Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study

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Abstract

Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 ( n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia‐Shigella ( p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution ( n = 6) ( p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound‐colonizing microorganisms.

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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Paul McMurdie, Susan Holmes (2013)

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

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Revised National Pressure Ulcer Advisory Panel Pressure Injury Staging System

Laura Edsberg, Joyce M Black, Margaret Goldberg … (2016)

Our understanding of pressure injury etiology and development has grown in recent years through research, clinical expertise, and global interdisciplinary expert collaboration. Therefore, the National Pressure Ulcer Advisory Panel (NPUAP) has revised the definition and stages of pressure injury. The revision was undertaken to incorporate the current understanding of the etiology of pressure injuries, as well as to clarify the anatomical features present or absent in each stage of injury. An NPUAP-appointed Task Force reviewed the literature and created drafts of definitions, which were then reviewed by stakeholders and the public, including clinicians, educators, and researchers around the world. Using a consensus-building methodology, these revised definitions were the focus of a multidisciplinary consensus conference held in April 2016. As a result of stakeholder and public input, along with the consensus conference, important changes were made and incorporated into the new staging definitions. The revised staging system uses the term injury instead of ulcer and denotes stages using Arabic numerals rather than Roman numerals. The revised definition of a pressure injury now describes the injuries as usually occurring over a bony prominence or under a medical or other device. The revised definition of a Stage 2 pressure injury seeks to clarify the difference between moisture-associated skin damage and injury caused by pressure and/or shear. The term suspected has been removed from the Deep Tissue Pressure Injury diagnostic label. Each definition now describes the extent of tissue loss present and the anatomical features that may or may not be present in the stage of injury. These important revisions reflect the methodical and collaborative approach used to examine the available evidence and incorporate current interdisciplinary clinical expertise into better defining the important phenomenon of pressure injury etiology and development.

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Polymicrobial Nature of Chronic Diabetic Foot Ulcer Biofilm Infections Determined Using Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP)

Scot Dowd, Randall D Wolcott, Yan-Yan Sun … (2008)

Background Diabetic extremity ulcers are associated with chronic infections. Such ulcer infections are too often followed by amputation because there is little or no understanding of the ecology of such infections or how to control or eliminate this type of chronic infection. A primary impediment to the healing of chronic wounds is biofilm phenotype infections. Diabetic foot ulcers are the most common, disabling, and costly complications of diabetes. Here we seek to derive a better understanding of the polymicrobial nature of chronic diabetic extremity ulcer infections. Methods and Findings Using a new bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) approach we have evaluated the bacterial diversity of 40 chronic diabetic foot ulcers from different patients. The most prevalent bacterial genus associated with diabetic chronic wounds was Corynebacterium spp. Findings also show that obligate anaerobes including Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp. are ubiquitous in diabetic ulcers, comprising a significant portion of the wound biofilm communities. Other major components of the bacterial communities included commonly cultured genera such as Streptococcus, Serratia, Staphylococcus and Enterococcus spp. Conclusions In this article, we highlight the patterns of population diversity observed in the samples and introduce preliminary evidence to support the concept of functional equivalent pathogroups (FEP). Here we introduce FEP as consortia of genotypically distinct bacteria that symbiotically produce a pathogenic community. According to this hypothesis, individual members of these communities when they occur alone may not cause disease but when they coaggregate or consort together into a FEP the synergistic effect provides the functional equivalence of well-known pathogens, such as Staphylococcus aureus, giving the biofilm community the factors necessary to maintain chronic biofilm infections. Further work is definitely warranted and needed in order to prove whether the FEPs concept is a viable hypothesis. The findings here also suggest that traditional culturing methods may be extremely biased as a diagnostic tool as they select for easily cultured organisms such as Staphylococcus aureus and against difficult to culture bacteria such as anaerobes. While PCR methods also have bias, further work is now needed in comparing traditional culture results to high-resolution molecular diagnostic methods such as bTEFAP.

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Author and article information

Contributors

Catherine Dunyach‐Remy: catherine.remy@chu-nimes.fr

Journal

Journal ID (nlm-ta): Int Wound J

Journal ID (iso-abbrev): Int Wound J

Journal ID (doi): 10.1111/(ISSN)1742-481X

Journal ID (publisher-id): IWJ

Title: International Wound Journal

Publisher: Blackwell Publishing Ltd (Oxford, UK )

ISSN (Print): 1742-4801

ISSN (Electronic): 1742-481X

Publication date (Electronic): 23 January 2024

Publication date Collection: January 2024

Volume: 21

Issue: 1 ( doiID: 10.1111/iwj.v21.1 )

Electronic Location Identifier: e14626

Affiliations

[ ¹ ] Department of Microbiology and Hospital Hygiene CHU Nîmes, Univ Montpellier Nîmes France

[ ² ] Department of Biostatistics, Epidemiology, Public Health, and Innovation in Methodology (BESPIM) CHU Nîmes, Univ Montpellier Nîmes France

[ ³ ] Centre Mutualiste Neurologique Propara Montpellier France

[ ⁴ ] VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene CHU Nîmes, Univ Montpellier Nîmes France

[ ⁵ ] bioMérieux SA Marcy‐l'Etoile France

[ ⁶ ] VBIC, INSERM U1047, Department of Infectious and Tropical Diseases CHU Nîmes, Univ Montpellier Nîmes France

Author notes

[*] [* ] Correspondence

Catherine Dunyach‐Remy, VBIC, INSERM U1047, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU de Nîmes, Nîmes, France.

Email: catherine.remy@ 123456chu-nimes.fr

Article

Publisher ID: IWJ14626

DOI: 10.1111/iwj.14626

PMC ID: 10805533

SO-VID: 6366a8c3-03be-47c5-a066-3fd86145a32c

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

History

Date received : 05 October 2023

Date accepted : 14 December 2023

Page count

Figures: 2, Tables: 2, Pages: 9, Words: 4374

Funding

Funded by: Centre Hospitalier Universitaire de Nîmes , doi 10.13039/501100022656;

Funded by: French Society of Pressure Ulcer

Custom metadata

source-schema-version-number 2.0

cover-date January 2024

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.6 mode:remove_FC converted:23.01.2024

ScienceOpen disciplines: Emergency medicine & Trauma

Keywords: anaerobic bacteria,episeq® 16s,metagenomics next‐generation sequencing,pressure ulcer, proteus sp,spinal cord injury,urinary microbiota,wound evolution

Data availability:

ScienceOpen disciplines: Emergency medicine & Trauma

Keywords: anaerobic bacteria, episeq® 16s, metagenomics next‐generation sequencing, pressure ulcer, proteus sp, spinal cord injury, urinary microbiota, wound evolution

Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study

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Irish Journal of Paramedicine

Most cited references 21

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Revised National Pressure Ulcer Advisory Panel Pressure Injury Staging System

Polymicrobial Nature of Chronic Diabetic Foot Ulcer Biofilm Infections Determined Using Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP)

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