Microbial profiling of combat wound infection through detection microarray and next-generation sequencing.
Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden.
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA be1@llnl.gov jaing2@llnl.gov.
Nicholas A
NA
Be
Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, USA.
Jonathan E
JE
Allen
Regenerative Medicine Department, Naval Medical Research Center, Silver Spring, Maryland, USA Surgical Critical Care Initiative, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.
Trevor S
TS
Brown
Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, USA.
Shea N
SN
Gardner
Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, USA.
Kevin S
KS
McLoughlin
Regenerative Medicine Department, Naval Medical Research Center, Silver Spring, Maryland, USA Surgical Critical Care Initiative, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.
Jonathan A
JA
Forsberg
Norman M. Rich Department of Surgery, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA Department of Wound Infections, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
Benjamin C
BC
Kirkup
Department of Pathology and Laboratory Medicine, School of Medicine, University of California at Davis, Davis, California, USA.
Brett A
BA
Chromy
Department of Pathology and Laboratory Medicine, School of Medicine, University of California at Davis, Davis, California, USA Center for Comparative Medicine, University of California at Davis, Davis, California, USA.
Paul A
PA
Luciw
Regenerative Medicine Department, Naval Medical Research Center, Silver Spring, Maryland, USA Surgical Critical Care Initiative, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA Norman M. Rich Department of Surgery, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.
Eric A
EA
Elster
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA be1@llnl.gov jaing2@llnl.gov.
Crystal J
CJ
Jaing
D000328:Adult; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D058491:Bacterial Load; D058448:Biota; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D008889:Military Personnel; D014945:Wound Healing; D014946:Wound Infection / Q000382:microbiology*; D055815:Young Adult