A novel decoy strategy for polymyxin resistance in Acinetobacter baumannii

  1. Jaeeun Park
  2. Misung Kim
  3. Bora Shin
  4. Mingyeong Kang
  5. Jihye Yang
  6. Tae Kwon Lee
  7. Woojun Park  Is a corresponding author
  1. Korea University, Republic of Korea
  2. Yonsei University, Republic of Korea

Abstract

Modification of the outer membrane charge by a polymyxin B (PMB)-induced PmrAB two-component system appears to be a dominant phenomenon in PMB-resistant Acinetobacter baumannii. PMB-resistant variants and many clinical isolates also appeared to produce outer membrane vesicles (OMVs). Genomic, transcriptomic, and proteomic analyses revealed that upregulation of the pmr operon and decreased membrane-linkage proteins (OmpA, OmpW and BamE) are linked to overproduction of OMVs, which also promoted enhanced biofilm formation. The addition of OMVs from PMB-resistant variants into the cultures of PMB-susceptible A. baumannii and the clinical isolates protected these susceptible bacteria from PMB. Taxonomic profiling of in vitro human gut microbiomes under anaerobic conditions demonstrated that OMVs completely protected the microbial community against PMB treatment. A Galleria mellonella-infection model with PMB treatment showed that OMVs increased the mortality rate of larvae by protecting A. baumannii from PMB. Taken together, OMVs released from A. baumannii functioned as decoys against PMB.

Data availability

1. Sequence reads for the experimentally evolved isolates are accessible from the NCBI sequence archives under accession numbers PRJNA530195 (Lab-WT), PRJNA530197 (PMRLow), and PRJNA530202 (PMRHigh).2. The RNA-seq data have been deposited in NCBI under Gene Expression Omnibus (GEO) accession number GSE163581.3. The bacterial community data have been deposited in NCBI under Sequence Read Archive (SRA) accession number SRX9819399 PRJNA689940, SRX9819397 PRJNA689944 and SRX9819398 PRJNA689944.

The following data sets were generated
    1. Kim M
    (2021) PMB
    NCBI Bioproject ID SRX9819397 PRJNA689944.
    1. Kim M
    (2021) OMV->PMB.
    NCBI Bioproject ID SRX9819398 PRJNA689944.

Article and author information

Author details

  1. Jaeeun Park

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  2. Misung Kim

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  3. Bora Shin

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  4. Mingyeong Kang

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  5. Jihye Yang

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  6. Tae Kwon Lee

    Environmental Engineering, Yonsei University, Wonju, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3845-7316
  7. Woojun Park

    Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
    For correspondence
    wpark@korea.ac.kr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3166-1528

Funding

National Research Foundation of Korea (NRF-2020M3A9H5104237)

  • Woojun Park

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Park et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,383
    views
  • 580
    downloads
  • 40
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Jaeeun Park
  2. Misung Kim
  3. Bora Shin
  4. Mingyeong Kang
  5. Jihye Yang
  6. Tae Kwon Lee
  7. Woojun Park
(2021)
A novel decoy strategy for polymyxin resistance in Acinetobacter baumannii
eLife 10:e66988.
https://doi.org/10.7554/eLife.66988

Share this article

https://doi.org/10.7554/eLife.66988

Further reading

    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease
    Saugat Poudel, Jason Hyun ... Bernhard O Palsson
    Research Article

    The Staphylococcus aureus clonal complex 8 (CC8) is made up of several subtypes with varying levels of clinical burden; from community-associated methicillin-resistant S. aureus USA300 strains to hospital-associated (HA-MRSA) USA500 strains and ancestral methicillin-susceptible (MSSA) strains. This phenotypic distribution within a single clonal complex makes CC8 an ideal clade to study the emergence of mutations important for antibiotic resistance and community spread. Gene-level analysis comparing USA300 against MSSA and HA-MRSA strains have revealed key horizontally acquired genes important for its rapid spread in the community. However, efforts to define the contributions of point mutations and indels have been confounded by strong linkage disequilibrium resulting from clonal propagation. To break down this confounding effect, we combined genetic association testing with a model of the transcriptional regulatory network (TRN) to find candidate mutations that may have led to changes in gene regulation. First, we used a De Bruijn graph genome-wide association study to enrich mutations unique to the USA300 lineages within CC8. Next, we reconstructed the TRN by using independent component analysis on 670 RNA-sequencing samples from USA300 and non-USA300 CC8 strains which predicted several genes with strain-specific altered expression patterns. Examination of the regulatory region of one of the genes enriched by both approaches, isdH, revealed a 38-bp deletion containing a Fur-binding site and a conserved single-nucleotide polymorphism which likely led to the altered expression levels in USA300 strains. Taken together, our results demonstrate the utility of reconstructed TRNs to address the limits of genetic approaches when studying emerging pathogenic strains.

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Malika Hale, Kennidy K Takehara ... Marion Pepper
    Research Article

    Pseudomonas aeruginosa (PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here, we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across three donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.