1
|
Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
Collapse
Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
2
|
Rimoldi SG, Brioschi D, Curreli D, Salari F, Pagani C, Tamoni A, Longobardi C, Bosari R, Rizzo A, Landonio S, Coen M, Passerini M, Gismondo MR, Gori A, Manzotti A. Traditional Cultures versus Next Generation Sequencing for Suspected Orthopedic Infection: Experience Gained from a Reference Centre. Antibiotics (Basel) 2023; 12:1588. [PMID: 37998790 PMCID: PMC10668678 DOI: 10.3390/antibiotics12111588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, data are scarce regarding the impact of molecular techniques in real-life scenarios. (Methods) We included cases of suspected orthopedic infection treated with surgery from May 2021 to September 2023. We combined traditional cultures with NGS. For NGS, we performed a metagenomic analysis of ribosomal 16s, and we queried dedicated taxonomic libraries to identify the species. To avoid false positive results, we set a cut-off of 1000 counts of the percentage of frequency of reads. (Results) We included 49 patients in our study. Our results show the presence of bacteria in 36/49 (73%) and 29/49 (59%) cases studied with NGS and traditional cultures, respectively. The concordance rate was 61%. Among the 19/49 discordant cases, in 11/19 cases, cultures were negative and NGS positive; in 4/19, cultures were positive and NGS negative; and in the remaining 4/19, different species were detected by traditional cultures and NGS. (Conclusions) Difficult-to-grow microorganisms, such as slow-growing anaerobic bacteria, were better detected by NGS compared to traditional culture in our study. However, more data to distinguish between true pathogens and contaminants are needed. NGS can be an additional tool to be used for the diagnosis of orthopedic infections and the choice of appropriate antimicrobial therapy.
Collapse
Affiliation(s)
- Sara Giordana Rimoldi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Davide Brioschi
- Orthopedic Unit, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy
| | - Daniele Curreli
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Federica Salari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Cristina Pagani
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Alessandro Tamoni
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Concetta Longobardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Raffaella Bosari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Simona Landonio
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
| | - Massimo Coen
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
| | - Matteo Passerini
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Andrea Gori
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
| | - Alfonso Manzotti
- Orthopedic Unit, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy
| |
Collapse
|
3
|
Tay ST, Merican AM, Abdul Jabar K, Velayuthan RD, Ayob KA, Lee JL, Chong J, Karunakaran R. Falsarthrobacter nasiphocae periprosthetic joint infection. Int J Infect Dis 2023; 136:77-80. [PMID: 37660726 DOI: 10.1016/j.ijid.2023.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
We report the isolation of a rare Gram-positive coccobacillary bacterium from synovial fluids of a patient with periprosthetic joint infection on three occasions over an 8-month period. As routine microbiological methods were not able to identify the isolate definitely, sequence analyses of the bacterial 16S ribosomal RNA gene and whole genome were performed. Analysis of the bacterial 16S ribosomal RNA gene showed the highest similarity (98.1%) with that of Falsarthrobacter (previously known as Arthrobacter) nasiphocae, which was first isolated from the nasal cavities of common seals (Phoca vitulina). The genome size of the strain (designated as UM1) is 2.4 Mb. With a high G+C content (70.4 mol%), strain UM1 is phylogenetically most closely related to F. nasiphocae based on whole genome analysis. Strain UM1 was susceptible to vancomycin, linezolid, trimethoprim-sulfamethoxazole, doxycycline, and intermediate to penicillin and ciprofloxacin. Ceftriaxone resistance was noted. The patient who was also on hemodialysis for his end stage kidney disease died approximately 3 weeks following implant removal and fusion with an external fixator. This study describes the first isolation of F. nasiphocae from human clinical samples. The use of emerging technologies has supported more definitive etiological diagnosis associated with rarely encountered organisms in periprosthetic joint infection.
Collapse
Affiliation(s)
- Sun Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
| | - Azhar Mahmood Merican
- Department of Orthopaedic Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Kartini Abdul Jabar
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rukumani Devi Velayuthan
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Khairul Anwar Ayob
- Department of Orthopaedic Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jiang Lin Lee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Chong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rina Karunakaran
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
4
|
Ponraj DS, Falstie-Jensen T, Brüggemann H, Lange J. The value of sonication on orthopaedic implants in an everyday clinical setting - an exploratory study. BMC Musculoskelet Disord 2023; 24:691. [PMID: 37644417 PMCID: PMC10464118 DOI: 10.1186/s12891-023-06796-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Sonication of removed orthopaedic implants in suspected implant-associated infections (IAI) is widely applied internationally. However, evaluation of the utility of sonication on all implants removed in everyday standard practice is scarce. This exploratory study was performed to evaluate the application of sonication fluid (SF) culture on removed orthopaedic implants, irrespective of the reason for removal. METHODS Out of 100 removed orthopaedic implants collected between August 2019 and September 2020, 77 implants with availability of concurrent tissue culture samples were included in the study. Removed implants were categorized into a confirmed or suspected IAI group and a presumed aseptic group based on pre-operative diagnosis by the responsible surgeon. Implants were sonicated and SF culture performed under both aerobic and anaerobic conditions. The significance of all bacterial isolates was evaluated based on the CFU/mL cut-offs of the EBJIS guidelines, except for C. acnes where additional investigations were performed. RESULTS The results of SF culture in the two groups were compared with their corresponding tissue cultures. Out of the 12 cases in the confirmed/suspected IAI group, SF culture was positive in 11 cases and had increased diagnostic yield in two (17%) cases compared to tissue culture. Increased diagnostic yield of SF compared to tissue culture was seen in seven (11%) of the 65 implants in the presumed aseptic group. If growth of Cutibacterium species isolates were interpreted based on EBJIS cut-off for SF culture instead of the study-specific criteria, then two isolates considered to represent infection might have been missed while three other isolates considered contaminants would have fallen under the 'infection confirmed' category in the EBJIS guidelines. CONCLUSION Sonication with SF culture has increased diagnostic yield compared to tissue cultures in all implants irrespective of reason for removal. However, positive SF cultures with Cutibacterium species should always be interpreted with extreme care.
