DOI: 10.5061/dryad.x3ffbg7r6
title: High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections

description: 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.
description: # 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.