Propionibacterium/Cutibacterium species-related positive samples, identification, clinical and resistance features: a 10-year survey in a French hospital

Comparative Genomic Analysis of Cutibacterium spp. Isolates in Implant-Associated Infections

Bacteria of the genus Cutibacterium are Gram-positive commensals and opportunistic pathogens that represent a major challenge in the diagnosis and treatment of implant-associated infections (IAIs). This study provides insight into the distribution of different sequence types (STs) of C. acnes, and the presence of virulence factors (VFs) in 64 Cutibacterium spp. isolates from suspected or confirmed IAIs obtained during routine microbiological diagnostics. Fifty-three C. acnes, six C. avidum, four C. granulosum, and one C. namnetense isolate, collected from different anatomical sites, were included in our study. Using whole-genome sequencing and a single-locus sequencing typing scheme, we successfully characterized all C. acnes strains and revealed the substantial diversity of STs, with the discovery of six previously unidentified STs. Phylotype IA1, previously associated with both healthy skin microbiome and infections, was the most prevalent, with ST A1 being the most common. Some minor differences in STs' distribution were observed in correlation with anatomical location and association with infection. A genomic analysis of 40 investigated VFs among 64 selected strains showed no significant differences between different STs, anatomical sites, or infection-related and infection undetermined/unlikely groups of strains. Most differences in VF distribution were found between strains of different Cutibacterium spp., subspecies, and phylotypes, with CAMP factors, biofilm-related VFs, lipases, and heat shock proteins identified in all analyzed Cutibacterium spp.

First case of Cutibacterium avidum-infected pelvic lymphocele post-lymphadenectomy for endometrial cancer: A case report

Background

Pelvic lymphocele (lymphocyst) infection after lymphadenectomy is a rare complication that can cause the spread of inflammation to neighboring organs whose microbiology is not well known. Cutibacterium avidum causes various infections. However, no case reports of C. avidum pelvic lymphocele infection are available; therefore, its clinical characteristics in pelvic lymphocele infections remain unknown.

Case presentation

A 38-year-old woman with obesity (body mass index: 38.1 kg/m2) and a history of pelvic lymphadenectomy and chemotherapy for endometrial cancer presented with worsening left lower quadrant (LLQ) pain with fever. Physical examination revealed decreased abdominal bowel sounds and tenderness on LLQ palpation with no signs of peritonitis. Computed tomography (CT) revealed an infected left pelvic lymphocele with inflammation spreading to the adjacent sigmoid colon. Following blood culture, ampicillin/sulbactam (2 g/1 g every 6 h) was administered intravenously. Anaerobic culture bottles revealed gram-positive rods on day 4 of incubation at 37 °C. No other disseminated foci were observed in enhanced whole-body CT and upon transthoracic echocardiography. The isolates grew aerobically and anaerobically on blood agar plates with strong hemolysis. The bacterium was identified as C. avidum using a combination of characteristic peak analysis with matrix-assisted laser desorption ionization (MALDI) and 16S rRNA gene sequencing. The patient was diagnosed with C. avidum pelvic lymphocele infection. Based on penicillin susceptibility, the patient was successfully treated with intravenous ampicillin/sulbactam and de-escalated with intravenous ampicillin (2 g every 6 h) for 10 days, followed by oral amoxicillin (2000 mg/day) for an additional 11 days without drainage.

Conclusions

C. avidum should be considered a causative microorganism of pelvic lymphocele infection. Peak analysis using MALDI and distinctive growth on blood agar plates are suitable for identifying C. avidum. Mild pelvic lymphocele caused by C. avidum can be treated with a short course of appropriate antimicrobial treatment without surgical intervention.

