Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics

Experimental evolution of Pseudomonas aeruginosa to colistin in spatially confined microdroplets identifies evolutionary trajectories consistent with adaptation in microaerobic lung environments

Antibiotic resistance is a continuing global health crisis. Identifying the evolutionary trajectories leading to increased antimicrobial resistance can be critical to the discovery of biomarkers for clinical diagnostics and new targets for drug discovery. While the combination of patient data and in vitro experimental evolution has been remarkably successful in extending our understanding of antimicrobial resistance, it can be difficult for in vitro methods to recapitulate the spatial structure and consequent microenvironments that characterize in vivo infection. Notably, in cystic fibrosis (CF) patients, changes to either the PmrA/PmrB or PhoP/PhoQ two-component systems have been identified as critical drivers for high levels of colistin and polymyxin resistance. When using microfluidic emulsions to provide spatially structured, low-competition environments, we found that adaptive mutations to phoQ were more successful than pmrB in increasing colistin resistance. Conversely, mutations to pmrB were readily identified using well-mixed unstructured cultures. We found that oxygen concentration gradients within the microdroplet emulsions favored adaptive changes to the PhoP/PhoQ pathway consistent with microaerobic conditions that can be found in the lungs of CF patients. We also observed mutations linked to hallmark adaptations to the CF lung environment, such as loss of motility and loss of O antigen biosynthesis (wbpL). Mutation to wbpL, in addition to causing loss of O antigen, was additionally shown to confer moderately increased colistin resistance. Taken together, our data suggest that distinct evolutionary trajectories to colistin resistance may be shaped by the microaerobic partitioning and spatial separation imposed within the CF lung.IMPORTANCEAntibiotic resistance remains one of the great challenges confronting public health in the world today. Individuals with compromised immune systems or underlying health conditions are often at an increased for bacterial infections. Patients with cystic fibrosis (CF) produce thick mucus that clogs airways and provides a very favorable environment for infection by bacteria that further decrease lung function and, ultimately, mortality. CF patients are often infected by bacteria such as Pseudomonas aeruginosa early in life and experience a series of chronic infections that, over time, become increasingly difficult to treat due to increased antibiotic resistance. Colistin is a major antibiotic used to treat CF patients. Clinical and laboratory studies have identified PmrA/PmrB and PhoP/PhoQ as responsible for increased resistance to colistin. Both have been identified in CF patient lungs, but why, in some cases, is it one and not the other? In this study, we show that distinct evolutionary trajectories to colistin resistance may be favored by the microaerobic partitioning found within the damaged CF lung.

Methyl halide transferase-based gas reporters for quantification of filamentous bacteria in microdroplet emulsions

The application of microfluidic techniques in experimental and environmental studies is a rapidly emerging field. Water-in-oil microdroplets can serve readily as controllable micro-vessels for studies that require spatial structure. In many applications, it is useful to monitor cell growth without breaking or disrupting the microdroplets. To this end, optical reporters based on color, fluorescence, or luminescence have been developed. However, optical reporters suffer from limitations when used in microdroplets such as inaccurate readings due to strong background interference or limited sensitivity during early growth stages. In addition, optical detection is typically not amenable to filamentous or biofilm-producing organisms that have significant nonlinear changes in opacity and light scattering during growth. To overcome such limitations, we show that volatile methyl halide gases produced by reporter cells expressing a methyl halide transferase (MHT) can serve as an alternative nonoptical detection approach suitable for microdroplets. In this study, an MHT-labeled Streptomyces venezuelae reporter strain was constructed and characterized. Protocols were established for the encapsulation and incubation of S. venezuelae in microdroplets. We observed the complete life cycle for S. venezuelae including the vegetative expansion of mycelia, mycelial fragmentation, and late-stage sporulation. Methyl bromide (MeBr) production was detected by gas chromatography-mass spectrometry (GC-MS) from S. venezuelae gas reporters incubated in either liquid suspension or microdroplets and used to quantitatively estimate bacterial density. Overall, using MeBr production as a means of quantifying bacterial growth provided a 100- to 1,000-fold increase in sensitivity over optical or fluorescence measurements of a comparable reporter strain expressing fluorescent proteins. IMPORTANCE Quantitative measurement of bacterial growth in microdroplets in situ is desirable but challenging. Current optical reporter systems suffer from limitations when applied to filamentous or biofilm-producing organisms. In this study, we demonstrate that volatile methyl halide gas production can serve as a quantitative nonoptical growth assay for filamentous bacteria encapsulated in microdroplets. We constructed an S. venezuelae gas reporter strain and observed a complete life cycle for encapsulated S. venezuelae in microdroplets, establishing microdroplets as an alternative growth environment for Streptomyces spp. that can provide spatial structure. We detected MeBr production from both liquid suspension and microdroplets with a 100- to 1,000-fold increase in signal-to-noise ratio compared to optical assays. Importantly, we could reliably detect bacteria with densities down to 106 CFU/mL. The combination of quantitative gas reporting and microdroplet systems provides a valuable approach to studying fastidious organisms that require spatial structure such as those found typically in soils.