Collapse
Affiliation(s)
| | | | | | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, 8000, Denmark.
- Department of Orthopaedic Surgery, Regional Hospital, Horsens, 8700, Denmark.
| |
Collapse
|
5
|
Bos MP, van Houdt R, Poort L, van der Stel AX, Peters EJ, Saouti R, Savelkoul P, Budding AE. Rapid Diagnostics of Joint Infections Using IS-Pro. J Clin Microbiol 2023; 61:e0015423. [PMID: 37154734 PMCID: PMC10281151 DOI: 10.1128/jcm.00154-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Diagnosis of bone and joint infections (BJI) relies on microbiological culture which has a long turnaround time and is challenging for certain bacterial species. Rapid molecular methods may alleviate these obstacles. Here, we investigate the diagnostic performance of IS-pro, a broad-scope molecular technique that can detect and identify most bacteria to the species level. IS-pro additionally informs on the amount of human DNA present in a sample, as a measure of leukocyte levels. This test can be performed in 4 h with standard laboratory equipment. Residual material of 591 synovial fluid samples derived from native and prosthetic joints from patients suspected of joint infections that were sent for routine diagnostics was collected and subjected to the IS-pro test. Bacterial species identification as well as bacterial load and human DNA load outcomes of IS-pro were compared to those of culture. At sample level, percent positive agreement (PPA) between IS-pro and culture was 90.6% (95% CI 85.7- to 94%) and negative percent agreement (NPA) was 87.7% (95% CI 84.1 to 90.6%). At species level PPA was 80% (95% CI 74.3 to 84.7%). IS-pro yielded 83 extra bacterial detections over culture for which we found supporting evidence for true positivity in 40% of the extra detections. Missed detections by IS-pro were mostly related to common skin species in low abundance. Bacterial and human DNA signals measured by IS-pro were comparable to bacterial loads and leukocyte counts reported by routine diagnostics. We conclude that IS-pro showed an excellent performance for fast diagnostics of bacterial BJI.
Collapse
Affiliation(s)
| | - Robin van Houdt
- Department of Medical Microbiology & Infection Control, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | | | - Edgar J. Peters
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Infectious Diseases, Amsterdam Infection & Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Rachid Saouti
- Department of Orthopedic Surgery, Amsterdam UMC, Amsterdam Movement Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul Savelkoul
- Department of Medical Microbiology & Infection Control, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht UMC, Maastricht, The Netherlands
| | | |
Collapse
|
6
|
Ponraj DS, Lund M, Lange J, Poehlein A, Himmelbach A, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H. Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent. Front Cell Infect Microbiol 2023; 13:1165017. [PMID: 37265503 PMCID: PMC10229904 DOI: 10.3389/fcimb.2023.1165017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.
Collapse
Affiliation(s)
| | - Michael Lund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Orthopaedic Surgery, Regional Hospital, Horsens, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - Christen Ravn
- Department of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, Denmark
| | | |
Collapse
|
7
|
Ahmed AH, Ahmed S, Barakat A, Mangwani J, White H. Inflammatory response in confirmed non-diabetic foot and ankle infections: A case series with normal inflammatory markers. World J Orthop 2023; 14:136-145. [PMID: 36998381 PMCID: PMC10044321 DOI: 10.5312/wjo.v14.i3.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/23/2022] [Accepted: 02/01/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND The distinction between foot and ankle wound healing complications as opposed to infection is crucial for the appropriate and efficacious allocation of antibiotic therapy. Multiple reports have focused on the diagnostic accuracy of different inflammatory markers, however, mainly in the diabetic population.
AIM To evaluate the diagnostic accuracy of white cell count (WCC) and C-reactive protein (CRP) as diagnostic tools for this distinction in the non-diabetic cohort.
METHODS Data was reviewed from a prospectively maintained Infectious Diseases Unit database of 216 patients admitted at Leicester University Hospitals–United Kingdom with musculoskeletal infections over the period between July 2014 and February 2020 (68 mo). All patients with confirmed diagnosis of diabetes were excluded while only those with confirmed microbiological or clinical diagnosis of foot or ankle infection were included in our study. For the included patients, we retrospectively retrieved the inflammatory markers (WCCs and CRP) at the time of presentation. Values of CRP 0-10 mg/L and WCC 4.0-11.0 × 109/L were considered normal.
