High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections
Data files
Sep 05, 2023 version files 28.34 KB
-
Dryad_raw_data.xlsx
24.78 KB
-
README.md
3.56 KB
Abstract
Chronic, highly antibiotic-resistant infections in cystic fibrosis (CF) lungs contribute to increasing morbidity and mortality. Pseudomonas aeruginosa, a common CF pathogen, exhibits resistance to multiple antibiotics, contributing to antimicrobial resistance (AMR). These bacterial populations display genetic and phenotypic diversity, but it is unclear how this diversity affects susceptibility to bacteriocins. R-pyocins, i.e. bacteriocins produced by P. aeruginosa, are phage-tail-like antimicrobials. R-pyocins have potential as antimicrobials, however, recent research suggests the diversity of P. aeruginosa variants within CF lung infections leads to varying susceptibility to R-pyocins. This variation may be linked to changes in lipopolysaccharide (LPS), acting as the R-pyocin receptor. Currently, it is unknown how frequently R-pyocin-susceptible strains are in chronic CF lung infection, particularly when considering the heterogeneity within these strains. In this study, we tested R2-pyocin susceptibility of 139 P. aeruginosa variants from 17 sputum samples of seven CF patients and analyzed LPS phenotypes. We found that 83% of sputum samples did not have R2-pyocin-resistant variants, while nearly all samples contained susceptible variants. There was no correlation between LPS phenotype and R2-pyocin susceptibility, though we estimate that about 76% of sputum-derived variants lack an O-specific antigen, 40% lack a common antigen, and 24% have altered LPS cores. The absence of a correlation between LPS phenotype and R-pyocin susceptibility suggests LPS packing density may play a significant role in R-pyocin susceptibility among CF variants. Our research supports the potential of R-pyocins as therapeutic agents, as many infectious CF variants are susceptible to R2-pyocins, even within diverse bacterial populations.
README: High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections
Dataset includes biological replicate measurements of R-pyocin susceptibility data, and raw images of SDS-page gels used in scoring lipopolysaccharide phenotype profiles for each variant.
Description of the data and file structure
An Excel spreadsheet titled "Dryad_raw_data.xlsx" includes a list of bacterial strains and variants used with biological replicates of susceptibility data.
Column headers within the file "Dryad_raw_data.xlsx" include:
PATIENT
- Numerical assignments for each patient, to further de-identify samples
Longitudinal Collection
- A number corresponding to the sequential collection of a population of bacterial from the same patient, at a different timepoint
Isolate ID
- Randomized 3-digit number corresponding to each patient (ie Patient 1 samples are bacterial populations 258), followed by an arbitrary sequential number to further distinguish each variant from within the same population
R-pyocin Genotype
- The subtype of R-pyocin that could be produced by a strain, determined by in silico genomic analysis comparing the strain's R-pyocin genes to known R-pyocin genes of each of the 3 functional subtypes of R-pyocin (R1, R2, R5) UT = Untypeable
R2-pyocin Susceptibility
- Binary description of whether a variant is R2-pyocin susceptible (S) or resistant (R) as determined by the average susceptibility metric
Susceptibility Metric (dilution level) n=1
- The lowest serial dilution level that gives a zone of inhibition on the variant tested, which was used as a metric for R2-pyocin susceptibility; Biological replicate #1
Susceptibility Metric (dilution level) n=2
- The lowest serial dilution level that gives a zone of inhibition on the variant tested, which was used as a metric for R2-pyocin susceptibility; Biological replicate #2
Susceptibility Metric (dilution level) n=3
- The lowest serial dilution level that gives a zone of inhibition on the variant tested, which was used as a metric for R2-pyocin susceptibility; Biological replicate #3
avg Susceptibility
- The average R2-pyocin susceptibility metric of all three replicates for each variant; we deem the R-pyocin Susceptibility variable as an ordinal variable, with a naturally ranking order (susceptibility levels 0-4).
A-band
- A binary score (0 absent, 1 present) to characterize the presence or absence of the common antigen or A-band of the lipopolysaccharide for each variant; a categorical variable
B-band
- A binary score (0 absent, 1 present) to characterize the presence or absence of the O-antigen or B-band of the lipopolysaccharide for each variant; a categorical variable
Core
- A binary score (0 Altered, 1 WT) to characterize the lipopolysaccharide core as either similar to the wild-type (WT) PAO1, or altered; a categorical variable
LPS Score
- A composite score to summarize the physical attributes of the lipopolysaccharide for each variant; determined by adding up each binary score for the A-band, B-band, and Core; a categorical variable; LPS = lipopolysaccharide
A folder titled "LPS_gels" includes labeled images of SDS-page gels stained with Pro-Q Emerald stain as described in the manuscript, used for scoring LPS phenotypes.
Sharing/Access information
This data is not accessible from another source.
Code/Software
No code was used in analyzing this data.