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After introducing the 13-valent pneumococcal conjugate vaccine (PCV13) for children, a change in the prevalence of different Streptococcus pneumoniae serotypes that cause invasive pneumococcal diseases (IPDs) has been observed. The prevalence of vaccine serotypes has decreased and that of non-vaccine serotypes has increased. Currently, serogroup 24 has become one of the major non-vaccine serotypes causing IPDs in children in Japan. The aim of this study was to characterize clinical and genomic features of S. pneumoniae serogroup 24 strains isolated from sterile body sites in Japanese children. Serotyping, multi-locus sequence typing and genomic analysis of capsular polysaccharides of 61 strains of serogroup 24 were performed from 2015 to 2021. Among the 61 strains, 36, 23 and two belonged to serotypes 24F, 24B and 24C, respectively. The 24F sequence type (ST) 2572 and 24B ST 2572 were the major serotypes and sequence types observed from 2015 to 2019. By contrast, 24F ST 162 and 24B ST 2754 were the two major serotypes and sequence types observed after 2020. Two strains of serotype 24C were detected for the first time in Japan. Sequence analysis of the abpA gene, which plays a role in the synthesis of capsular polysaccharides in S. pneumoniae , was performed to distinguish different strains of serogroup 24. After the introduction of PCV13 in Japan, serogroup 24 has become one of the most prevalent non-vaccine serotypes causing IPDs in children. This serogroup has not been targeted in the next-generation pneumococcal conjugate vaccines. Therefore, monitoring of S. pneumoniae serogroup 24 that causes IPDs in children is essential.

Skin flora bacteria, such as Cutibacterium acnes , are the predominant contaminants of blood products used for transfusion. Platelet concentrates (PCs), a therapeutic product used to treat patients with platelet deficiencies, are stored at ambient temperature under agitation, providing ideal conditions for bacterial proliferation. At Canadian Blood Services, PCs are screened for microbial contamination using the automated BACT/ALERT culture system. Positive cultures are processed and contaminating organisms are identified using the VITEK 2 system. Over a period of approximately 2 years, several PC isolates were identified as Atopobium vaginae to a high level of confidence. However, since A. vaginae is associated with bacterial vaginosis and is not a common PC contaminant, a retrospective investigation revealed that in all cases C. acnes was misidentified as A. vaginae . Our investigation demonstrated that the media type used to grow PC bacterial isolates can have a significant impact on the results obtained on the VITEK 2 system. Furthermore, other identification methods such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALD-TOF MS) and PCR amplification of the 16S RNA gene were only partially successful in the identification of C. acnes . Therefore, our findings support a multiphasic approach when PC isolates are identified as A. vaginae by the VITEK 2 system for proper identification of C. acnes using macroscopic, microscopic and other biochemical analyses.

Streptococcus pneumoniae is one of the pathogenic bacteria causing invasive pneumococcal diseases such as pneumonia, sepsis, and meningitis, which are commonly reported in children and adults. In this study, we investigated the nasopharyngeal carriage rates, serotype distribution, and antimicrobial susceptibility profiles of S. pneumoniae among children with pneumonia and healthy children under 5 years old in Padang, West Sumatra, Indonesia. Nasopharyngeal swabs were collected from 65 hospitalized children with pneumonia in a referral hospital and from 65 healthy children at two day-care centers from 2018 to 2019. S. pneumoniae was identified by conventional and molecular methods. Antibiotic susceptibility was performed with the disc diffusion method. Out of 130 children, S. pneumoniae strains were carried by 53% and 9.2 % in healthy children (35/65) and children with pneumonia (6/65), respectively. Serotype 19F was the most common serotype among the isolated strains (21%) followed by 6C (10%), 14, 34 (7 % each), and 1, 23F, 6A, 6B (5 % each). Moreover, 55 % of the strains (23/42) were covered by the 13-valent pneumococcal conjugate vaccine. Most isolates were susceptible to vancomycin (100%), chloramphenicol (93%), clindamycin (76%), erythromycin (71%), and tetracycline (69%). Serotype 19F was commonly found as a multi-drug resistant strain.

Biofilms are naturally occurring communities of micro-organisms, attached to a surface and often embedded in a matrix of self-produced polymeric substances. Biofilms are widely implicated in human infections, particularly on prostheses and medical implants. Such biofilms are difficult to eradicate, often leading to replacement of the prosthesis and resulting in a significant burden to healthcare. Here we present a fun and engaging interactive activity targeted toward primary school/early secondary school children, introducing the concept of natural and healthcare-associated biofilms, using dental plaque as an archetypal example. Dental plaque forms as a result of poor oral/dental hygiene, and develops according to a typical series of defined stages: attachment and adherence to the surface, followed by colonization and maturation of the biofilm structure, and eventually, dispersal. This activity uses dental disclosing tablets to visualize real biofilms (plaque) on the participants teeth, and uses interlocking building-blocks to represent microorganisms, where children build three-dimensional 'biofilms' of varying shapes and structural integrities. Each of the stages of development are discussed in detail, and after building the biofilms, balls of different shapes, sizes and weights can be used as 'antimicrobials' to disrupt the biofilm structure. The outcomes of the activity are to enhance knowledge and general understanding of biofilms; their ubiquitous presence in the natural environment, development, implications in healthcare, and challenges of treatment. The various 'antimicrobial' balls also provide a basis to introduce and discuss drug selection for infections, and the importance of using the correct antimicrobial for different infections to avoid development of resistance.

