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Background Suicide research aims to contribute to a better understanding of suicidal behaviour and its prevention. However, there are many ethical challenges in this research field, for example, regarding consent and potential risks to participants. While studies to-date have focused on the perspective of the researchers, this study aimed to investigate the views and experiences of members of Human Research Ethics Committees (HRECs) in dealing with suicide-related study applications. Methods This qualitative study entailed a thematic analysis using an inductive approach. We conducted semi-structured interviews with a purposive sample (N = 15) of HREC Chairs or their delegates from Australian research-intensive universities. The interview guide included questions regarding the ethical concerns and challenges in suicide-related research raised by HREC members, how they dealt with those challenges and what advice they could give to researchers. Results The analysis identified four main themes: (1) HREC members’ experiences of reviewing suicide-related study applications, (2) HREC members’ perceptions of suicide, suicide research, and study participants, (3) Complexity in HREC members’ decision-making processes, and (4) HREC members’ relationships with researchers. Conclusions Reliance on ethical guidelines and dialogue with researchers are crucial in the assessment of suicide-related study applications. Both researchers and HREC members may benefit from guidance and resources on how to conduct ethically sound suicide-related studies. Developing working relationships will be likely to help HRECs to facilitate high quality, ethical suicide-related research and researchers to conduct such research.

Persistent human papillomavirus (HPV) infections is necessary for the development of cervical cancers. Consequently, understanding the biologic mechanisms resulting in clearance is key in cancer prevention. Similar to other mucosal sites, it is expected that the local microbiome plays a significant role in shaping the immune response responsible for HPV clearance. Using cervical wash repository samples from a prospective study of HPV in women, this study investigates the microbiome and its associated inflammatory milieu during HPV 16 pre-acquisition, persistence and clearance states. For comparison, samples from women with no history of HPV ever during the study period were selected. We showed that 9 of 13 inflammatory cytokines were found to be significantly increased in the immediate post-clearance visit compared to the pre-acquisition or infection visits. Gardnerella vaginalis was associated with higher levels of inflammatory cytokines. Women with no history of HPV infection had similar cytokine profiles as those with HPV 16 post-clearance. This in vivo study documented an immune response shortly after HPV 16 clearance. G. vaginalis appeared to be involved in shaping this immune response. The appearance of G. vaginalis may have resulted from a shift from anti-microbial to anti-viral immune response with loss of bacterial control. The similar high levels of cytokines seen in women with no history of HPV suggest that a certain level of inflammatory surveillance is required to maintain an HPV negative state. This data may inform therapies such as probiotics or pro-inflammatory agents for treatment of persistent HPV.

Porphyrins are a group of metabolites essential to the biosynthesis of heme, cobalamin, and chlorophyll in living organisms. Bacterial porphyrins can be proinflammatory, with high levels linked to human inflammatory diseases, including the common skin condition acne vulgaris. Propionibacteria are among the most abundant skin bacteria. Variations in propionibacteria composition on the skin may lead to different porphyrin levels and inflammatory potentials. This study characterized porphyrin production in all lineages of Propionibacterium acnes, the most dominant skin Propionibacterium, and other resident skin propionibacteria, including P. granulosum, P. avidum, and P. humerusii. We revealed that P. acnes type I strains produced significantly more porphyrins than did type II and III strains and other Propionibacterium species. The findings from this study shed light on the proinflammatory potential of the skin microbiome and can be used to guide the development of effective acne treatments by modulating the skin microbiome and its metabolic activities., Porphyrins are intermediate metabolites in the biosynthesis of vital molecules, including heme, cobalamin, and chlorophyll. Bacterial porphyrins are known to be proinflammatory, with high levels linked to inflammatory skin diseases. Propionibacterium species are dominant skin commensals and play essential roles in defending against pathogens and in triggering an inflammatory response. To better understand how the inflammatory potential of the skin microbiome may vary depending on its propionibacterial composition, we compared the production levels of porphyrins among Propionibacterium acnes, Propionibacterium granulosum, Propionibacterium avidum, and Propionibacterium humerusii strains. We found that porphyrin production varied among these species, with P. acnes type I strains producing significantly larger amounts of porphyrins than P. acnes type II and III strains and other Propionibacterium species. P. acnes strains that are highly associated with the common skin condition acne vulgaris responded to vitamin B12 supplementation with significantly higher porphyrin production. In contrast, vitamin B12 supplementation had no effect on the porphyrin production of health-associated P. acnes strains and other propionibacteria. We observed low-level porphyrin production in most Propionibacterium strains harboring the deoR repressor gene, with the exception of P. acnes strains belonging to type I clades IB-3 and IC. Our findings shed light on the proinflammatory potential of distinct phylogenetic lineages of P. acnes as well as other resident skin propionibacteria. We demonstrate that the overall species and strain composition is important in determining the metabolic output of the skin microbiome in health and disease. IMPORTANCE Porphyrins are a group of metabolites essential to the biosynthesis of heme, cobalamin, and chlorophyll in living organisms. Bacterial porphyrins can be proinflammatory, with high levels linked to human inflammatory diseases, including the common skin condition acne vulgaris. Propionibacteria are among the most abundant skin bacteria. Variations in propionibacteria composition on the skin may lead to different porphyrin levels and inflammatory potentials. This study characterized porphyrin production in all lineages of Propionibacterium acnes, the most dominant skin Propionibacterium, and other resident skin propionibacteria, including P. granulosum, P. avidum, and P. humerusii. We revealed that P. acnes type I strains produced significantly more porphyrins than did type II and III strains and other Propionibacterium species. The findings from this study shed light on the proinflammatory potential of the skin microbiome and can be used to guide the development of effective acne treatments by modulating the skin microbiome and its metabolic activities.

