pathogens Article A New Type of Chronic Wound Infection after Wisdom Tooth Extraction: A Diagnostic Approach with 16S-rRNA Gene Analysis, Next-Generation Sequencing, and Bioinformatics Sebastian Böttger 1,*, Silke Zechel-Gran 2, Philipp Streckbein 1 , Michael Knitschke 1, Torsten Hain 2,3, Markus Weigel 2 , Jan-Falco Wilbrand 4 , Eugen Domann 2,3, Hans-Peter Howaldt 1 and Sameh Attia 1 1 Department of Oral and Maxillofacial Surgery, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg, Location Giessen, Klinikstrasse 33, D-35392 Giessen, Germany; [email protected] (P.S.); [email protected] (M.K.); [email protected] (H.-P.H.); [email protected] (S.A.) 2 Institute of Medical Microbiology, Justus-Liebig-University Giessen, Biomedical Research Facility Seltersberg (BFS), Schubertstrasse 81, D-35392 Giessen, Germany; [email protected] (S.Z.-G.); [email protected] (T.H.); [email protected] (M.W.); [email protected] (E.D.) 3 German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, D-35392 Giessen, Germany 4 Department for Cranio-Maxillofacial Surgery-Plastic Surgery, Diakonie Klinikum Jung-Stilling, Wichernstr. 40, D-57074 Siegen, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-641-9854-6271 Received: 20 August 2020; Accepted: 26 September 2020; Published: 28 September 2020 Abstract: Delayed-onset infections are rare postoperative complications of lower third molar extractions. This article presents a case of a chronic combined hard and soft tissue infection after the extraction of a third molar, where the causative organisms could only be elucidated by molecular methods. Experimental 16S-rRNA gene analysis with next-generation sequencing and bioinformatics was used to identify the bacterial spectrum of the infection. 16S-rRNA gene analysis delivered the microbiome of the abscessing inflammation while standard culture and laboratory examinations were all sterile. The microbiome showed a mixed bacterial infection with a dominance of Delftia and Alcanivorax (spp.) besides other bacteria of the normal oral flora. Using 16S-rRNA-gene analysis, next-generation sequencing, and bioinformatics, a new type of chronic wound infection after wisdom tooth extraction was found. The property of Delftia and Alcanivorax (spp.) as water-affine environmental bacteria raises suspicion of infection from contaminated water from a dental unit. Thus, osteotomies of teeth should only be done with sterile cooling water. The 16S-rRNA gene analysis should become a part of the routine diagnostics in medical microbiology. Keywords: 16S-rRNA gene analysis; third molar surgery; environmental bacteria; postoperative wound infection 1. Introduction Bacterial infections in the field of oral and maxillofacial surgery are very common. With the application of antibiotics, the implementation of incision and drainage of abscesses, and with the removal of infected teeth, most infections can usually be treated fast and successfully [1–5]. Nevertheless, sometimes persistent subacute and chronic infections occur, where adequate therapy Pathogens 2020, 9, 798; doi:10.3390/pathogens9100798 www.mdpi.com/journal/pathogens Pathogens 2020, 9, x W 2 of 12 1. Introduction Bacterial infections in the field of oral and maxillofacial surgery are very common. With the application of antibiotics, the implementation of incision and drainage of abscesses, and with the removalPathogens 2020 of , 9infected, 798 teeth, most infections can usually be treated fast and successfully [1–5].2 of 12 Nevertheless, sometimes persistent subacute and chronic infections occur, where adequate therapy can be a great challenge for practitioners and where treatment can take a long time [6]. Especially, delayed-onsetcan be a great wound challenge infections for after practitioners third molar and extraction, where treatmentwhich occur can several take weeks a long after time suture [6]. removalEspecially, and delayed-onset after discharge wound [7], can infections cause varying after third symptoms molar extraction,affecting hard which and occur soft tissues several [7–11]. weeks Figueiredoafter suture et removal al. reported and that after those discharge infections [7], canare normally cause varying caused symptoms by anaerobic affecting bacteria hard of andthe oral soft flora,tissues e.g., [7– Fusobacterium,11]. Figueiredo Peptostreptococcus et al. reported that, Porphyromonas, those infections and are Prevotella normally causedstrains, bywhich anaerobic in most bacteria cases canof the be oralsuccessfully flora, e.g., treatedFusobacterium, with combinations Peptostreptococcus of surgical, Porphyromonas, revision andand antibioticsPrevotella [9].strains, Other whichauthors in havemost shown cases can that be specific successfully infections treated like with Actinomy combinationscosis, which of surgical need specific revision therapy, and antibiotics have to [be9]. consideredOther authors [6,12,13]. have shownAdditionally, that specific cases infectionsof osteom likeyelitis Actinomycosis, of the jaw after which third need molar specific surgery therapy, have beenhave topreviously be considered described [6,12 ,13[14].]