In Vivo Emergence of Dual Resistance to Rifampin and Levofloxacin in Osteoarticular Cutibacterium avidum

Cutibacterium avidum is an emerging causative agent of orthopedic device-related infections (ODRIs). There are no guidelines for the antimicrobial treatment of C. avidum ODRI, but oral rifampin is frequently used in combination with a fluoroquinolone following intravenous antibiotics. We describe the in vivo emergence of combined resistance to rifampin and levofloxacin in a C. avidum strain isolated from a patient with early-onset ODRI treated with debridement, antibiotic treatment, and implant retention (DAIR) using rifampin combined with levofloxacin as the oral treatment. Whole-genome sequencing of C. avidum isolates before and after antibiotic exposure confirmed strain identity and identified new mutations in rpoB and gyrA, leading to amino acid substitutions previously reported to be associated with resistance to rifampin (S446P) and fluoroquinolones (S101L), respectively, in other microbial agents, in the posttherapy isolate. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing a DAIR procedure for C. avidum ODRI and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens. IMPORTANCE In this study, we report for the first time the in vivo emergence of dual resistance to levofloxacin and rifampin in C. avidum isolated from a patient who received both antibiotics orally in the setting of a salvage debridement and implant retention of an ODRI. Aside from the molecular insights reported here, this study highlights potential limitations of the combination of oral rifampin and levofloxacin in patients undergoing these surgical procedures and the potential need to evaluate specific optimal therapy for emerging ODRI pathogens.

Recent Trends in Antimicrobial Resistance among Anaerobic Clinical Isolates

Anaerobic bacteria are normal inhabitants of the human commensal microbiota and play an important role in various human infections. Tedious and time-consuming, antibiotic susceptibility testing is not routinely performed in all clinical microbiology laboratories, despite the increase in antibiotic resistance among clinically relevant anaerobes since the 1990s. β-lactam and metronidazole are the key molecules in the management of anaerobic infections, to the detriment of clindamycin. β-lactam resistance is usually mediated by the production of β-lactamases. Metronidazole resistance remains uncommon, complex, and not fully elucidated, while metronidazole inactivation appears to be a key mechanism. The use of clindamycin, a broad-spectrum anti-anaerobic agent, is becoming problematic due to the increase in resistance rate in all anaerobic bacteria, mainly mediated by Erm-type rRNA methylases. Second-line anti-anaerobes are fluoroquinolones, tetracyclines, chloramphenicol, and linezolid. This review aims to describe the up-to-date evolution of antibiotic resistance, give an overview, and understand the main mechanisms of resistance in a wide range of anaerobes.

Multidrug Resistance Plasmid pTZC1 Could Be Pooled among Cutibacterium Strains on the Skin Surface

Acne vulgaris is a chronic inflammatory skin disease that is exacerbated by Cutibacterium acnes. Although antimicrobials such as macrolides, clindamycin, and tetracyclines are used to treat acne caused by C. acnes, the increasing prevalence of antimicrobial-resistant C. acnes strains has become a global concern. In this study, we investigated the mechanism by which interspecies transfer of multidrug-resistant genes can lead to antimicrobial resistance. Specifically, the transfer of pTZC1 between C. acnes and C. granulosum isolated from specimens of patients with acne was investigated. Among the C. acnes and C. granulosum isolated from 10 patients with acne vulgaris, 60.0% and 70.0% of the isolates showed resistance to macrolides and clindamycin, respectively. The multidrug resistance plasmid pTZC1, which codes for macrolide-clindamycin resistance gene erm(50) and tetracycline resistance gene tet(W), was identified in both C. acnes and C. granulosum isolated from the same patient. In addition, whole-genome sequencing revealed that the pTZC1 sequences of C. acnes and C. granulosum showed 100% identity using comparative whole-genome sequencing analysis. Therefore, we hypothesize that the horizontal transfer of pTZC1 between C. acnes and C. granulosum strains may occur on the skin surface. The plasmid transfer test revealed a bidirectional transfer of pTZC1 between C. acnes and C. granulosum, and transconjugants that obtained pTZC1 exhibited multidrug resistance. In conclusion, our results revealed that the multidrug resistance plasmid pTZC1 could be transferred between C. acnes and C. granulosum. Furthermore, since pTZC1 transfer among different species may aid in the prevalence of multidrug resistant strains, antimicrobial resistance genes may have been pooled on the skin surface. IMPORTANCE The emergence of antimicrobial resistance not only in Cutibacterium acnes strain but also other skin bacteria such as Staphylococcus epidermidis is a big concern due to antimicrobial use for the treatment of acne vulgaris. Increased prevalence of macrolides-clindamycin resistant C. acnes relates to the acquisition of exogenous antimicrobial resistance genes. erm(50) is harbored by the multidrug resistance plasmid pTZC1, which has been found in C. acnes and C. granulosum strains isolated from patients with acne vulgaris. In this study, C. acnes and C. granulosum with pTZC1 were found in the same patient, and plasmid transfer between C. acnes and C. granulosum was proved by transconjugation assay. This study showed plasmid transfer between other species and the possibility of further prevalence antimicrobial resistance between Cutibacterium species.