RESULTS After exclusion of patients with confirmed diabetes, 25 patients with confirmed foot or ankle infections were included. All infections were confirmed microbiologically with positive intra-operative culture results. 7 (28%) patients with osteomyelitis (OM) of the foot, 11 (44%) with OM of the ankle, 5 (20%) with ankle septic arthritis and 2 (8%) patients with post-surgical wound infection were identified. Previous bony surgery was identified in 13 (52%) patients, either a corrective osteotomy or an open reduction and internal fixation for a foot or ankle fracture with the infection developing on top of the existing metalwork. 21 (84%) patients did have raised inflammatory markers while 4 (16%) patients failed to mount an inflammatory response even with subsequent debridement and removal of metal work. CRP sensitivity was 84%, while WCC sensitivity was only 28%.
CONCLUSION CRP has a relatively good sensitivity in the diagnosis of foot and ankle infections in non-diabetic patients, whereas WCC is a poor inflammatory marker in the detection of such cases. In presence of clinically high level of suspicion of foot or ankle infection, a normal CRP should not rule out the diagnosis of OM.
Collapse
Affiliation(s)
- Amr Hassan Ahmed
- Department of Trauma and Orthopedics, Leicester University Hospitals-NHS Trust, Leicester LE1 5WW, Leicestershire, United Kingdom
| | - Shah Ahmed
- Department of Trauma and Orthopedics, Leicester University Hospitals-NHS Trust, Leicester LE1 5WW, Leicestershire, United Kingdom
| | - Ahmed Barakat
- Department of Trauma and Orthopedics, Leicester University Hospitals-NHS Trust, Leicester LE1 5WW, Leicestershire, United Kingdom
| | - Jitendra Mangwani
- Department of Trauma and Orthopedics, Leicester University Hospitals-NHS Trust, Leicester LE1 5WW, Leicestershire, United Kingdom
| | - Helena White
- Department of Infectious Diseases and Tropical Medicine, Leicester Royal Infirm, Leicester LE1 5WW, Leicestershire, United Kingdom
| |
Collapse
|
8
|
Ponraj DS, Lange J, Falstie-Jensen T, Jørgensen NP, Ravn C, Poehlein A, Brüggemann H. Amplicon-Based Next-Generation Sequencing as a Diagnostic Tool for the Detection of Phylotypes of Cutibacterium acnes in Orthopedic Implant-Associated Infections. Front Microbiol 2022; 13:866893. [PMID: 35464945 PMCID: PMC9022064 DOI: 10.3389/fmicb.2022.866893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 01/04/2023] Open
Abstract
The diagnosis of orthopedic implant-associated infections (OIAIs) caused by the slow-growing anaerobic bacterium Cutibacterium acnes is challenging. The mild clinical presentations of this low-virulent bacterium along with its ubiquitous presence on human skin and human-dominated environments often make it difficult to differentiate true infection from contamination. Previous studies have applied C. acnes phylotyping as a potential avenue to distinguish contamination from infection; several studies reported a prevalence of phylotypes IB [corresponding to type H in the single-locus sequence typing (SLST) scheme] and II (SLST type K) in OIAIs, while a few others found phylotype IA1 (more specifically SLST type A) to be abundant. However, phylotype determination has mainly been done in a culture-dependent manner on randomly selected C. acnes isolates. Here, we used a culture-independent amplicon-based next-generation sequencing (aNGS) approach to determine the presence and relative abundances of C. acnes phylotypes in clinical OIAI specimens. As amplicon, the SLST target was used, a genomic fragment that is present in all C. acnes strains known to date. The aNGS approach was applied to 30 sonication fluid (SF) samples obtained from implants removed during revision surgeries, including 17 C. acnes culture-positive and 13 culture-negative SF specimens. In 53% of the culture-positive samples, SLST types were identified: relative abundances were highest for K-type C. acnes, followed by H- and D-type C. acnes. Other types, including A- and C-type C. acnes that are more prevalent on human skin, had low relative abundances. The aNGS results were compared with, and confirmed by a culture-dependent approach, which included the isolation, whole genome sequencing (WGS) and phylotyping of 36 strains of C. acnes obtained from these SF samples. Besides serving as a powerful adjunct to identify C. acnes phylotypes, the aNGS approach could also distinguish mono- from heterotypic infections, i.e., infections caused by more than one phylotype of C. acnes: in eight out of nine culture-positive SF samples multiple C. acnes types were detected. We propose that the aNGS approach, along with the patient’s clinical information, tissue and SF cultures and WGS, could help differentiate C. acnes contamination from true infection.
Collapse
Affiliation(s)
| | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Orthopedic Surgery, Horsens Regional Hospital, Horsens, Denmark
| | | | | | - Christen Ravn
- Department of Orthopedic Surgery, Aarhus University Hospital, Aarhus, Denmark.,Department of Orthopedic Surgery, Lillebaelt Hospital, Kolding, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | | |
Collapse
|