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Next Generation Sequencing Results Require Higher.1239
Next Generation Sequencing Results Require Higher.1239
DOI 10.1097/CORR.0000000000002738
Basic Research
Anaerobic Culture
Diana Fernández-Rodrı́guez MD1,2, Jeongeun Cho BS1, Niosha Parvizi BS1,
Adam Z. Khan MD1 , Javad Parvizi MD, FRCS1, Surena Namdari MD1
stKpJaykxPO0dTmG52Wz9uWv8= on 06/24/2023
Received: 26 October 2022 / Revised: 16 April 2023 / Accepted: 22 May 2023 / Published online: 21 June 2023
Copyright © 2023 by the Association of Bone and Joint Surgeons
Abstract
Background Cutibacterium acnes has been described as than for anaerobic conventional culture? (2) What duration
the most common causative microorganism in prosthetic of incubation is necessary for anaerobic culture to detect all
shoulder infections. Conventional anaerobic culture or C. acnes loads?
molecular-based technologies are usually used for this Methods Five C. acnes strains were tested for this study:
purpose, but little to no concordance between these meth- Four strains were causing infection and were isolated from
odologies (k = 0.333 or less) has been observed. surgical samples. Meanwhile, the other was a reference
Questions/purposes (1) Is the minimum C. acnes load for strain commonly used as a positive and quality control in
detection higher for next-generation sequencing (NGS) microbiology and bioinformatics. To create inoculums
Each author certifies that there are no funding or commercial associations (consultancies, stock ownership, equity interest, patent/licensing
arrangements, etc.) that might pose a conflict of interest in connection with the submitted article related to the author or any immediate
family members.
Outside the submitted work, one of the authors (SN) certifies receipt of payments or benefits, during the study period, in an amount of less than
USD 10,000 from ACI, personal fees in an amount of less than USD 10,000 from Aevumed, research support in an amount of less than USD 10,000
from Arthrex, Inc, personal fees in an amount of less than USD 10,000 from Biederman Motech, personal fees in an amount of less than USD 10,000
from Coracoid Solutions, research support in an amount of less than USD 10,000 from DePuy, personal fees and research support in an amount of
less than USD 10,000 from DJ Orthopaedics, research support in an amount of less than USD 10,000 from Integra, personal fees in an amount of less
than USD 10,000 from MediFlix, personal fees in an amount of less than USD 10,000 from Miami Device Solutions/Biederman Motech, personal fees
in an amount of less than USD 10,000 from Pacira, research support in an amount of less than USD 10,000 from Roche, personal fees in an amount
of less than USD 10,000 from Saunders/Mosby-Elsevier, personal fees in an amount of less than USD 10,000 from SLACK Incorporated, research
support in an amount of less than USD 10,000 from Smith & Nephew, personal fees in an amount of less than USD 10,000 from Synthes, personal
fees in an amount of less than USD 10,000 from Tigon, personal fees in an amount of less than USD 10,000 from Wolters Kluwer Health, research
support in an amount of less than USD 10,000 from Wright Medical Technology, Inc, and research support in an amount of less than USD 10,000
from Zimmer. In addition, SN certifies ownership interest of Actabond, Aevumed, CLEU Diagnostics, Coracoid Solutions, HealthExl, MD Valuate,
MediFlix, Parvizi Surgical Innovations, SurgiWipe, and Tangen.
1
Rothman Orthopaedic Institute, Philadelphia, PA, USA
2
Plan de Estudios Combinados en Medicina (PECEM) MD/PhD, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico
City, Mexico
S. Namdari ✉, Rothman Orthopaedic Institute, 925 Chestnut Street, Philadelphia, PA 19107, USA, Email: Surena.namdari@rothmanortho.com
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
2 Fernández-Rodrı́guez et al. Clinical Orthopaedics and Related Research®
with varying degrees of bacterial load, we began with a agar plates and determined the minimum incubation time in
standard bacterial suspension at 1.5 x 108 colony-forming days required for CFU detection in all strains and loads
units (CFU)/mL and created six more diluted suspensions examined in this study. Growth detection and bacterial
(from 1.5 x 106 CFU/mL to 1.5 x 101 CFU/mL). Briefly, to CFU counting were performed by three laboratory per-
XcPwNfwdA02jL8IwmI9oyE6Ap+nPRE3GrPdJ5t9sQToC+rXW4P92yOvyEPfXNpHQwwjeaiq1uuQ8z0IHxYgGr/EGogc447WGXnYZ
do so, we transferred 200 mL from the tube with the highest sonnel, with a high intraobserver and interobserver agree-
inoculum (for example, 1.5 x 106 CFU/mL) to the fol- ment (k > 0.80). A two-tailed p value below 0.05 was
lowing dilution tube (1.5 x 105 CFU/mL; 1800 mL of
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incubated at 37°C in an anaerobic chamber and assessed for Conclusion When NGS is negative and culture is positive
growth after 3 days of incubation and daily thereafter until for C. acnes, there is likely a low bacterial load. Holding
positive or Day 14. The remaining volume of each bacterial cultures beyond 7 days is likely unnecessary.
suspension was sent for NGS analysis to identify bacterial Clinical Relevance This is important for treating physi-
DNA copies. We performed the experimental assays in cians to decide whether low bacterial loads necessitate
duplicate. We calculated mean DNA copies and CFUs for aggressive antibiotic treatment or whether they are more
each strain, bacterial load, and incubation timepoint likely contaminants. Cultures that are positive beyond
assessed. We reported detection by NGS and culture as a 7 days likely represent contamination or bacterial loads
qualitative variable based on the identification or absence even below the dilution used in this study. Physicians may
of DNA copies and CFUs, respectively. In this way, we benefit from studies designed to clarify the clinical im-
identified the minimum bacterial load detected by NGS and portance of the low bacteria loads used in this study at
culture, regardless of incubation time. We performed a which both methodologies’ detection differed. Moreover,
qualitative comparison of detection rates between meth- researchers might explore whether even lower C. acnes
odologies. Simultaneously, we tracked C. acnes growth on loads have a role in true periprosthetic joint infection.
Outside the submitted work, one of the authors (JP) certifies receipt of payments or benefits, during the study period, in an amount of less
than USD 10,000 from Corentec, personal fees in an amount of less than USD 10,000 from Data Trace, personal fees in an amount of less than
USD 10,000 from Elsevier, personal fees in an amount of less than USD 10,000 from Jaypee Publishers, personal fees in an amount of less
than USD 10,000 from SLACK Incorporated, personal fees in an amount of less than USD 10,000 from Wolters Kluwer, personal fees in an
amount of less than USD 10,000 from Becton Dickensen, personal fees and non-financial support in an amount of less than USD 10,000 from
Zimmer Biomet, personal fees in an amount of less than USD 10,000 from Ethicon, personal fees in an amount of less than USD 10,000 from
Tenor, personal fees in an amount of less than USD 10,000 from KCI/3M (Acelity), personal fees in an amount of less than USD 10,000 from
MicroGenDx, personal fees in an amount of less than USD 10,000 from Jointstem, personal fees in an amount of less than USD 10,000 from
Becton Dickenson, personal fees in an amount of less than USD 10,000 from Cardinal Health, research support in an amount of less than USD
10,000 from the NIH, research support in an amount of less than USD 10,000 from OREF, research support in an amount of less than USD
10,000 from 3M, research support in an amount of less than USD 10,000 from Aesculap, research support in an amount of less than USD
10,000 from AO Spine, research support in an amount of less than USD 10,000 Biomet, research support in an amount of less than USD
10,000 from Cempra, research support in an amount of less than USD 10,000 from DePuy, research support in an amount of less than USD
10,000 from Integra, research support in an amount of less than USD 10,000 from Lima, research support in an amount of less than USD
10,000 from Myoscience, research support in an amount of less than USD 10,000 from NDRI, research support in an amount of less than USD
10,000 from Novartis, research support in an amount of less than USD 10,000 from Pfizer, research support in an amount of less than USD
10,000 from Rotation Medical, research support in an amount of less than USD 10,000 from Simplify Medical, research support in an amount
of less than USD 10,000 from Smith & Nephew, research support in an amount of less than USD 10,000 from Stelkast, research support in an
amount of less than USD 10,000 from Stryker Orthopedics, research support in an amount of less than USD 10,000 from Synthes, research
support in an amount of less than USD 10,000 from TissueGene, research support in an amount of less than USD 10,000 from Tornier, and
research support in an amount of less than USD 10,000 from Orthospace. In addition, JP certifies ownership interest of Parvizi Surgical
Innovation and Subsidiaries, Hip Innovation Technology, Alphaeon/Strathsby Crown, Elute, Ceribell, Acumed, PRN-Veterinary, Illuminus,
Intellijoint, Osteal, Nanooxygenic, Sonata, Molecular Surface Technologies, and Peptilogic.
All ICMJE Conflict of Interest Forms for authors and Clinical Orthopaedics and Related Research® editors and board members are on file with
the publication and can be viewed on request.
Clinical Orthopaedics and Related Research® neither advocates nor endorses the use of any treatment, drug, or device. Readers are
encouraged to always seek additional information, including FDA approval status, of any drug or device before clinical use.
Ethical approval for this study was waived by the Thomas Jefferson University Institutional Review Board.
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
Volume 00, Number 00 C. acnes NGS Versus Culture 3
dergoing primary THA and TKA, respectively [22]. In (k = 0.333 or less [15, 16]).
fact, infection may be the leading cause of more than Therefore, we asked: (1) Is the minimum C. acnes load
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25% of revision procedures in those joints [3, 23]. for detection higher for NGS than for anaerobic conven-
Cutibacterium acnes is an anaerobic organism fre- tional culture? (2) What duration of incubation is necessary
quently isolated from joint implants, especially but not for anaerobic culture to detect all C. acnes loads?
limited to the upper extremity [20]. Patients with peri-
prosthetic joint infection (PJI) secondary to C. acnes
present with vague clinical symptoms compared with Materials and Methods
those with other pathogens, including pain, stiffness,
and less commonly, elevated serum and synovial bio- Study Overview
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Fig. 1 Five C. acnes strains were diluted and assessed in parallel using NGS and
anaerobic conventional culture. ATCC 6919 = American Type Culture Collection 6919;
CSF = cerebrospinal fluid; CFU = colony-forming unit; NGS = next-generation
sequencing.
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
4 Fernández-Rodrı́guez et al. Clinical Orthopaedics and Related Research®
suspensions at different known concentrations (Fig. 1). To create inoculums with varying degrees of bacterial
The volume of each bacterial suspension was processed load, we began with the standard bacterial suspension (1.5
for anaerobic conventional culture and NGS analysis. x 108 CFU/mL) and created six more diluted suspensions
Three laboratory personnel with a high intra- and in- (from 1.5 x 106 CFU/mL to 1.5 x 101 CFU/mL). To do so,
XcPwNfwdA02jL8IwmI9oyE6Ap+nPRE3GrPdJ5t9sQToC+rXW4P92yOvyEPfXNpHQwwjeaiq1uuQ8z0IHxYgGr/EGogc447WGXnYZ
terobserver agreement (k > 0.80) assessed growth; we transferred 200 mL from the tube with the highest
meanwhile, NGS analysis was performed by a certified inoculum (1.5 x 106 CFU/mL) to the following dilution
tube (1.5 x 105 CFU/mL, containing 1800 mL of sterile
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time necessary to detect C. acnes growth by anaerobic lution tube for each assay. Moreover, a vial with sterile
conventional culture. All bacterial suspensions prepared phosphate-buffered saline solution without inoculum was
for this study (Fig. 1) were inoculated into brain heart in- used as negative control. All plates were incubated at
fusion agar with horse blood and taurocholate (Anaerobe 37°C in an anaerobic chamber.
Systems) agar plates and incubated in an anaerobic atmo- Plates were examined after 72 hours and daily thereafter
sphere at 37°C. Growth was evaluated at Day 3 and daily until positive or Day 14. Colony morphology, hemolysis, and
thereafter until positive or Day 14. The time necessary for the CFUs at each timepoint were assessed as qualitative
C. acnes growth on agar plates was determined according variables by three laboratory personnel (DFR, JC, and NP)
to the minimum incubation time in days required for CFU with high intraobserver and interobserver agreement (k >
detection in all strains and loads used in this study. 0.80). Briefly, colony morphology was focused on the size
(diameter in millimeters), surface appearance (for example,
mucoid or wrinkled), shape (such as punctiform, circular, or
Strains of C. acnes irregular), color, and hemolysis pattern [25]. Hemolysis was
graded according to the characteristics of the area surrounding
We tested five C. acnes strains in this study. We included the the CFUs: A clear area denoted complete hemolysis (beta), a
reference strain American Type Culture Collection (ATCC) greenish area indicated incomplete hemolysis (alpha), and no
6919. This C. acnes strain is used as a positive and quality changes indicated nonhemolytic (gamma) strains [18].
control in microbiology and bioinformatics [12]. In addition, We performed the experimental assays in duplicate. For
four strains isolated from surgical procedures were provided each assay, we tested 30 tubes (five strains and six bacterial
from our biobank and used for this study. The number and suspensions per strain), which were incubated in two agar
type of strains eligible for our study was limited because of plates per tube and processed for NGS analysis (description
the growth requirements of C. acnes and its perception as a below).
contaminant. Thus, our study only included strains that were We calculated mean DNA copies and CFUs for each
confirmed as the causative microorganism of monobacterial strain, bacterial load, and incubation timepoint that were
infections. We were able to include two isolates causing PJI assessed. Then, we reported detection by NGS and culture
(knee and shoulder) and two more strains isolated from as a qualitative variable, based on the identification or ab-
surgical samples of the heart and vertebral column (cere- sence of DNA copies and CFUs, respectively. In this way,
brospinal fluid). we identified the minimum bacterial load detected by NGS
and culture, regardless of incubation time. For our second
research question, C. acnes growth was tracked on agar
Culture Protocol plates, and the time in days for positivity was recorded for
each bacterial suspension. Then, the minimum incubation
We used monobacterial cultures in agar plates to stir bac- time required for CFU detection was identified, regardless of
teria into a tube with Brucella broth (Anaerobe Systems) strain and load assessed in this study.
using a loop. Bacteria in the broth were incubated in an-
aerobic conditions at 150 rpm and 37°C for 4 days. We
assessed growth (cloudy broth) at 4 days. Bacterial sus- NGS
pensions were prepared using the cloudy broth and sterile
phosphate-buffered saline solution to achieve a 0.5 The remaining volume of each bacterial suspension was
McFarland turbidity standard (1.5 x 108 CFU/mL). processed at the MicrogenDx facility for NGS analysis to
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
Volume 00, Number 00 C. acnes NGS Versus Culture 5
identify bacterial DNA copies. Each bacterial suspension merging, as well as chimera detection) and diversity anal-
was mechanically lysed using the Qiagen TissueLyser ysis (operational taxonomic unit selection and taxonomic
(Qiagen). Then, we spiked each sample with a positive assignment) using MicroGen Dx’s curated microbial
internal control to ensure the success of the extraction database.
XcPwNfwdA02jL8IwmI9oyE6Ap+nPRE3GrPdJ5t9sQToC+rXW4P92yOvyEPfXNpHQwwjeaiq1uuQ8z0IHxYgGr/EGogc447WGXnYZ
process. In addition, negative controls were run along with Total bacterial CFUs and DNA copies are summarized
samples to identify contamination associated with the ex- with a descriptive analysis. We calculated the mean and SD
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traction process. DNA was then extracted using a for each bacterial suspension and timepoint assessed. Then,
KingFisher Flex Purification System (ThermoFisher positivity or detection by conventional anaerobic culture
Scientific). DNA was amplified using forward and reverse and NGS was recorded for each bacterial suspension as a
primers specific to regions flanking the 16S rRNA gene for qualitative variable, regardless of incubation time. Relative
bacteria and the internal transcribed spacer gene for fungi and absolute frequencies are reported, and the positivity
on a LightCycler 480 II (Roche Life Sciences) with the rate was compared (conventional anaerobic culture versus
following thermal cycling profile: 95°C for 5 minutes; 35 NGS) using the chi-squared test. A two-tailed p value be-
cycles of 94°C for 30 seconds, 52°C for 40 seconds, and low 0.05 was considered statistically significant.
stKpJaykxPO0dTmG52Wz9uWv8= on 06/24/2023
Our study was exempt from institutional review board Conventional cultures can detect C. acnes at a load of 1.5 x
approval because we only used frozen bacterial strains and 101 CFU/mL, whereas NGS can detect this bacterium only
did not collect or share clinical information or tissue when the concentration was higher, at 1.5 x 102 CFU/mL
samples. (Fig. 2). This was represented by a lower positive detection
proportion (73% [22 or 30]) for NGS than for cultures
(100% [30 of 30]); p = 0.004). For the ATCC 6919 and
Statistical Analysis knee isolate, NGS analysis could identify C. acnes in
bacterial suspensions as low as 1.5 x 102 CFU/mL.
Bacterial counts were performed by three laboratory per- However, DNA copies of cerebrospinal fluid and shoul-
sonnel (DFR, JC, and NP), with high intraobserver and der and heart isolates were detected in bacterial suspen-
interobserver agreement (k > 0.80). Herein, we report the sions at 1.5 x 103 CFU/mL and above.
total CFUs at 3, 4, 5, 6, and 7 days of incubation. Cultures
were held until Day 14 to answer our secondary goal;
however, no changes were seen in the positivity rate or Duration to Hold Cultures to Detect C. acnes
CFU counts after Day 7.
After sequencing, we ran sample data through By Day 7, the most-diluted C. acnes suspension was
MicroGen Dx’s bioinformatic pipeline consisting of detected by conventional anaerobic cultures in all strains
Q-score assessment, denoising (quality trimming and read (Fig. 3). In our observations on Day 3, concentrations of
Fig. 2 DNA copies and CFUs per C. acnes load and strain were determined by NGS and conventional anaerobic culture,
respectively. ATCC 6919 = American Type Culture Collection 6919; CSF = cerebrospinal fluid; CFU = colony-forming unit; NGS
= next-generation sequencing.
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
6 Fernández-Rodrı́guez et al. Clinical Orthopaedics and Related Research®
Copyright © 2023 by the Association of Bone and Joint Surgeons. Unauthorized reproduction of this article is prohibited.
Volume 00, Number 00 C. acnes NGS Versus Culture 7
treating physicians to decide whether low bacterial loads likely unnecessary. Cultures that are positive beyond 7 days
necessitate aggressive antibiotic treatment or whether they likely represent contamination or bacterial loads lower than
are more likely contaminants. Moreover, the inconsis- the concentrations tested in our study. Clinicians have a
tencies between methods may be the result of the bacterial challenge in deciding whether to act on these low-level
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load required for C. acnes detection. Similar to our culture results, which may not represent true PJI. Future
findings, a prior clinical study demonstrated that the NGS studies should determine the clinical relevance of the low
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positive detection rate for C. acnes was lower than for bacteria loads tested in this study and explore whether even
culture (2.5% versus 15%) [17]. Gaston et al. [8] showed lower C. acnes loads might be found for true PJI.
NGS detection could be as low as 67.1% for fastidious
microorganisms such as C. acnes. Still, if NGS is positive,
the suspicion toward contamination or low inoculums that References
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stKpJaykxPO0dTmG52Wz9uWv8= on 06/24/2023
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