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.

Cryptic Oral Microbiota: What Is Its Role as Obstructive Sleep Apnea-Related Periodontal Pathogens?

Periodontitis has been commonly linked to periodontopathogens categorized in Socransky's microbial complexes; however, there is a lack of knowledge regarding "other microorganisms" or "cryptic microorganisms", which are rarely thought of as significant oral pathogens and have been neither previously categorized nor connected to illnesses in the oral cavity. This study hypothesized that these cryptic microorganisms could contribute to the modulation of oral microbiota present in health or disease (periodontitis and/or obstructive sleep apnea (OSA) patients). For this purpose, the presence and correlation among these cultivable cryptic oral microorganisms were identified, and their possible role in both conditions was determined. Data from oral samples of individuals with or without periodontitis and with or without OSA were obtained from a previous study. Demographic data, clinical oral characteristics, and genera and species of cultivable cryptic oral microorganisms identified by MALDI-TOF were recorded. The data from 75 participants were analyzed to determine the relative frequencies of cultivable cryptic microorganisms' genera and species, and microbial clusters and correlations tests were performed. According to periodontal condition, dental-biofilm-induced gingivitis in reduced periodontium and stage III periodontitis were found to have the highest diversity of cryptic microorganism species. Based on the experimental condition, these findings showed that there are genera related to disease conditions and others related to healthy conditions, with species that could be related to different chronic diseases being highlighted as periodontitis and OSA comorbidities. The cryptic microorganisms within the oral microbiota of patients with periodontitis and OSA are present as potential pathogens, promoting the development of dysbiotic microbiota and the occurrence of chronic diseases, which have been previously proposed to be common risk factors for periodontitis and OSA. Understanding the function of possible pathogens in the oral microbiota will require more research.

Preoperative topical benzoyl peroxide treatment is effective in reducing Cutibacterium acnes in shoulder surgery: a systematic review

BACKGROUND

Cutibacterium acnes (C acnes) colonization can have a significant impact on patients undergoing both arthroscopic and open shoulder surgery with regard to postoperative infection. Its resistance to standard preoperative skin preparations and prophylactic antibiotics has led to a need for a more targeted therapy. Topical benzoyl peroxide (BPO) has been used by dermatologists in the treatment for acnes due to its bactericidal and penetrative effects through the dermal layer. The aim of this systematic review is to review the effectiveness of topical BPO preoperatively in shoulder surgery in reducing C acnes colonization and postoperative infection.

METHODS

A review of the online databases Medline and Embase was conducted on December 15, 2021, according to Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. The review was registered prospectively in the PROSPERO database. Clinical studies reporting superficial and deep sample microbiology and postoperative complications were included. The studies were appraised using the revised Cochrane Risk of Bias 2 (ROB 2) tool for randomized studies and the Methodological Index for Non-Randomized Studies (MINORS) tool.

RESULTS

The search strategy identified 10 studies for inclusion (6 randomized control trials, 2 prospective cohort studies, and 2 case series), including a total of 482 patients. Seven studies were comparable, testing BPO against alternative standard skin preparations. Of the 10 studies, 7 showed a decrease in the load of C acnes on the skin and/or deep tissues, of which 6 demonstrated statistical significance. Men were shown to have a statistically significant increase in the colonization rate of C acnes. Scheer et al (2021) demonstrated 4500 colony-forming units/mL in males and 900 colony-forming units/mL in females. In studies where the number of BPO applications was higher, BPO appeared more effective. Dizay et al demonstrated C acnes elimination in 78.9% with more than 1 application compared with 66.7% if only applied once. Three studies looked at the effectiveness of BPO during the operative timeline with 1 demonstrating its statistically significant effectiveness at reducing colonization 2 hours into the operation (P = .048).

