Persistence and evolution of following initiation of highly effective modulator therapy in cystic fibrosis.

Unlabelled: Today, more than 90% of people with cystic fibrosis (pwCF) are eligible for the highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy called elexacaftor/tezacaftor/ivacaftor (ETI) and its use is widespread. Given the drastic respiratory symptom improvement experienced by many post-ETI, clinical studies are already underway to reduce the number of respiratory therapies, including antibiotic regimens, that pwCF historically relied on to combat lung disease progression. Early studies suggest that bacterial burden in the lungs is reduced post-ETI, yet it is unknown how chronic populations are impacted by ETI.

sp. nov., a novel proteolytic, non-sulphur-reducing bacterium isolated from a marine aquaculture solid waste bioreactor.

A new strain, designated F2B, was isolated from an anaerobic digester for treating solid waste from a marine recirculating aquaculture system. The motile, Gram-negative, non-spore-forming curved rods were 2-7 µm long and 1 µm in diameter. Growth occurred at temperatures ranging from 20 to 40 °C with a maximum rate of growth at 30 °C.

Plant Growth-Promoting Activity of Bacteria Isolated from Asian Rice (Oryza sativa L.) Depends on Rice Genotype.

Asian rice is one of the most important crops because it is a staple food for almost half of the world's population. To have production of rice keep pace with a growing world population, it is anticipated that the use of fertilizers will also need to increase, which may cause environmental damage through runoff impacts. An alternative strategy to increase crop yield is the use of plant growth-promoting bacteria.

Evolved resistance to a novel cationic peptide antibiotic requires high mutation supply.

Background And Objectives: A key strategy for resolving the antibiotic resistance crisis is the development of new drugs with antimicrobial properties. The engineered cationic antimicrobial peptide WLBU2 (also known as PLG0206) is a promising broad-spectrum antimicrobial compound that has completed Phase I clinical studies. It has activity against Gram-negative and Gram-positive bacteria including infections associated with biofilm.

Immunosuppression broadens evolutionary pathways to drug resistance and treatment failure during Acinetobacter baumannii pneumonia in mice.

Acinetobacter baumannii is increasingly refractory to antibiotic treatment in healthcare settings. As is true of most human pathogens, the genetic path to antimicrobial resistance (AMR) and the role that the immune system plays in modulating AMR during disease are poorly understood. Here we reproduced several routes to fluoroquinolone resistance, performing evolution experiments using sequential lung infections in mice that are replete with or depleted of neutrophils, providing two key insights into the evolution of drug resistance.

Performance of Conventional Urine Culture Compared to 16S rRNA Gene Amplicon Sequencing in Children with Suspected Urinary Tract Infection.

Because some organisms causing urinary tract infection (UTI) may be difficult to culture, examination of bacterial gene sequences in the urine may provide a more accurate view of bacteria present during a UTI. Our objective was to estimate how often access to 16S rRNA gene amplicon sequencing alters diagnosis and/or clinical management. The study was designed as a cross-sectional study of a convenience sample of children with suspected UTI.

Adaptation and genomic erosion in fragmented Pseudomonas aeruginosa populations in the sinuses of people with cystic fibrosis.

Pseudomonas aeruginosa notoriously adapts to the airways of people with cystic fibrosis (CF), yet how infection-site biogeography and associated evolutionary processes vary as lifelong infections progress remains unclear. Here we test the hypothesis that early adaptations promoting aggregation influence evolutionary-genetic trajectories by examining longitudinal P. aeruginosa from the sinuses of six adults with CF.

The roles of history, chance, and natural selection in the evolution of antibiotic resistance.

History, chance, and selection are the fundamental factors that drive and constrain evolution. We designed evolution experiments to disentangle and quantify effects of these forces on the evolution of antibiotic resistance. Previously, we showed that selection of the pathogen in both structured and unstructured environments containing the antibiotic ciprofloxacin produced distinct genotypes and phenotypes, with lower resistance in biofilms as well as collateral sensitivity to β-lactam drugs (Santos-Lopez et al.

Evolution towards Virulence in a Two-Component System.

