- Volume 4, Issue 8, 2022

Increasing numbers of patents directed to bacteria and bacterial products are being filed and granted, many of which claim specific deposited strains of bacteria. However, there remains significant uncertainty regarding exactly what scope patent claims limited to deposited strains might have. A claim limited to a specific deposited strain could be interpreted extremely narrowly, extending only to descendants of that deposit. However, a review of the available guidance from courts across the globe suggests that in practice such claims are likely to be infringed by competitor products. The commercial value of patent claims to bacteria depends on the regulatory and competitive landscape, and can be strengthened by appropriate details in patent applications.

Objectives. Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.

Methods. A range of open source bioinformatics tools were used to ‘mine’ genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.

Results. As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a ‘deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R ‘deleterious’ mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7 kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8 kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.

Conclusions. This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.

How we teach science and engage with the public, particularly in fast moving subjects such as microbiology, are constantly being reflected upon, improved and innovated. This has led to a significant increase of pedagogy publications by microbiology educators in higher education that have had a positive impact on teaching quality, student retention, progression and course satisfaction as well as how science is communicated with the public. In this paper we describe the different types of pedagogical manuscripts that biological scientists could write and the benefits that derive from doing so. We provide a glossary of terms often seen in educational literature. Project design and qualitative and quantitative research methodologies are discussed, highlighting ethical and General Data Protection Regulation (GDPR) considerations. Suggestions are made regarding how to network with colleagues who are also keen on writing pedagogical papers as well as examples of good practice. Lastly, a handy how-to-start guide aims to help with first steps. We hope that this paper will be a useful survival manual for colleagues who wish to engage in exciting pedagogical research in the field of microbiology and the broader biological sciences.

Introduction. Saprochaete capitata is an emerging opportunistic fungus that is responsible for an uncommon mycosis known as geotrichosis, mainly reported in patients with haematological malignancies. It is a life-threatening condition associated with a high mortality rate of over 52 %. S. capitata may affect any organ, with a predilection for the lungs.

Case presentation. Here we report a case of pulmonary geotrichosis in a neutropenic HIV-infected patient with a prior history of treated tuberculosis. The main risk factor for pulmonary geotrichosis is profound and prolonged neutropenia. To our knowledge, this is the first reported case of S. capitata infection occurring on top of probable active miliary tuberculosis.

Conclusion. The clinical and radiological features are non-specific and similar to those of other pulmonary fungal diseases, hence the importance of mycological examination to confirm the diagnosis. Through this report, we urge clinicians to vigilantly consider S. capitata as an aetiological agent in the differential diagnosis of fungal infections in HIV-infected individuals and to routinely screen for associated infections.