. Additionally,As delayed-ons caseset ofinfections osteomyelitis occur ofonly the jawseveral after weeks third molarpost- interventionsurgery have [7,10], been previously other diseases described of [14non-odontogenic]. As delayed-onset origin infections like atypical occur only mycobacteriosis, several weeks tuberculosis,post-intervention or cat [scratch7,10], other disease, diseases which of can non-odontogenic present with similar origin symptoms, like atypical also have mycobacteriosis, to be taken intotuberculosis, account [15,16]. or cat scratch disease, which can present with similar symptoms, also have to be taken intoThe account present [15, 16study]. shows a new type of delayed-onset wound infection after third molar surgery. This infectionThe present was study resistant shows to aantibiotic new type therapy of delayed-onset and surgical wound revision. infection It was after not third possible molar to surgery.clarify theThis cause infection with was standard resistant culture to antibiotic and therapylaboratory and examinations. surgical revision. The It wasstudy not aimed possible to toclarify clarify this the enigmaticcause with infection standard cultureby using and 16S-rRNA laboratory examinations.gene analysis Thewith study next-generation aimed to clarify sequencing this enigmatic and bioinformatics.infection by using 16S-rRNA gene analysis with next-generation sequencing and bioinformatics. 2.2. Patient Patient and and Methods Methods AA 23-year-old 23-year-old woman woman in in otherwise good good genera generall condition without without any any pre-existing illness visitedvisited the the ambulance ambulance of of oral oral and and maxillofacial maxillofacial surg surgeryery at at the the university university ho hospital.spital. She She suffered suffered from from inflammatoryinflammatory swelling swelling and and pain pain in in the the area area of ofthe the wisdom wisdom tooth tooth 38, 38,which which had had been been extracted extracted by her by dentisther dentist in a dental in a dental practice practice six months six months ago. After ago. a After post-operative a post-operative symptom-free symptom-free interval intervalof several of weeks,several renewed weeks, renewed swelling swelling in the area in the of the area extrac of theted extracted tooth and tooth the and adjacent the adjacent cheek appeared. cheek appeared. Thus, theThus, dentist the dentist decided decided to start to an start antibiotic an antibiotic therapy therapy on the on patient, the patient, which which was unsuccessful was unsuccessful as anas oral an abscessoral abscess formed, formed, which which was incised was incised and drained. and drained. Since all Since attempts all attempts to treat the to delayed-onset treat the delayed-onset infection failed,infection the failed, patient the was patient referred was to referred the university to the university hospital. hospital. AtAt the the first first consultation, chronic chronic inflammatory inflammatory and and rough rough tissue tissue could could be be investigated investigated in in the the areaarea of of the the former former tooth tooth 38 without 38 without evidence evidence of abscessing. of abscessing. Panoramic Panoramic radiograph radiograph (Figure 1) (Figure showed1) ashowed non-ossified a non-ossified alveolus alveolusof tooth 38 of while tooth 38the while other the alveoli other of alveoli the wi ofsdom the wisdomteeth were teeth already were ossified already regularly.ossified regularly. Figure 1. Panoramic radiograph at the first consultation. Alveolus of tooth 48 shows complete healing while ossification is missing in the area of tooth 38. PathogensPathogens2020 2020, 9,, 798 9, x W 3 of 12 3 of 12 Pathogens 2020, 9, x W 3 of 12 Figure 1. Panoramic radiograph at the first consultation. Alveolus of tooth 48 shows complete healing while ossification is missing in the area of tooth 38. WithFigure the suspicion1. Panoramic of radiograph an inflammatory at the first consultation. tumor, a surgical Alveolus incisionof tooth 48 was shows first complete carried healing out and tissue while ossification is missing in the area