Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance.

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.

Pseudomonas aeruginosa's adaptive trajectory: diverse origins, convergent paths.

Does genetic background contribute to populations following the same or divergent adaptive trajectories? A recent study by Filipow et al. evolved multiple genetically distinct Pseudomonas aeruginosa strains to an artificial cystic fibrosis lung sputum media. The strains adapted at different rates but converged on similar phenotypes despite their initial diversity.

Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity.

The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections-known as rewiring-that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system with the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify 3 key properties-high activation, high expression, and preexisting low-level affinity for novel target genes-that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by preexisting GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.

Natural selection on crosstalk between gene regulatory networks facilitates bacterial adaptation to novel environments.

At the level of the gene, mutation is the raw material for natural selection. However, at the level of the gene regulatory network (GRN), variation is revealed to selection via promiscuous regulator activity ('crosstalk'), which creates opportunities for genetic innovation that can facilitate adaptation. Many genetic and environmental features can contribute to increasing potential for crosstalk by facilitating non-cognate interactions between regulatory elements. If a novel interaction provides a fitness benefit, rewired GRNs with strengthened affinity for newly forged connections can be selected. Here, we identify factors that facilitate opportunities for crosstalk and rewiring between GRNs, consider whether features of some GRNs make them more 'rewireable' than others and if these features might constrain evolution towards convergent outcomes. We explore patterns from laboratory and natural microbial populations that show changes within GRNs during adaptation. Finally, we discuss the prospects and open questions in the field.

Pseudomonas aeruginosa adapts to octenidine via a combination of efflux and membrane remodelling.

Pseudomonas aeruginosa is an opportunistic pathogen capable of stably adapting to the antiseptic octenidine by an unknown mechanism. Here we characterise this adaptation, both in the laboratory and a simulated clinical setting, and identify a novel antiseptic resistance mechanism. In both settings, 2 to 4-fold increase in octenidine tolerance was associated with stable mutations and a specific 12 base pair deletion in a putative Tet-repressor family gene (smvR), associated with a constitutive increase in expression of the Major Facilitator Superfamily (MFS) efflux pump SmvA. Adaptation to higher octenidine concentrations led to additional stable mutations, most frequently in phosphatidylserine synthase pssA and occasionally in phosphatidylglycerophosphate synthase pgsA genes, resulting in octenidine tolerance 16- to 256-fold higher than parental strains. Metabolic changes were consistent with mitigation of oxidative stress and altered plasma membrane composition and order. Mutations in SmvAR and phospholipid synthases enable higher level, synergistic tolerance of octenidine.

Computer-Based and Online Therapy for Depression and Anxiety in Children and Adolescents.

OBJECTIVE: The purpose of this study was to provide an overview of computer-based and online therapies (e-therapy) to treat children and adolescents with depression and/or anxiety, and to outline programs that are evidence based or currently being researched. METHODS: We began by defining the topic and highlighting the issues at the forefront of the field. We identified computer and Internet-based interventions designed to prevent or treat depression or anxiety that were tested with children and young people <18 years of age (or inclusive of this age range together with emerging adults). We included randomized controlled trials (RCTs). We summarized available relevant systematic reviews. RESULTS: There is an increasing body of evidence that supports the use of computers and the Internet in the provision of interventions for depression and anxiety in children and adolescents. A number of programs have been shown to be effective in well-designed RCTs. Replication and long-term follow-up studies are needed to confirm results. CONCLUSIONS: There are now a range of effective computerized interventions for young people with depression and anxiety. This is likely to impact positively on attempts to make psychological therapies widely available to children and young people. We expect to see increased program sophistication and a proliferation of programs in the coming years. Research efforts, when developing programs, need to align with technological advances to maximize appeal. Implementation research is needed to determine the optimal modes of delivery and effectiveness of e-therapies in clinical practice. Given the large number of unproven program on the Internet, ensuring that there is clear information for patients about evidence for individual programs is likely to present a challenge.

A qualitative study of sexual minority young people's experiences of computerised therapy for depression.

OBJECTIVE: To describe the experiences of lesbian, gay, bisexual or sexual minority youth who used a form of computerised therapy (Rainbow SPARX) for depression. METHODS: 25 adolescents (20 with significant depressive symptoms) who had trialled Rainbow SPARX took part in semi-structured interviews. The general inductive approach was used to analyse interview data. RESULTS: Feedback consisted of five main themes: 'appealing aspects'; 'applying it to real life'; 'things to improve'; 'aspects that did not appeal'; and 'other themes'. Young people suggested that there should be more sexuality-specific ('rainbow') content in the computer program. Seventeen participants thought computerised therapy helped them feel better or less depressed. CONCLUSIONS: Consumer perspectives are increasingly being sought and this user input is especially useful for improving services. Our study provides important in-depth feedback on Rainbow SPARX from the perspective of sexual minority youth, and it highlights that computerised therapies can be successfully modified for groups traditionally under-served by mainstream mental health interventions.