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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