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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Here are the selected readings for the summer:

• In 2012, Botswana introduced the 13-valent pneumococcal conjugate vaccine (PCV-13) into its childhood immunization program, achieving coverage rates above 90% by 2014. Despite this success, this vaccination campaign has been followed by an increase in infections caused by non-vaccine serotypes, including some with a high prevalence of antibiotic resistance. The study by Hurst and colleagues examined the serotype distribution and antibiotic resistance of pneumococcal isolates from infants in the African country between 2016 and 2019, by collecting nasopharyngeal swabs and performing capsular serotyping and AST with E-tests. At the time of sample collection, more than four infants out of five had received at least one dose of PCV-13, and more than half had completed the three-dose series. Among the pneumococcal isolates identified, vaccine serotypes accounted for 27%. Penicillin resistance increased from 41% in 2016 to 71% in 2019, and non-susceptibility to trimethoprim-sulfamethoxazole rose from 55% in 2016 to 79% in 2019. Multi-drug resistance and amoxicillin resistance were found in 1% of the isolates. In conclusion, the researchers discovered that PCV-13 serotypes still accounted for a significant portion of isolates years after the vaccine’s introduction. The increase in penicillin resistance and low ceftriaxone resistance support using third-generation cephalosporins for empirically treating suspected bacterial meningitis.
• Self-sampling has the potential to overcome declining participation and inequalities in cervical screening programs; still, pilot studies are necessary to overcome variables and highlight the real-world benefits of this innovative testing method. YouScreen is a HPV screening program we have been partnering with for years, aiming to assess the impact of offering self-sampling to non-attenders. Between January and November 2021, self-sampling kits were distributed to non-attenders either opportunistically during any consultation in primary care or via direct mail 15 months after routine invitation. Primary outcomes included the monthly proportion of non-attenders screened, change in coverage, and uptake within 90 days. The study found that more than 8000 women provided self-samples, and responders represented the ethnically diverse non-attendee population. Kits offered opportunistically in primary care had a return rate of 65.5%, while directly mailed kits had a return rate of 12.9%. The self-sampling intervention increased the number of non-attenders screened per month, improving HPV screening coverage without any adverse effects. Dr Lim and colleagues concluded that opportunistic offering self-sampling in primary care could enhance coverage and potentially reach underserved populations in England.
• Multi-drug-resistant E. coli poses a significant global public health challenge, especially in the southern countries of the world – although these strains often spread to other regions through travelers. To understand the full extent of the genetic diversity of E. coli colonizing local populations, Tamim Khawaja and colleagues quantified genetic diversity and associated antimicrobial resistance (AMR) of E. coli individuals in the Punjab province, Pakistan, assessing the impact of antibiotic use. Rectal swab and stool samples were cultured, and DNA extracted from these cultures was sequenced to capture the genetic and AMR diversity of E. coli. The study assembled 5,247 E. coli genomes from 1,411 samples, revealing significant genetic diversity in gut colonization. The genetic lineages and AMR determinants in the Punjabi population differed notably from those in high-income countries. Antibiotic use increased the prevalence of well-known globally circulating MDR clinical strains. These findings suggest that longitudinal, multi-regional genomics-based surveillance of both colonization and infections is necessary to develop a mechanistic understanding of the interplay between ecology and evolution in maintaining and disseminating MDR E. coli.

