PMID- 27821087 OWN - NLM STAT- MEDLINE DCOM- 20170724 LR - 20220321 IS - 1471-2334 (Electronic) IS - 1471-2334 (Linking) VI - 16 IP - 1 DP - 2016 Nov 8 TI - Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections. PG - 652 LID - 652 AB - BACKGROUND: Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture. METHODS: In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples. RESULTS: For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum. CONCLUSION: The study emphasizes that many pathogens can be involved in NSTIs, and that no specific "NSTI causing" combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI. FAU - Rudkjobing, Vibeke Borsholt AU - Rudkjobing VB AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark. FAU - Thomsen, Trine Rolighed AU - Thomsen TR AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark. AD - Life Science Division, The Danish Technological Institute, Taastrup, Denmark. FAU - Xu, Yijuan AU - Xu Y AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark. AD - Life Science Division, The Danish Technological Institute, Taastrup, Denmark. FAU - Melton-Kreft, Rachael AU - Melton-Kreft R AD - Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, USA. FAU - Ahmed, Azad AU - Ahmed A AD - Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, USA. FAU - Eickhardt, Steffen AU - Eickhardt S AD - Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark. FAU - Bjarnsholt, Thomas AU - Bjarnsholt T AD - Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark. AD - Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark. FAU - Poulsen, Steen Seier AU - Poulsen SS AD - Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark. FAU - Nielsen, Per Halkjaer AU - Nielsen PH AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark. FAU - Earl, Joshua P AU - Earl JP AD - Center for Genomic Sciences, Philadelphia, PA, USA. AD - Departments of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Philadelphia, PA, USA. AD - Departments of Microbiology and Immunology, Philadelphia, PA, USA. FAU - Ehrlich, Garth D AU - Ehrlich GD AD - Center for Genomic Sciences, Philadelphia, PA, USA. AD - Departments of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Philadelphia, PA, USA. AD - Departments of Microbiology and Immunology, Philadelphia, PA, USA. AD - Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, USA. FAU - Moser, Claus AU - Moser C AD - Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark. moser@dadlnet.dk. LA - eng GR - R01 AI080935/AI/NIAID NIH HHS/United States GR - R01 DC002148/DC/NIDCD NIH HHS/United States GR - R01 DC004173/DC/NIDCD NIH HHS/United States PT - Comparative Study PT - Journal Article DEP - 20161108 PL - England TA - BMC Infect Dis JT - BMC infectious diseases JID - 100968551 RN - 0 (RNA, Ribosomal, 16S) SB - IM MH - Aged MH - Bacteriological Techniques/*methods MH - Debridement MH - Humans MH - In Situ Hybridization, Fluorescence/*methods MH - Middle Aged MH - Necrosis/microbiology MH - RNA, Ribosomal, 16S/genetics MH - Real-Time Polymerase Chain Reaction/*methods MH - Sensitivity and Specificity MH - Soft Tissue Infections/*microbiology MH - Streptococcal Infections/microbiology MH - Streptococcus pyogenes/genetics/isolation & purification/pathogenicity PMC - PMC5100109 OTO - NOTNLM OT - 16S rRNA OT - 454 pyrosequencing OT - Cloning OT - Direct Sanger sequencing OT - FISH OT - Ibis T5000 biosensor OT - Microorganisms OT - Necrotizing soft tissue infections OT - qPCR EDAT- 2016/11/09 06:00 MHDA- 2017/07/25 06:00 PMCR- 2016/11/08 CRDT- 2016/11/09 06:00 PHST- 2016/07/19 00:00 [received] PHST- 2016/10/26 00:00 [accepted] PHST- 2016/11/09 06:00 [entrez] PHST- 2016/11/09 06:00 [pubmed] PHST- 2017/07/25 06:00 [medline] PHST- 2016/11/08 00:00 [pmc-release] AID - 10.1186/s12879-016-1976-2 [pii] AID - 1976 [pii] AID - 10.1186/s12879-016-1976-2 [doi] PST - epublish SO - BMC Infect Dis. 2016 Nov 8;16(1):652. doi: 10.1186/s12879-016-1976-2.