serving 60 dental chairs in total. They performed two subsequent shock treatments and resampling procedures by increasing disinfectant dosage and contact time, identifying the sources of contamination and allowing a better focus on the maintenance and disinfection procedures.

Discover the complete studies below:

This month we bring you two studies on the pediatric use of FecalSwab, and an outstanding paper illustrating the innovations introduced in forensic science by the French gendarmerie:

• Diarrheagenic Escherichia coli strains are a common cause of disease in children. Jenna Diaz et al. evaluated their epidemiology and impact in Haiti, assessing the infection in control and diarrheal subjects with PCR, at enrollment and one month later at follow-up. Plus, the group evaluated the association between specific biomarkers, choline and docosahexaenoic acid, and diarrheal burden. Enterotoxigenic, enteroaggregative, and typical enteropathogenic Escherichia coli prevalence showed to be slightly higher in diarrheal subjects compared to controls, while biomarkers were not associated with the diarrheal burden. Furthermore, multivariate linear regression found a significant association of enterotoxigenic, enteroaggregative E.coli with unfavorable anthropometric measures, with possible synergistic interactions.
• The second study aimed to evaluate the difference in gut microbiomes between preterm and term infants seven days and one month after birth. Using third-generation long-read sequencing and comparing this method with the gold standard, the study showed that the third-generation long-read sequencing results highly correlate with the gold standard, thus suggesting its potential use for pathogen detection in neonates in clinical settings. Finally, a bioinformatic analysis identified features that differed between preterm and term infants which accentuated one month after birth, with the transition of prenatal babies towards a pathogenic bacteria environment and the increase of beneficial bacteria in term babies.
• The third paper is all about the IRCGN. IRCGN is a forensic science institute created by the French Gendarmerie, in charge of working on the crime scene to collect and analyze evidence. During the past 10 years, its experts in genetics have developed innovative engineering technologies to be applied in forensic sciences. This review explores these new ideas and innovations for human identification, which are fully suited to the French Gendarmerie’s needs – and not only: new protocols, mobile labs, NGS, and also our MicroFLOQ!

Discover the complete studies below:

The focus of this Microbiology Time is N. gonorrhoeae and its collection. So why did we decide to focus on this organism? Well, that’s clear: N. gonorrhoeae antimicrobial resistance has hugely increased in recent years, reducing the options for treatment and affecting more than eighty million new people in 2020, especially in the African and Western Pacific Regions. One key action WHO proposed to fight N. gonorrhoeae and its multi-resistant strains – gonorrhea superbugs or super gonorrhea – is to strengthen and make more effective surveillance screenings to control the microorganism’s spread and its resistance. Let’s explore three studies tackling the complex topic of N. gonorrhoeae sample collection:

• The first study used eSwab to preserve samples that resulted positive for Gonorrhoea after a smear test. By analyzing these samples by culture and NAAT, Jett-Goheen and colleagues demonstrated that eSwab can maintain gonorrhoeae viability for at least 24 hours and stabilized nucleic acids to be analyzed by NAAT for up to five days.
• The second paper analyzed the suitability of the eSwab for molecular diagnostics and deferred targeted gonorrhoeae culture, to allow selective and efficient culture based on MDX results. The Dutch researchers collected urogenital and rectal samples from almost 2000 patients visiting the STI Clinic in Amsterdam, using the standard method and eSwab. Showing that a targeted deferred N. gonorrhoeae culture is possible from clinical samples stored for up to 3 days in eSwab and that eSwab preservation is compatible with NAAT, this study was one of the first to confirm that eSwab allows prolonged transport time, preselection with NAAT, and subsequent N. gonorrhoeae culture.
• The third study comes from South Africa. Here, the researchers evaluated the survival of gonorrhoeae from male urethral specimens collected using eSwab® at both room and refrigerator temperatures. The survival of N. gonorrhoeae at different temperatures was compared to culture obtained by ‘gold standard’ direct plate inoculation with a Dacron swab. Preserving eSwab samples for up to 7 days at different temperatures, L. Gumede and colleagues concluded that eSwab®-preserved samples should be transported and maintained at refrigerator temperatures and must reach the processing laboratory by at least (5 days) after collection.

Discover the complete studies below:

ECCMID 2023 was pretty awesome!

We were blown away by the number of attendees at our symposia, and we enjoyed chatting with many of you at our booth. It’s fulfilling to know that Copenhagen has fostered such valuable connections!

So, a massive thank you to everyone for making it such a great time.

The Centers for Disease Control and Prevention recently warned about a drug-resistant strain of Candida auris, a fungus spreading at an alarming rate in the United States and many other countries worldwide, including Italy.

Candida auris is a highly contagious pathogenic fungus within healthcare facilities that spreads from one individual to another via direct contact or contaminated surfaces. Although it is not a threat to healthy people, this fungus can cause severe systemic infections in debilitated patients or those with invasive medical devices, leading to high mortality sepsis in 15% of them.

Moreover, although most Candida auris infections are treatable with antifungal drugs, some strains exhibit resistance to initial drug treatments – as happens with MDR bacteria – leading to the failure of first-line therapies.