CONCLUSION

BPO is effective as a topical treatment at reducing C acnes colonization before shoulder surgery. However, the relationship between duration of treatment, frequency of application, and gender requires further research.

Fast and Sensitive Multiplex Real-Time Quantitative PCR to Detect Cutibacterium Periprosthetic Joint Infections

Diagnosis of Cutibacterium periprosthetic joint infections (PJIs) is challenging due to a long cultivation time of up to 14 days. Faster culture-independent diagnosis would improve patient care with early and accurate treatment. Specific primers and probes were designed for Cutibacterium acnes, Cutibacterium avidum, and Cutibacterium granulosum and evaluated in a multiplex TaqMan real-time quantitative PCR (qPCR) format on 57 skin swabs and 20 culture-negative cerebrospinal fluid samples. The multiplex qPCR was tested in a PJI cohort of 41 sonication fluid samples from removed implants infected with different pathogens. All five culture-positive Cutibacterium PJIs were detected with the corresponding Cutibacterium-specific probe (100% positive percent agreement). The multiplex qPCR additionally detected C. avidum in two PJI sonication fluid samples that were diagnosed as Staphylococcus species infections according to culture (95% negative percent agreement). The new multiplex qPCR can provide a Cutibacterium PJI diagnosis within 1 day, allowing early and accurate antibiotic treatment. A prospective diagnostic trial in PJI with a high number of Cutibacterium species infections (shoulder PJI) is needed for further evaluation.

True infection or contamination in patients with positive Cutibacterium blood cultures-a retrospective cohort study

Cutibacterium is a genus often considered a contaminant when present in blood cultures, but it can also cause severe infections, especially related to implanted foreign materials. We investigated the incidence and features of patients with true Cutibacterium infection. Patients with positive Cutibacterium blood cultures between the years 2015-2020 in southern Sweden were identified through microbiology records and medical records were studied retrospectively. Cutibacterium isolates were species determined using MALDI-TOF MS. Patients were classified as having true infection or contamination according to a definition considering both clinical and microbiological features and these groups were compared. A total of 313 episodes of positive Cutibacterium blood cultures were identified in 312 patients. Of these, 49 (16%, corresponding to an incidence of 6 cases per million inhabitants per year) were classified as true infections. The most common species was Cutibacterium acnes (87%), and the majority were elderly men with comorbidities. Patients with true Cutibacterium infection often had an unknown focus of infection (n = 21) or a focus in the respiratory tract (n = 18). We identified one episode of ventriculo-peritoneal shunt infection, three episodes of aortic stent-graft infection, and one episode of infective endocarditis. Two patients, where Cutibacterium was isolated at the site of infection, had only one positive blood culture. The finding of positive Cutibacterium blood cultures should not always be considered contamination. Definitions of true Cutibacterium bacteremia with a demand that more than one blood culture must be positive may miss true infections.

Multidrug-resistant Cutibacterium avidum isolated from patients with acne vulgaris and other infections

OBJECTIVES

Cutibacterium avidum, a human skin bacterium, rarely causes infectious diseases. It has been recently shown that C. acnes, another member of the genus Cutibacterium, acts as an opportunistic pathogen in surgical site infections. However, the antimicrobial susceptibility and pathogenicity of C. avidum remain unknown. Here, we investigated the epidemiological features of C. avidum.

RESULTS

C. avidum strains were isolated from patients with acne vulgaris (29 strains) and patients with other infections (12 strains). Antimicrobial susceptibility testing showed clarithromycin and clindamycin resistance in 65.9% of the tested strains (27/41). In addition, ciprofloxacin resistance was found in 34.1% of the strains (14/41), and 13 of those strains additionally exhibited resistance to both macrolides and clindamycin. Notably, the macrolides-clindamycin resistance gene erm(X) was found on the chromosomes of 92.6% (25/27) of the clindamycin-resistant strains and may be prevalent owing to transmission among C. avidum strains. Ciprofloxacin-resistant strains developed amino acid substitutions in GyrA owing to the use of antimicrobial agents. Pulsed-field gel electrophoresis (PFGE) analysis revealed that only a few strains exhibited 100% similarity. Additionally, no clustering associated with antimicrobial resistance, biofilm-forming ability, and type of infection was observed.