All-electrical antibiotic susceptibility and resistance profiling of electrogenic Pseudomonas aeruginosa

There is a pressing need for evidence-based, non-surgical therapy guidance for biofilm-based infections. Conventional phenotypic or genotypic or emerging antibiotic susceptibility testing (AST) techniques cannot provide clinically relevant guidelines and widely adaptable stewardship for effective biofilm treatment because they are mainly limited to planktonic bacteria and suffer from many technical and operational challenges. Here, we created an all-electrical, reliable, rapid AST device to monitor antibiotic efficacy in bacterial biofilms that can be practically translatable to clinical settings and industrial antibiotic developments. The electrons metabolically produced by a Pseudomonas aeruginosa biofilm provided a strong signal for monitoring bacterial growth and treatment efficacy while a 3-D paper-based culturing platform provided a new strategy for rapid biofilm formation through capillary action. When antibiotics are effective against the pathogenic biofilm, their metabolic activities are inhibited, decreasing their electron transfer reactions. The changes in electrical outputs can be measured to assess the treatment effectiveness against pathogenic biofilms. Within 100 minutes, our six-well AST device successfully distinguished antibiotic-susceptible and -resistant P. aeruginosa biofilms, provided a quantifiable minimum inhibitory concentration (MIC) of antibiotics, and characterized the bacterial antibiotic action mechanisms.

Indirect Enrichment of Desirable, but Less Fit Phenotypes, from a Synthetic Microbial Community Using Microdroplet Confinement

Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was composed of three strains: a "Producer" that makes the diffusible quorum sensing molecule (N-(3-oxododecanoyl)-l-homoserine lactone, C12-oxo-HSL) or AHL; a "Receiver" that is killed by AHL; and a Non-Producer or "cheater" that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allows a more efficient but transient enrichment of more rare and slower-growing Producer subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology.

Intracellular Experimental Evolution of Francisella tularensis Subsp. holarctica Live Vaccine Strain (LVS) to Antimicrobial Resistance

In vitro experimental evolution has complemented clinical studies as an excellent tool to identify genetic changes responsible for the de novo evolution of antimicrobial resistance. However, the in vivo context for adaptation contributes to the success of particular evolutionary trajectories, especially in intracellular niches where the adaptive landscape of virulence and resistance are strongly coupled. In this work, we designed an ex vivo evolution approach to identify evolutionary trajectories responsible for antibiotic resistance in the Live Vaccine Strain (LVS) of Francisella tularensis subsp. holarctica while being passaged to increasing ciprofloxacin (CIP) and doxycycline (DOX) concentrations within macrophages. Overall, adaptation within macrophages advanced much slower when compared to previous in vitro evolution studies reflecting a limiting capacity for the expansion of adaptive mutations within the macrophage. Longitudinal genomic analysis identified resistance conferring gyrase mutations outside the Quinolone Resistance Determining Region. Strikingly, FupA/B mutations that are uniquely associated with in vitro CIP resistance in Francisella were not observed ex vivo, reflecting the coupling of intracellular survival and resistance during intracellular adaptation. To our knowledge, this is the first experimental study demonstrating the ability to conduct experimental evolution to antimicrobial resistance within macrophages. The results provide evidence of differences in mutational profiles of populations adapted to the same antibiotic in different environments/cellular compartments and underscore the significance of host mediated stress during resistance evolution.

Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement

Spatial structure within microbial communities can provide nearly limitless opportunities for social interactions and are an important driver for evolution. As metabolites are often molecular signals, metabolite diffusion within microbial communities can affect the composition and dynamics of the community in a manner that can be challenging to deconstruct. We used encapsulation of a synthetic microbial community within microdroplets to investigate the effects of spatial structure and metabolite diffusion on population dynamics and to examine the effects of cheating by one member of the community. The synthetic community was comprised of three strains: a 'Producer' that makes the diffusible quorum sensing molecule ( N -(3-Oxododecanoyl)-L-homoserine lactone, C12-oxo-HSL) or AHL; a 'Receiver' that is killed by AHL and a Non-Producer or 'cheater' that benefits from the extinction of the Receivers, but without the costs associated with the AHL synthesis. We demonstrate that despite rapid diffusion of AHL between microdroplets, the spatial structure imposed by the microdroplets allow a more efficient but transient enrichment of more rare and slower growing 'Producer' subpopulations. Eventually, the Non-Producer population drove the Producers to extinction. By including fluorescence-activated microdroplet sorting and providing sustained competition by the Receiver strain, we demonstrate a strategy for indirect enrichment of a rare and unlabeled Producer. The ability to screen and enrich metabolite Producers from a much larger population under conditions of rapid diffusion provides an important framework for the development of applications in synthetic ecology and biotechnology.

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Droplet-based methods for tackling antimicrobial resistance

Application of droplet-based methods enables (i) faster detection, (ii) increased sensitivity, (iii) characterization of the level of heterogeneity in response to antibiotics by bacterial populations, and (iv) expanded screening of the effectiveness of antibiotic combinations. Hereby, we discuss the key steps and parameters of droplet-based experiments to investigate antimicrobial resistance. We also review recent findings accomplished with these methods and highlight their advantages and capacity to yield new insights into the problem of antimicrobial resistance.