Bacterial Strain Diversity Within Wounds

Abstract

Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.

Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease

“…Improvements could also be made through application of one sampling method (skin biopsies) on a fixed location (or multiple locations) within the ulcers in order to control for the microhabitats within the wound, each of which is characterized by their physiological parameters and bacterial composition. [ 44 , 45 ] Finding which area is most relevant for sampling is difficult, but warrants investigation. However, comparisons between healthy samples (likely swabs) and lesions (routinely biopsies) may be difficult, especially as even some biopsies did not contain adequate bacterial DNA for use within this study (as can be seen with exclusion at the rarefaction stage).…”

Gallium–Carbenicillin Framework Coated Defect‐Rich Hollow TiO2 as a Photocatalyzed Oxidative Stress Amplifier against Complex Infections

“…In general, an infected wound always contains several kinds of bacteria. [ 2 ] The two most common bacteria in wounds are methicillin‐resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PA). [ 3 ] They are known to easily form biofilms that can lower antibiotic efficacy, impair wound healing, and even be insusceptible to various antibiotics.…”

Genomic Epidemiology with Mixed Samples

“…When more complex strain-level diversity is present, benchmarking these tools shows reduced performance in both taxonomic binning and metagenomic assembly [16][17][18][19]. In practice, natural strain-level variation is harbored ubiquitously in epidemiologically relevant samples [20][21][22][23][24][25][26][27][28][29] and it is reflected by the transmission events occurring between individuals and their environment [30]. Although some sample types may be dominated by one or two strains [31], direct sequencing of clinical samples may result in an overabundance of host DNA [28,[32][33][34], or lack detection power for strains with low abundance in environments with high species diversity [18,32,35].…”