CONCLUSIONS

Our study revealed that erm(X) may be frequently disseminated in C. avidum, and multidrug-resistant C. avidum strains may colonize the skin of patients with acne vulgaris and patients with other infections. Therefore, the prevalence of multidrug-resistant C. avidum and the use of antimicrobial agents for the treatment of acne vulgaris and other infections associated with C. avidum should be monitored.

Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes

In 2016, a new species name Cutibacterium acnes was coined for the well-documented species, Propionibacterium acnes, one of the most successful and clinically important skin commensals. The nomenclatural changes were brought about through creation of the genus Cutibacterium, when a group of propionibacteria isolates from the skin were transferred from the genus Propionibacterium and placed in the phylum Actinobacteria. Almost simultaneously, the discovery of two novel species of Cutibacterium occurred and the proposal of three subspecies of C. acnes were reported. These dramatic changes that occurred in a long-established taxon made it challenging for the non-specialist to correlate the huge volume of hitherto published work with current findings. In this review, we aim to correlate the eco-specificity and pathophysiological properties of these newly circumscribed taxa. We envisage that this information will shed light on the pathogenic potential of new isolates and enable better assessment of their clinical importance in the foreseeable future. Currently, five species are recognized within the genus: Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, Cutibacterium modestum (previously, "Propionibacterium humerusii"), and Cutibacterium namnetense. These reside in different niches reflecting their uniqueness in their genetic makeup. Their pathogenicity includes acne inflammation, sarcoidosis, progressive macular hypomelanosis, prostate cancer, and infections (bone, lumbar disc, and heart). This is also the case for the three newly described subspecies of C. acnes, which are C. acnes subspecies acnes (C. acnes type I), subspecies defendens (C. acnes type II), and subspecies elongatum (C. acnes type III). C. acnes subspecies acnes is related to inflamed acne and sarcoidosis, while subspecies defendens to prostate cancer and subspecies elongatum to progressive macular hypomelanosis. Because the current nomenclature is based upon polyphasic analyses of the biochemical and pathogenic characteristics and comparative genomics, it provides a sound basis studying the pathophysiological roles of these species.

Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors

Cutibacterium acnes is a member of the skin microbiota found predominantly in regions rich in sebaceous glands. It is involved in maintaining healthy skin and has long been considered a commensal bacterium. Its involvement in various infections has led to its emergence as an opportunist pathogen. Interactions between C. acnes and the human host, including the human skin microbiota, promote the selection of C. acnes strains capable of producing several virulence factors that increase inflammatory capability. This pathogenic property may be related to many infectious mechanisms, such as an ability to form biofilms and the expression of putative virulence factors capable of triggering host immune responses or enabling C. acnes to adapt to its environment. During the past decade, many studies have identified and characterized several putative virulence factors potentially involved in the pathogenicity of this bacterium. These virulence factors are involved in bacterial attachment to target cells, polysaccharide-based biofilm synthesis, molecular structures mediating inflammation, and the enzymatic degradation of host tissues. C. acnes, like other skin-associated bacteria, can colonize various ecological niches other than skin. It produces several proteins or glycoproteins that could be considered to be active virulence factors, enabling the bacterium to adapt to the lipophilic environment of the pilosebaceous unit of the skin, but also to the various organs it colonizes. In this review, we summarize current knowledge concerning characterized C. acnes virulence factors and their possible implication in the pathogenicity of C. acnes.

Low prevalence of Cutibacterium acnes in prostatic tissue biopsies in a French hospital

We evaluated the Cutibacterium acnes prevalence in prostatic biopsies and characterized the strains at a molecular level. 18 out of 36 biopsies (50%) were sterile after seven days in culture. C. acnes was observed in only two biopsies. Its prevalence was low (5.6%). Finally, the molecular characterization revealed diverse clusters including phylotypes IA₁, IB and II.