Background: The optimal management strategy for multiple sclerosis (MS), and many other chronic diseases, likely involves health behavior modification. Multimodal behavioral interventions may be most effective, but little is known about long-term adherence in people with MS.Methods: This qualitative study assessed barriers and enablers to long-term adherence by people with MS who self-selected for a 5-day health behavior intervention 3-5 years prior. Thirteen women and five men participated in semi-structured phone interviews, which were transcribed and thematically analyzed.Results: The experience was described as useful for information gathering, decision making, and practical strategies regarding health behaviors. The majority still followed supplementation and dietary recommendations most of the time, although consuming non-recommended food while eating out was common. Support at home, ability and enjoyment in food preparation, and ability to resist unhealthy foods were both barriers and enablers. Adherence to "time-consuming" exercise and meditation recommendations were less common and episodic. Many reported competing interests on time from work and family; and barriers including injuries and symptoms, weather, financial or geographical barriers, and lack of person-centred support and motivation. Increased fitness and mobility, weight loss, and a sense of accomplishment and control were advantages and motivators. Practical and attitudinal strategies employed included planning, tailoring activities to ability and preference, and self-monitoring.Conclusion: While most people attempted to engage with all components of the intervention initially, only some still engaged with all components, and none to the recommended levels. These data can inform future quantitative studies and health behavior interventions.Implications for rehabilitationA multimodal group lifestyle intervention may be useful to assist people with multiple sclerosis in information gathering, decision making, attitudinal changes, and practical strategies regarding health behaviors; as well as providing a sense of hope for the future and control over wellbeing.While participants are unlikely to engage with all components of a multimodal intervention to the recommended level, they are likely to make improvements to one or more health behaviors.Experiential learning, including going through recipes and ingredient lists, and practicing meditation and physical exercises, is helpful to instigate behavior change.The initiation and maintenance of behavior change was assisted by support from family, friends, and health practitioners; and practical strategies employed by participants, including planning, self-monitoring, and tailoring activities to ability and preference.

Type 2 diabetes mellitus (T2DM) is a systemic disease, predisposing patients to other inflammatory conditions including periodontitis. The subgingival microbiome, a key player in periodontitis pathogenesis, is not well characterized in T2DM population. To better understand whether the subgingival microbiome is different between T2DM and systemically healthy, nondiabetic (ND) subjects, we performed a longitudinal analysis of the subgingival microbiome in T2DM patients (n = 15) compared with ND subjects (n = 16). Using metagenomic shotgun sequencing, we investigated the microbiome in the healthy periodontal state, periodontitis state, and resolved state after treatment. We found that in the periodontitis state, the shift in the subgingival microbiome from the healthy state was less prominent in T2DM compared with ND subjects, yet the clinical signs of disease were similar for both. Furthermore, we revealed highly correlated presence of pathogenic species in relative abundance not only in the periodontitis state, but also in the healthy state in T2DM, suggesting an elevated risk of progression to periodontitis in this cohort. We further investigated the functional potentials of the subgingival microbiome and identified a set of microbial marker genes associated with the clinical states. These genes were significantly enriched in 21 pathways, some of which are associated with periodontitis and some potentially link T2DM and periodontitis. This study identified the longitudinal changes of the subgingival microbiome associated with periodontitis in T2DM and suggests that T2DM patients are more susceptible to shifts in the subgingival microbiome toward dysbiosis, potentially due to impaired host metabolic and immune regulation.

