Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with ß-lactams.

OBJECTIVE: Determining the mechanisms that modulate ß-lactam resistance in clinical Pseudomonas aeruginosa (P. aeruginosa) isolates can be challenging, as the molecular profiles identified in mutation-based or expression-based resistance determinant screens may not correlate with in vitro phenotypes. One of the lesser studied resistance mechanisms in P. aeruginosa is the modification of penicillin-binding protein 3 (pbpB/ftsI). This study reported that nonsynonymous polymorphisms within pbpB frequently occur among ß-lactam resistant sputum isolates, and are associated with unique antibiotic susceptibility patterns. METHODS: Longitudinally collected isolates (n = 126) from cystic fibrosis (CF) patients with or without recent ß-lactam therapy or of non-clinical origin were tested for susceptibility to six ß-lactams (aztreonam, ceftazidime, cefsulodin, cefepime, meropenem, and piperacillin). Known ß-lactam resistance mechanisms were characterised by polymerase chain reaction (PCR)-based methods, and polymorphisms in the transpeptidase-encoding domain of pbpB identified by sequencing. RESULTS: Twelve nonsynonymous polymorphisms were detected among 86 isolates (67%) from five CF patients with a history of ß-lactam therapy, compared with one polymorphism in 30 (3.3%) from three patients who had not received ß-lactam treatments. No nonsynonymous polymorphisms were found in ten environmental isolates. Multiple pbpB alleles, often with different combinations of polymorphisms, were detected within the population of strains from each CF patient for up to 2.6 years. Traditional patterns of ampC or mexA de-repression reduced expression of oprD or the presence of extended-spectrum ß-lactamases were not observed in resistant isolates with nonsynonymous polymorphisms in pbpB. CONCLUSION: This study's findings suggest that pbpB is a common adaptive target, and may contribute to the development of ß-lactam resistance in P. aeruginosa.

Constructing and Analyzing Microbiome Networks in R.

Microbiomes are complex microbial communities whose structure and function are heavily influenced by microbe-microbe and microbe-host interactions mediated by a range of mechanisms, all of which have been implicated in the modulation of disease progression and clinical outcome. Therefore, understanding the microbiome as a whole, including both the complex interplay among microbial taxa and interactions with their hosts, is essential for understanding the spectrum of roles played by microbiomes in host health, development, dysbiosis, and polymicrobial infections. Network theory, in the form of systems-oriented, graph-theoretical approaches, is an exciting holistic methodology that can facilitate microbiome analysis and enhance our understanding of the complex ecological and evolutionary processes involved. Using network theory, one can model and analyze a microbiome and all its complex interactions in a single network. Here, we describe in detail and step by step, the process of building, analyzing and visualizing microbiome networks from operational taxonomic unit (OTU) tables in R and RStudio, using several different approaches and extensively commented code snippets.

Porphysome nanoparticles for enhanced photothermal therapy in a patient-derived orthotopic pancreas xenograft cancer model: a pilot study.

Local disease control is a major challenge in pancreatic cancer treatment, because surgical resection of the primary tumor is only possible in a minority of patients and radiotherapy cannot be delivered in curative doses. Despite the promise of photothermal therapy (PTT) for focal ablation of pancreatic tumors, this approach remains underinvestigated. Using photothermal sensitizers in combination with laser light irradiation for PTT can result in more efficient conversion of light energy to heat and improved spatial confinement of thermal destruction to the tumor. Porphysomes are self-assembled nanoparticles composed mainly of pyropheophorbide-conjugated phospholipids, enabling the packing of ∼80,000 porphyrin photosensitizers per particle. The high-density porphyrin loading imparts enhanced photonic properties and enables high-payload tumor delivery. A patient-derived orthotopic pancreas xenograft model was used to evaluate the feasibility of porphysome-enhanced PTT for pancreatic cancer. Biodistribution and tumor accumulation were evaluated using fluorescence intensity measurements from homogenized tissues and imaging of excised organs. Tumor surface temperature was recorded using IR optical imaging during light irradiation to monitor treatment progress. Histological analyses were conducted to determine the extent of PTT thermal damage. These studies may provide insight into the influence of heat-sink effect on thermal therapy dosimetry for well-perfused pancreatic tumors.