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Here we are, with the three studies selected for the July Microbiology Time:

• To explore the effects of surface characteristics on the deposition and persistence of touch DNA, Dr. Recipon and colleagues selected a range of substrates commonly found at crime scenes to be analyzed in vitro. The researchers discovered that these surface features influence cell deposition, morphology, retention, and the subsequent genetic analysis of touch DNA. Remarkably, while cell-derived fragments and fingermarks were detectable on various substrates for up to two months by targeting proteins and carbohydrates, swabbing and genetic analysis of mock traces yielded the most informative profiles primarily from substrates with the highest surface free energy. The researchers conclude that understanding the intrinsic properties of substrates is crucial for comprehending the transfer and persistence of biological traces, and appropriate methodologies and sampling devices are necessary for improving their detection and collection.
• The second study from the US assessed the performance of self-collected vaginal swabs for HPV detection using the Cobas 6800 system. The researchers found minimal variability in swabs self-collected by the same individual, as determined by the amplification of HPV and human β-globin control DNA, and high concordance between self-collected vaginal swabs and professional-collected cervical samples. The duration of dry storage did not affect HPV amplification; even the exposure of self-collected dry swabs to extreme summer and winter temperatures did not impact testing outcomes. These findings are another piece of evidence that suggests the use of self-collected vaginal samples for accurate clinical HPV testing, even after extreme temperature storage.
• To understand the impact of self-collection on HPV test outcomes, the authors of the third study selected and tested different swab collection workflows. What did they find? Depositing the collection swab into a resuspension buffer improved the PCR detection of human beta-hemoglobin compared to the “swirl-and-toss” method. Additionally, reducing the swab resuspension volume from 10 mL to 3 mL resulted in a PCR threshold reduction in the detection of human beta-globin. In a second step, the researchers performed a systematic literature search followed by data extraction and analysis to assess further the impact of resuspension volume on performance following self-collection. The article suggests that self-collection conditions can be optimized to improve sample recovery and performance, thereby enhancing cervical cancer screening.

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HPV self-collection in Mongolia, DNA methylation for detecting uterine cancer, and automated Antibiotic Susceptibility Testing with Radian: read the three studies we selected in this edition.

• The high prevalence of Human Papillomavirus (HPV) in the country makes cervical cancer the third most common tumor among women in Mongolia. The study by Batmunkh and colleagues evaluated the acceptance of self-sampling for HPV detection among young Mongolian women and assessed their knowledge about HPV and cervical cancer. Enrolling more than 200 women, the researchers showed that 95.1% found the self-sampling easy to perform, 98.5% found the instructions clear, and 94.1% experienced no pain. However, 67.8% preferred to perform the self-sampling in a clinic rather than at home. Despite the high acceptance of self-sampling, the participants displayed low knowledge about HPV and moderate knowledge about cervical cancer, urging the need for enhanced educational efforts about HPV and cervical cancer in Mongolia.
• Endometrial cancer EC is the most common gynecological cancer in high-income countries, with a rapidly increasing incidence. In the second study we selected, the British researchers demonstrated that the DNA methylation-based women’s cancer risk identification – quantitative polymerase chain reaction test for endometrial cancer (WID-qEC) test’s stability is consistent regardless of the collection device and sample media used, whether the specimen is collected by a gynecologist or the patient, and the precise sampling site. The test shows sample stability in eNAT medium for seven days at room temperature, facilitating integration into diagnostic workflows. Using FLOQSwabs and eNAT sample collection media, the test’s sensitivity and specificity for detecting uterine cancers in gynecologist-taken samples are 92.9% and 98.6%, respectively, while in patient self-samples, sensitivity and specificity are 75.0% and 100.0%, respectively. These findings confirm the robustness and clinical potential of the WID-qEC test.
• The third study, published in Current Microbiology, evaluated Radian® against manual disk diffusion using EUCAST 2021 breakpoints. Kim Callebaut and colleagues tested 135 bacterial strains from various sources, including Enterobacterales, Enterococcus faecalis, Enterococcus faecium, Pseudomonas aeruginosa, Staphylococcus aureus, coagulase-negative staphylococci, and Streptococcus spp. Radian® showed categorical agreement rates of 95.3% to 98.0% across different bacterial groups, with major error rates of ≤ 5% for all antibiotics. Additionally, antibiotic disk thermostability was confirmed for up to 4 days in the Radian® Carousel. Thus, the Radian® In-Line Carousel offers a fully automated, accurate, and standardized solution for disk diffusion AST, reducing workload and improving traceability.

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In this edition of our Microbiology Time, we selected three papers that showcase the diverse applications of our products.

• The first study we selected is from the Netherlands. Here, Laura Hughes and colleagues reported three cases of chronic follicular conjunctivitis caused by the zoonotic transmission of Chlamydia felis from domestic cats. The study aimed to increase awareness about the possible zoonotic transmission of C. felis and suggest PCR and subsequent sequence analysis as a valuable method to accurately identify the pathogen. Moreover, the researchers discussed the factors contributing to the potential under-diagnosis of C. felis infections and proposed treatment options for C. felis-related conjunctivitis cases.
• In the second study, the Slovenian researchers discussed the application of gene electrotransfer (GET) of plasmids encoding IL12 in treating tumors and as a DNA vaccine adjuvant. In previous studies, they had already developed a plasmid encoding human IL12, now in a phase I clinical study. In this study, they aimed to validate previous findings in mice by using a porcine model, which better mimics human skin. Nine pigs underwent GET of IL12 using different concentrations and types of electrodes. Results showed that needle electrodes induced the highest IL12 expression. The plasmid was distributed to all organs, but its concentration decreased over time. Based on these findings, the researchers concluded that IL12 GET is safe in pigs, making them a valuable model for human gene therapy safety studies.
• We move to Italy for the third study, conducted in Milan. The researchers aimed to compare the performance of a self-administered POC test for anal HPV screening with a laboratory gold-standard test in pre-exposure prophylaxis (PrEP) users. Participants self-collected anal swabs and completed anonymous questionnaires on self-sampling feasibility. Afterward, participants underwent standard viral genotyping at local clinics. 68.2% of the subjects tested positive for at least one high-risk HPV genotype on POCT, compared to 77% with the gold-standard test. The feasibility questionnaire revealed that 92.7% found self-swabbing easy. The agreement between POCT and the gold-standard test was moderate, with POCT showing a sensitivity of 81.0%, specificity of 73.8%, positive predictive value of 91.0%, and negative predictive value of 54.4%. The study concludes that POCT could serve as a valuable and feasible additional tool for HPV screening, particularly in low-resource and community-based settings.

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Discover the three studies we selected in April’s Microbiology Time.

• The first study we selected explored the potential of using tongue swabbing as a substitute for sputum in tuberculosis (TB) testing. Previous research indicated that the Cepheid Xpert Ultra platform performs well compared to reference standards on buffer-preserved sputum samples. Here, the researchers assessed the same platform on 245 self-collected and dry-stored tongue swabs and compared the results with the Molbio Truenat MTB Ultima (MTB Ultima) assay. Xpert Ultra showed 75.5% sensitivity and 100% specificity compared to sputum testing, while MTB Ultima demonstrated 71.6% sensitivity and 96.9% specificity, improving to 79.1% sensitivity after re-testing frozen samples initially yielding false-negative or invalid results. These findings highlight the feasibility of using tongue swabs as easy-to-collect samples for TB testing.
• For the second study, we move to Indonesia, where Dr. Wulandri and colleagues investigated the pathogens causing acute diarrhea in children, comparing HIV-infected and non-HIV-infected cases at an Indonesian tertiary hospital. Conducted from March 2019 to April 2020, the cross-sectional study utilized multiplex RT-PCR, showing that almost 60% of the samples were positive, with more positive results in HIV-infected children than in non-HIV-infected children (70% vs. 54.7%). Overall, 72 enteropathogens were detected, with non-HIV cases primarily showing bacterial infections with enteroaggregative Escherichia coli as predominant, followed by viral infections. In contrast, HIV-infected children exhibited a mix of viruses, bacteria, and parasites with Cryptosporidium spp. solely detected in this group. Notably, non-HIV children predominantly presented with invasive bacterial pathogens, while HIV-infected children showed more viral and parasitic infections, often attributed to opportunistic pathogens.
• The last study investigated the relationship between gut microbiome composition and clinical outcomes in COVID-19 patients. Stool samples and patient records were collected from 24 hospitalized individuals with confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the Illumina MiSeq. The results revealed that female COVID-19 patients had lower gut bacterial microbiota richness compared to males, possibly influenced by differences in hospital admission timing. Both sexes exhibited associations with opportunistic bacterial pathogens like Enterococcus and Streptococcus. The Candida genus dominated the gut mycobiota of COVID-19 patients, with adults showing higher fungal diversity than the elderly. Notably, Saccharomycetales unassigned fungal genera correlated with bacterial short-chain fatty acid producers and negatively with proinflammatory bacteria like Bilophila. Patients harboring this fungal taxon were not admitted to high-intensity units. The study underscores the association between COVID-19 and opportunistic bacterial pathogens, highlights Candida dominance in the gut, and suggests a potential protective role for specific fungal taxa, warranting further investigation into their role in gastrointestinal health and disease outcomes.

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This month, we bring you a new oral microbiota sampling method, a study on saliva and Long COVID, and yet another paper highlighting the importance of self-collection in the fight against cervical cancer.

• This first study investigated the association between COVID-19 and Long COVID in children. The Italian researchers conducted a prospective study involving 167 pediatric patients hospitalized with confirmed acute SARS-CoV-2 infection, and collecting saliva samples with LolliSponge. A telephone survey was conducted at 3-6-12 months after discharge. Of the patients, 95.5% presented with symptoms upon admission. Regarding patients for whom it was feasible to determine the SARS-CoV-2 variant, the study identified the Delta variant in 21.6% and the Omicron variant in 78.4%. About 16.5% of patients reported symptoms indicative of Long COVID, such as weight loss, inappetence, chronic cough, fatigue, and others. Only 4 patients with Long COVID had a specific SARS-CoV-2 variant identified. The study emphasizes the significant concern of Long COVID in the pediatric population, highlighting the need for continuous monitoring and tailored symptom investigation based on age.
• For the second study, we remain in Italy. Marianna Martinelli and colleagues assessed the accuracy of the BD Onclarity HPV assay on self-collected vaginal FLOQSwabs compared to cervical samples for detecting cervical intraepithelial neoplasia (CIN). Testing was conducted on two automated platforms, BD Viper LT and BD COR, and included 300 women. Self-sampling was performed with two vaginal swabs to assess, with the second one, the influence of freezing on the results. The results showed similar sensitivity for ≥CIN2 between vaginal and cervical samples, regardless of the platform used. Specificity was initially slightly lower for self-collected samples compared to cervical samples, but cut-off optimization for HPV positivity improved relative specificity without compromising sensitivity. No significant differences were observed between self-samples tested with the two platforms and between first- and second-collected (frozen) swabs. The study concludes that Onclarity assay on self-collected FLOQSwabs samples showed similar sensitivity and specificity (with cut-off optimization) to detect ≥CIN2 compared to cervical samples.
• The third study addressed the challenge of standardizing oral microbiome analysis due to the variability in microbiota compositions across different oral habitats and the lack of standardized collection methods. The study proposes a standardized protocol for dental examination and material collection for next-generation sequencing (NGS) from various oral sites. The researchers involved 60 patients grouped into COVID-19 convalescents with and without antibiotics and healthy individuals. The collected biological samples were then used to conduct NGS (16S rRNA). Alpha and beta diversity analyses reveal notable differences in microbial communities, particularly in the supragingival plaque. The study emphasizes the importance of precise procedures during dental exams and material collection to avoid technical errors and contamination in NGS results. Dental indices like DMFT, D number, PI, and BOP are highlighted as valuable prognostic parameters for assessing oral health. The developed procedures are suggested for use in future studies by future studies.

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