Relationships of trust between research participants and researchers are often considered paramount to successful research; however, we know little about participants’ perspectives. We examined whom research participants trusted when taking part in research. Using a qualitative approach, we interviewed 36 research participants, including eight Indigenous participants. Thematic analysis was used to analyze the data. This article focuses on findings related to non-Indigenous participants. In contrast to Indigenous participants, non-Indigenous participants placed their trust in research institutions because of their systems of research ethics, their reputation and prestige. Researchers working in non-Indigenous contexts need to be cognizant that the trust that participants place in them is closely connected with the trust that participants have in the institution.

Background. Propionibacteria are important members of the human skin microbiota, but are also opportunistic pathogens associated with periprosthetic joint infections (PJI). While the role of Propionibacterium acnes in PJI has been widely described, insight into the capacity of Propionibacterium avidum to cause PJI is limited. Methods. An unusual cluster of four hip PJIs caused by P. avidum in one orthopedic center in 2015 prompted us to retrospectively identify and analyze clinical data related to previous P. avidum PJI cases (1997-2015). We also characterized the hemolytic and biofilm-producing capacity of our four clinical P. avidum strains isolated in 2015, and investigated their phylogenetic relationships by whole genome sequencing. Results. We retrospectively identified 13 P. avidum PJIs, with the majority being hip-related infections (n=11). Preoperative synovial fluid cultures were P. avidum positive in 63.6% of cases. Six out of 12 patients (50%) with available case histories were treated with an exchange of the prosthesis. In all but one of the six patients treated with debridement-retention of the prosthesis, treatment failed thus requiring a two-stage revision. The isolated P. avidum strains showed a more pronounced hemolytic activity, but a similar biofilm-forming ability when compared to P. acnes. Whole genome sequencing identified two phylogenetic clusters highly related to P. avidum PJI strains isolated in Sweden. Conclusions. We describe the largest series of P. avidum PJI predominantly located in the hip. Phylogenetic similarity of our P. avidum strains to PJI strains isolated elsewhere suggests these invasive lineages may be common.

The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA 1 , IA 2 , IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA 1 , IA 2 , and IC), sodA (types IA 2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA 1 ( n = 145), IA 2 ( n = 20), IB ( n = 65), IC ( n = 7), II ( n = 45), and III ( n = 30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.

Trust in research is important but not well understood. We examine the ways that researchers understand and practice trust in research. Using a qualitative research design, we interviewed 19 researchers, including eight researchers involved in Australian Indigenous research. The project design focused on sensitive research including research involving vulnerable participants and sensitive research topics. Thematic analysis was used to analyze the data. We found that researchers' understanding of trust integrates both the conceptual and concrete; researchers understand trust in terms of how it relates to other similar concepts and how they practice trust in research. This provides a sound basis to better understand trust in research, as well as identifying mechanisms to regain trust when it is lost in research.

Progressive macular hypomelanosis (PMH) is a common skin disorder that causes hypopigmentation in a variety of skin types. Although the underlying aetiology of this condition is unclear, there is circumstantial evidence that links the skin bacterium Propionibacterium acnes to the condition. We now describe the first detailed population genetic analysis of P. acnes isolates recovered from paired lesional and non-lesional skin of PMH patients. Our results demonstrate a strong statistical association between strains from the type III phylogenetic lineage and PMH lesions (P = 0.0019), but not those representing other phylogroups, including those associated with acne (type IA1). We also demonstrate, based on in silico 16S rDNA analysis, that PMH isolates previously recovered from patients in Europe are also consistent with the type III lineage. Using comparative genome analysis, we identified multiple genomic regions that are specific for, or absent from, type III strains compared to other phylogroups. In the former case, these include open reading frames with putative functions in metabolism, transport and transcriptional regulation, as well as predicted proteins of unknown function. Further study of these genomic elements, along with transcriptional and functional analyses, may help to explain why type III strains are associated with PMH.

