Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds

Abstract

Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.

The influence of microbial colonization on inflammatory versus pro-healing trajectories in combat extremity wounds

“…Only wounds that can overcome initial pro-inflammatory environments regardless of colonization status and properly balance the proliferative processes through coordinated processes heal. Beyond providing more information to the wound healing process, these data provide novel functions and individual biomarkers (i.e., differentially expressed genes between failed vs. healed wounds) that can be further evaluated and incorporated into machine learning models to predict when to close the wound and whether or not there are early signs that the wound has a higher likelihood of failure as has been demonstrated previously 12 , 13 , 20 . These types of investigations will lay the foundation for precision medicine tools to improve clinical outcomes in traumatic wound care for both combat casualties and in civilian trauma centers.…”

“…Further, infected wounds, such as those with either bacterial, or invasive fungal infections, frequently have more complications and worse outcomes, requiring additional surgeries or even amputation 19 . Our group has previously investigated the influence of microbial colonization in combat casualty extremity wounds using metagenomic sequencing 20 . It was found that there was not a single defining microbial profile that was associated with failed wounds, but trends such as Pseudomonas and Acinetobacter colonization were seen at higher prevalence, as well as lower observed alpha and beta diversities.…”

“…One potential solution to improve the current methods is to develop clinical decision support tools or novel therapies. Our group has previously used circulating serum biomarker data 12 , gene expression data 13 , and microbial metagenomic signatures 20 , as features in machine learning models that enable the prediction of wound failure. To further understand the mechanisms of the wound healing process and predict novel biomarkers, this study utilized RNA sequencing of wound tissue biopsies collected longitudinally during treatment of U.S. military service members who sustained combat extremity injuries.…”

Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system

“…To date, there have only been two reports of isolation of Mycoplasma canis from dog bite wounds in humans [6,7] and one report of the isolation of M. canis and Mycoplasma spumans from a dog bite wound in a cat. Recent advances in culture-free sequencing of clinical material have advanced the aetiological diagnosis of infectious diseases [8][9][10][11] and wound infections [12][13][14][15], and ultimately are likely to lead to improved treatment outcomes.…”

“…canis and Mycoplasma spumans from a dog bite wound in a cat. Recent advances in culture-free sequencing of clinical material have advanced the aetiological diagnosis of infectious diseases [8–11] and wound infections [12–15], and ultimately are likely to lead to improved treatment outcomes.…”