Introduction: Diagnosis of COVID-19 (coronavirus disease 2019) is best performed with real-time (quantitative) PCR (qPCR), the most sensitive method for detection and quantification of viral RNA. Using the Centers for Disease Control and Prevention (CDC) protocol, for each sample tested for the virus, three qPCR tests are performed, targeting the viral genes N1 and N2, in addition to the internal control gene RNase P. Samples in which internal control fails to amplify should be labelled 'invalid'.

Methods: This study aims to determine the frequency of inhibition of the RNase P gene used as an internal control in qPCR tests for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in a reference hospital in Southern Brazil during the COVID-19 pandemic (1 February 2021 to 31 March 2021).

Results: A total 10, 311 samples were available for analysis. The mean cycle threshold (Ct) value for the RNAse P gene was 26.65 and the standard deviation was 3.18. A total of 252 samples were inhibited (2.4%) during the study period: amongst these, 77 (30.5%) showed late amplifications (beyond 2 standard deviations from the mean Ct value), and 175 (69.4%) revealed no fluorescence at all for the RNase P gene.

Conclusions: This study showed a low percentage of inhibition using RNase P as an internal control in COVID-19 PCRs using the CDC protocol, thus proving the effectiveness of this protocol for identification of SARS-CoV-2 in clinical samples. Re-extraction was efficacious for samples that showed little or no fluorescence for the RNase P gene.

Introduction: Brain abscess is the most common focal infectious neurological injury. Until the nineteenth century this condition was fatal, however the development of neuroimaging for early diagnosis, neurosurgery and antibiotic therapy in the twentieth century has led to new therapeutic strategies decreasing mortality from 50 % in the 1970s to less than 10 % nowadays. In this context we report a case of brain abscess with a dental origin.

Case report: A immunocompetent man without any addiction presented to the emergency department with dysarthria and frontal headache at home. The clinical examination was normal. Further investigations revealed a polymicrobial brain abscess as a consequence of an ear, nose or throat (ENT) infection with locoregional extension with a dental starting point involving Actinomyces israelii and Fusobacterium nucleatum . In spite of a rapid diagnosis and a neurosurgical management associated with an optimal treatment by a dual therapy made of ceftriaxone and metronidazole the patient unfortunately died.

Conclusion: This case report shows that despite a low incidence and a good prognosis following the diagnosis, brain abscesses can lead to patient's death. Thereby, when the patient's condition and urgency allow, a thorough dental examination of patients with neurological signs following the recommendations would improve the diagnosis made by the clinician. The use of microbiological documentation, the respect of pre-analytical conditions, the interaction between the laboratory and the clinicians are indispensable for an optimal management of these pathologies.

Background: Escherichia coli is a common cause of urinary tract infections. Due to the increase in antimicrobial resistance (AMR) and global differences in antimicrobial susceptibility data, routine assessment of local antimicrobial susceptibility patterns is necessary to guide the selection of appropriate empirical therapy. The aim of this study was to evaluate the antimicrobial susceptibility patterns of community-acquired uropathogenic Escherichia coli within a catchment area in Dublin over a 13 year period, 2010-2022.

Methods: All mid-stream urine samples received from local general practitioners in which there was significant E. coli bacteriuria during the study period, 2010-2022, were included in the analysis. Antimicrobial susceptibility testing was performed by disc diffusion as per the European Committee on Antimicrobial Susceptibility Testing recommendations.

Results: An average of 11 407 urine samples per month had significant bacteriuria, with E. coli accounting for an average of 67 % of those. Overall AMR rates were highest for ampicillin (53.9 %), followed by trimethoprim (32.4 %), gentamicin (18.6 %), co-amoxiclav (16.5 %), ciprofloxacin (12.3 %), cephalexin (8.3 %), cefpodoxime (6.8 %) and nitrofurantoin (2 %). While rates appeared grossly static, statistically significant reduced resistance rates were noted for co-amoxiclav (r_s=-0.95; P=<0.001), cephalexin prior to 2019 (r_s=-0.783; P=0.013) and trimethoprim (r_s=-0.639; P=0.019), with a statistically significant increase in non-susceptibility to cefpodoxime (r_s=0.802; P=0.001).

Conclusions: In order to generate efficient empirical antimicrobial prescribing guidelines, knowledge of region-specific contemporaneous antimicrobial susceptibility patterns is pivotal. Our findings support the use of nitrofurantoin or cephalexin as empirical antimicrobial therapy within our setting.

Alternative methods for arbuscular mycorrhizal (AM) fungal colonized root staining have recently gained more attention for the reduction of hazard exposure to the user. Sheaffer blue ink has been employed for such an identification and quantification, having shown an increased degree of image clarity. However, sourcing Sheaffer blue ink is becoming problematic, leading to the need to find alternative inks that are readily available. Parker ink is a well-known brand, providing comparable colour options to Sheaffer. Two Parker inks, blue and washable blue, were employed alongside Sheaffer blue for comparative AM fungal colonized root staining. From quantified AM fungal vesicles and arbuscles, along with the degree of stained image clarity under microscopy, none of the inks utilized for this comparison produce a significantly (P=0.97) different AM fungal quantification or change in image clarity. Therefore, the results of the present communication suggest that Parker blue and washable blue inks are alternative ink stains for the viewing and quantification of AM fungi in host cortical root tissues.

We have sequenced the whole genome of Streptomyces sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana. The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate Streptomyces sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to Streptomyces prasinus and Streptomyces viridosporus . It is known that the genus Streptomyces possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.