Background It is important for researchers to understand the motivations and decision-making processes of participants who take part in their research. This enables robust informed consent and promotes research that meets the needs and expectations of the community. It is particularly vital when working with Indigenous communities, where there is a history of exploitative research practices. In this paper, we examine the accounts of Australian Indigenous and non-Indigenous research participants in terms of how and why they agree to take part in research. Methods A qualitative research approach was employed to undertake individual interviews with 36 research participants in Victoria, Australia. Eight participants identified as Indigenous and 28 were non-Indigenous. Thematic analysis was used to interpret the data. Results There were stark differences between Indigenous and non-Indigenous research participants in terms of why and how they decided to participate in research. For Indigenous participants, taking part in research was primarily to benefit their communities rather than for personal interests. Indigenous participants often started from a position of caution, and showed a considered and deliberate process of decision making. In weighing up their decision to participate, some Indigenous participants clearly articulated what was valued in conducting research with Indigenous communities, for example, honesty, reciprocity, and respect; these values were explicitly used to assist their decision whether or not to participate. This was in contrast to non-Indigenous participants who took researchers’ claims on face value, and for whom deciding to participate in research was relatively straightforward. The motivations to participate of non-Indigenous participants were due to personal interests, a desire to help others, or trust in the medical practitioner who recruited them for the research project. Conclusion Understanding research participants’ motivations about taking part in research is important. This is particularly relevant for Indigenous communities where there is a reported history of research abuse leading to mistrust. This understanding can lead to research practice that is more respectful and responsive to the needs of Indigenous communities and abides by the values of Indigenous communities. Moreover it can lead to more ethical and respectful research practice for all.

The skin is the largest organ in the human body and provides the first line of defence against environmental attack and pathogen invasion. It harbor multiple commensal microbial communities at different body sites, which play important roles in sensing the environment, protecting against colonization and infection of pathogens, and guiding the host immune system in response to foreign invasions. The skin microbiome is largely variable between individuals and body sites, with several core commensal members commonly shared among individuals at the healthy state. These microbial commensals are essential to skin health and can potentially lead to disease when their abundances and activities change due to alterations in the environment or in the host. While recent advances in sequencing technologies have enabled a large number of studies to characterize the taxonomic composition of the skin microbiome at various body sites and under different physiological conditions, we have limited understanding of the microbiome composition and dynamics at the strain level, which is highly important to many microbe‐related diseases. Functional studies of the skin microbial communities and the interactions among community members and with the host are currently scant, warranting future investigations. In this review, we summarize the recent findings on the skin microbiome, highlighting the roles of the major commensals, including bacteria, fungi and bacteriophages, in modulating skin functions in health and disease. Functional studies of the skin microbiota at the metatranscriptomic and proteomic levels are also included to illustrate the interactions between the microbiota and the host skin.

The anaerobic skin commensalPropionibacterium acnesis an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised from each of 64 patients with lumbar disc herniation.P. acnesand other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence ofP. acnesin their excised herniated disc tissue. UsingrecAand mAb typing methods, 52% of the isolates were type II (50% of culture-positive patients), while type IA strains accounted for 28% of isolates (42% patients). Type III (11% isolates; 21% patients) and type IB strains (9% isolates; 17% patients) were detected less frequently. The MIC values for all isolates were lowest for amoxicillin, ciprofloxacin, erythromycin, rifampicin, tetracycline, and vancomycin (≤1mg/L). The MIC for fusidic acid was 1-2 mg/L. The MIC for trimethoprim and gentamicin was 2 to ≥4 mg/L. The demonstration that type II and III strains, which are not frequently recovered from skin, predominated within our isolate collection (63%) suggests that the role ofP. acnesin lumbar disc herniation should not be readily dismissed.

Propionibacterium acnes , a non-spore-forming, anaerobic Gram-positive bacterium, is most notably recognized for its association with acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821–832, 2009). We now present the draft genome sequence of an antibiotic-resistant P. acnes strain, PRP-38, isolated from an acne patient in the United Kingdom and belonging to the novel type IC cluster.

Propionibacterium acnes is an anaerobic Gram-positive bacterium that has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris (I. Kurokawa et al., Exp. Dermatol. 18:821–832, 2009). We now present the whole-genome sequences of three P. acnes strains from the type IA 2 cluster which were recovered from ophthalmic infections (A. McDowell et al., Microbiology 157:1990–2003, 2011).

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 64 % of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants, which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore support an association between acne and P. acnes strains from the type IA cluster and highlight the role of a widely disseminated clonal genotype in this condition. Characterization of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST4) that correctly predicted the phylogroup (IA1, IA2, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST4 method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated 'virulence' factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages.

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two ‘putative virulence’ genes (eMLST) that provides improved high resolutiontyping (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA1 clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA2 strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA1 and IA2 strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications.