Amplicon-Based Next-Generation Sequencing as a Diagnostic Tool for the Detection of Phylotypes of Cutibacterium acnes in Orthopedic Implant-Associated Infections

Increased biofilm formation in dual-strain compared to single-strain communities of Cutibacterium acnes

Cutibacterium acnes is a known opportunistic pathogen in orthopedic implant-associated infections (OIAIs). The species of C. acnes comprises distinct phylotypes. Previous studies suggested that C. acnes can cause single- as well as multi-typic infections, i.e. infections caused by multiple strains of different phylotypes. However, it is not known if different C. acnes phylotypes are organized in a complex biofilm community, which could constitute a multicellular strategy to increase biofilm strength and persistency. Here, the interactions of two C. acnes strains belonging to phylotypes IB and II were determined in co-culture experiments. No adverse interactions between the strains were observed in liquid culture or on agar plates; instead, biofilm formation in both microtiter plates and on titanium discs was significantly increased when combining both strains. Fluorescence in situ hybridization showed that both strains co-occurred throughout the biofilm. Transcriptome analyses revealed strain-specific alterations of gene expression in biofilm-embedded cells compared to planktonic growth, in particular affecting genes involved in carbon and amino acid metabolism. Overall, our results provide first insights into the nature of dual-type biofilms of C. acnes, suggesting that strains belonging to different phylotypes can form biofilms together with additive effects. The findings might influence the perception of C. acnes OIAIs in terms of diagnosis and treatment.

2023 Neer Award for Basic Science: Genetics of Cutibacterium acnes in revision shoulder arthroplasty: a large-scale bacterial whole-genome sequencing study

BACKGROUND

Cutibacterium acnes is the bacterium most commonly responsible for shoulder periprosthetic joint infection (PJI) and is often cultured from samples obtained at the time of revision for failed shoulder arthroplasty. We sought to determine whether these bacteria originate from the patient or from exogenous sources. We also sought to identify which C. acnes genetic traits were associated with the development of shoulder PJI.

METHODS

We performed bacterial whole-genome sequencing of C. acnes from a single-institution repository of cultures obtained before or during primary and revision shoulder arthroplasty and correlated the molecular epidemiology and genetic content of strains with clinical features of infection.

RESULTS

A total of 341 isolates collected over a 4-year period from 88 patients were sequenced. C. acnes cultured from surgical specimens demonstrated significant similarity to the strains colonizing the skin of the same patient (P < .001). Infrequently, there was evidence of strains shared across unrelated patients, suggesting that exogenous sources of C. acnes culture-positivity were uncommon. Phylotypes IB and II were modestly associated with clinical features of PJI, but all phylotypes appeared inherently capable of causing disease. Chronic shoulder PJI was associated with the absence of common C. acnes genes involved in bacterial quorum-sensing (luxS, tqsA).

CONCLUSION

C. acnes strains cultured from deep intraoperative sources during revision shoulder arthroplasty demonstrate strong genetic similarity to the strains colonizing a patient's skin. Some phylotypes of C. acnes commonly colonizing human skin are modestly more virulent than others, but all phylotypes have a capacity for PJI. C. acnes cultured from cases of PJI commonly demonstrated genetic hallmarks associated with adaptation from acute to chronic phases of infection. This is the strongest evidence to date supporting the role of the patient's own, cutaneous C. acnes strains in the pathogenesis of shoulder arthroplasty infection. Our findings support the importance of further research focused on perioperative decolonization and management of endogenous bacteria that are likely to be introduced into the arthroplasty wound at the time of skin incision.

The value of sonication on orthopaedic implants in an everyday clinical setting - an exploratory study

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.

Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent

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.

Prevalence of antimicrobial-resistant Cutibacterium isolates and development of multiplex PCR method for Cutibacterium species identification

INTRODUCTION

Cutibacterium species such as C. acnes, C. avidum, and C. granulosum are known anaerobic skin inhabitants and often cause surgical site infections. These species are genetically similar and are difficult to identify rapidly. In addition, their pathogenicity and antimicrobial resistance remain unknown. In this study, antimicrobial resistance in Cutibacterium isolates was studied and a multiplex PCR method for their identification was developed.

METHODS

A total of 497 C. acnes, 71 C. avidum, and 25 C. granulosum strains which were isolated from the acne pustule and infectious regions, were used.

RESULTS

The antimicrobial resistance rates of C. acnes, C. avidum, and C. granulosum strains isolated from patients with acne vulgaris were higher than those of strains isolated from patients with infectious diseases. In particular, macrolide-clindamycin-resistant strains were isolated most frequently from all species. Among the resistant strains, strains with 23S rRNA mutations were the most common in C. acnes (24.3%, 71/292), whereas C. avidum and C. granulosum strains were most frequently found with erm(X). For the first time, a C. granulosum strain carrying pTZC1, which codes erm(50) and tet(W), was isolated from patients with acne vulgaris. Regarding the rapid identification of causative pathogens from infectious regions, three Cutibacterium species were identified with 100% sensitivity and specificity using multiplex PCR method.

CONCLUSIONS

Our data showed that antimicrobial resistance differed among Cutibacterium species. The multiplex PCR method may contribute to the rapid detection of Cutibacterium species and selection of appropriate antimicrobial agents.