Bacteria in the Burkholderia cepacia complex (BCC) are significant pathogens for people with cystic fibrosis (CF) and are often extensively antibiotic resistant. Here, we assess the impacts of clinically observed mutations in , which encodes the sensor histidine kinase FixL. FixL along with FixJ compose a two-component system that regulates multiple phenotypes.

Rampant prophage movement among transient competitors drives rapid adaptation during infection.

Interactions between bacteria, their close competitors, and viral parasites are common in infections, but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny.

Draft Genome Sequence of Staphylococcus succinus Strain GN1, Isolated from a Basement Floor in Milwaukee, WI.

A strain of Staphylococcus succinus was sampled from the floor of the basement of a house and isolated in an undergraduate classroom in Milwaukee, WI. Here, we report the draft genome sequence of this strain.

Draft Genome Sequence of sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium.

We present here the draft genome sequence of a pyridine-degrading bacterium, ATCC 49442, which was reclassified as sp. strain ATCC 49442 based on its draft genome sequence. Its genome length is 4.

Defining Genomic and Predicted Metabolic Features of the Genus.

Acetogens are anaerobic bacteria capable of fixing CO or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). is the type strain of the genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus.

Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading sp. Strain ATCC 49987.

Here, we report the draft genome sequence of sp. strain ATCC 49987, consisting of three contigs with a total length of 4.4 Mbp.

Parallel Evolution of Tobramycin Resistance across Species and Environments.

Different species exposed to a common stress may adapt by mutations in shared pathways or in unique systems, depending on how past environments have molded their genomes. Understanding how diverse bacterial pathogens evolve in response to an antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics, combined with periodic whole-population genome sequencing, can be used to identify many contending routes to antimicrobial resistance.

Microbiome for the Electrosynthesis of Chemicals from Carbon Dioxide.

The price for renewable electricity is rapidly decreasing, and the availability of such energy is expected to increase in the coming years. This is a welcomed outcome considering that mitigation of climate disruption due to the use of fossil carbon is reaching a critical stage. However, the economy will remain dependent on carbon-based chemicals and the problem of electricity storage persists.

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle.

Bacterial populations vary in their stress tolerance and population structure depending upon whether growth occurs in well-mixed or structured environments. We hypothesized that evolution in biofilms would generate greater genetic diversity than well-mixed environments and lead to different pathways of antibiotic resistance. We used experimental evolution and whole genome sequencing to test how the biofilm lifestyle influenced the rate, genetic mechanisms, and pleiotropic effects of resistance to ciprofloxacin in populations.

Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection.

Opportunistic pathogens establishing new infections experience strong selection to adapt, often favoring mutants that persist. Capturing this initial dynamic is critical for identifying the first adaptations that drive pathogenesis. Here we used a porcine full-thickness burn wound model of chronic infection to study the evolutionary dynamics of diverse infections.

A method of processing nasopharyngeal swabs to enable multiple testing.

Objective: To develop a method to perform multiple tests on a single nasopharyngeal (NP) swab.

Methods: We collected a NP swab on children aged 2-12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA-sequencing, which we accomplished by cutting the tip of the swab.

Draft Genome Sequence of sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, sp. strain ATCC 49988.

A Pilot-Scale Field Study: In Situ Treatment of PCB-Impacted Sediments with Bioamended Activated Carbon.

A combined approach involving microbial bioaugmentation and enhanced sorption was demonstrated to be effective for in situ treatment of polychlorinated biphenyls (PCBs). A pilot study was conducted for 409 days on PCB impacted sediments in four 400 m plots located in a watershed drainage pond in Quantico, VA. Treatments with activated carbon (AC) agglomerate bioamended with PCB dechlorinating and oxidizing bacteria decreased the PCB concentration in the top 7.

Improved Detection of Culprit Pathogens by Bacterial DNA Sequencing Affects Antibiotic Management Decisions in Severe Pneumonia.

BACKGROUND Severe pneumonia requiring admission to an intensive care unit carries high morbidity and mortality. Evidence-based management includes early administration of empiric antibiotics against plausible bacterial pathogens while awaiting results of microbiologic cultures. However, in over 60% of pneumonia cases, no causative pathogen is identified with conventional diagnostic techniques.

Parallel genetic adaptation across environments differing in mode of growth or resource availability.

Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments.