Clinical significance of Propionibacterium acnes recovered from blood cultures: analysis of 524 episodes. J Clin Microbiol. 2011;49:1598-1601. [PMID: 21325550 DOI: 10.1128/jcm.01842-10]

Whole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates

Introduction

Cutibacterium acnes can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are C. acnes strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results.

Methods

In the present study, we prospectively collected C. acnes strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality.

Results

Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups.

Discussion

Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits.

Microbial growth on temporary pacemaker leads post-TAVR: pathogen spectrum and clinical implications

BACKGROUND AND OBJECTIVE

Transcatheter aortic valve replacement (TAVR) is an established treatment option for patients with symptomatic severe aortic stenosis across all stages of surgical risk. Rapid pacing during the procedure and the risk for the occurrence of conduction disturbances after TAVR requires the pre-interventional insertion of a temporary pacemaker (TP). However, this approach poses risks, including the risk of infection. For this reason, the following study aimed to investigate microbial growth on temporary pacemaker leads and its association with outcome post-TAVR and to identify associated pathogens and related risk factors.

METHODS

A prospective study was conducted including 344 patients undergoing TAVR at the Heart Centre Bonn. Of these, 97 patients did not require TP leads as they already had permanent pacemakers; this group was considered as comparison group. The TP leads of the remaining 247 patients were removed, sonicated, and cultured to investigate bacterial growth over a period of 14 days. Finally, we compared patients without microbial growth (n = 184) and patients with microbial growth (n = 63). The primary endpoint of the study was 30-day all-cause mortality, secondary endpoints were periprocedural infections, the length of the postprocedural hospital stay, 30-day major vascular complications and the 30-day stroke rate.

RESULTS

The majority of cases (74.5%) showed no bacterial growth. In the remaining cases (25.5%), diverse microorganisms were identified, mostly non-pathogenic bacteria. The statistical analysis revealed no significant differences between groups according to microbial growth in terms of 30-day mortality (p = 0.446), postprocedural hospital stay (p = 0.401), periprocedural infections (p = 0.434), 30-day major vascular complications (p = 1.0), and 30-day stroke rate (p = 1.0). Notably, the timing of sheath insertion was significantly associated with microbial growth; sheath placement more than 2 days prior to the procedure was associated with a significantly higher risk of microbial growth (OR: 2.1; 95% CI 1.1-4.3) (p = 0.030).

CONCLUSIONS

The presence of temporary leads does not significantly impact clinical outcomes, irrespective of bacterial growth on the lead. However, the timing and duration of sheath placement plays a crucial role in contamination incidence. Thus, temporary leads/sheaths should be placed shortly before the procedure and removed promptly to reduce the risk of contamination/infection.

The operational and financial impact of adding anaerobic screening of platelets

BACKGROUND AND OBJECTIVES

We evaluated the operational and safety impact of implementing anaerobic culture screening of apheresis and pooled platelets at the American Red Cross on the already established use of the aerobic culture screening of each donation performed no sooner than 24 h following collection.

MATERIALS AND METHODS

Platelets were screened for bacterial contamination with the BACT/ALERT 3D® (bioMérieux, Durham, NC) microbial detection testing system. The addition of anaerobic culture to the already existing aerobic culture resulted in sampling an additional 8-10 mL from each donation.

RESULTS

Implementation of anaerobic testing resulted in an approximate 3.5-fold increased rate of False Positive BACT/ALERT alarms. There was a modest increase in the rate of True Positive alarms of 1.4-fold with increased detection of Klebsiella and Propionibacterium species, including Cutibacterium acnes. In addition, there was an approximate 3.5-fold increase rate of False Positives and a 13.5-fold increase rate of Indeterminates, the majority (~57%) were due to Cutibacterium acnes. The combined costs and lost revenue associated with adding anaerobic screening increased by ~$1,000,000/year due to testing cost and product discards.

CONCLUSION

The addition of anaerobic culture to aerobic culture to the original donation (without the introduction of sampling delay) resulted in a significant increase in the rate of alerts. The 40% increased rate of True Positive alarms may have modestly improved platelet safety. However, there was a disproportionate increase in the rate of False Positive and Indeterminate bacterial culture alarms, which added substantial cost and overall loss of platelet products.

Infective endocarditis: prevention strategy and risk factors in an animal model

INTRODUCTION

Infective endocarditis is a serious infection of the endocardium, especially the heart valves, which is associated with a high mortality rate. It generally occurs in patients with altered and abnormal cardiac architecture combined with exposure to bacteria from trauma and other potentially high-risk activities with transient bacteremia.

Prospective Study of the Detection of Bacterial Pathogens in Pediatric Clinical Specimens Using the Melting Temperature Mapping Method

The melting temperature (Tm) mapping method is a novel technique that uses seven primer sets without sequencing to detect dominant bacteria. This method can identify pathogenic bacteria in adults within 3 h of blood collection without using conventional culture methods. However, no studies have examined whether pathogenic bacteria can be detected in clinical specimens from pediatric patients with bacterial infections. Here, we designed a new primer set for commercial use, constructed a database with more bacterial species, and examined the agreement rate of bacterial species in vitro. Moreover, we investigated whether our system could detect pathogenic bacteria from pediatric patients using the Tm mapping method and compared the detection rates of the Tm mapping and culture methods. A total of 256 pediatric clinical specimens from 156 patients (94 males and 62 females; median age, 2 years [<18 years of age]) were used. The observed concordance rates between the Tm mapping method and the culture method for both positive and negative samples were 76.4% (126/165) in blood samples and 79.1% (72/91) in other clinical specimens. The Tm mapping detection rate was higher than that of culture using both blood and other clinical specimens. In addition, using the Tm mapping method, we identified causative bacteria in pediatric clinical specimens quicker than when using blood cultures. Hence, the Tm mapping method could be a useful adjunct for diagnosing bacterial infections in pediatric patients and may be valuable in antimicrobial stewardship for patients with bacterial infections, especially in culture-negative cases. IMPORTANCE This study provides novel insights regarding the use of the melting temperature (Tm) mapping method to identify the dominant bacteria in samples collected from pediatric patients. We designed a new set of primers for commercial use and developed a database of different bacteria that can be identified using these primers. We show that the Tm mapping method could identify bacteria from blood samples and other clinical specimens. Moreover, we provide evidence that the Tm mapping method has a higher detection rate than that of the culture-based methods and can achieve a relatively high agreement rate. We believe that our study makes a significant contribution to this field because rapid identification of the source of bacterial infections can drastically improve patient outcomes and impede the development of antibiotic-resistant bacteria.

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.

Bacterial pericarditis and empyema caused by Cutibacterium acnes in a patient with metastatic lung cancer

Bacterial pericarditis and empyema due to Cutibacterium acnes has rarely been reported. C.acnes, a normal component of human skin flora, is often considered a contaminant when isolated from body fluids and thus cases may be underreported. We report the first case of concurrent purulent pericarditis and empyema caused by C. acnes in a patient with newly diagnosed metastatic lung cancer. Our patient underwent pericardial window creation and placement of pericardial and bilateral chest tubes and was successfully treated with culture directed antibiotic therapy.

Prevalence and Predictors of Bacterial Contamination in Excisional Lymph Node Biopsies: Implications for Diagnosis and Management

Routine tissue handling exposes lymph node specimens to microbial contamination that can confound microbiological culture results and interfere with diagnosis. The scope and impact of this problem remain poorly understood. We combined over 13 years of lymph node pathology, culture data, and patient records to define the prevalence, predisposing factors, microbiology, and clinical management of false-positive lymph node cultures at a large academic medical center. Nearly one third (31.9%) of 216 cultured lymph nodes yielded bacterial growth. Approximately 90% of positive bacterial cultures grew 1 of 2 common skin-resident taxa-coagulase-negative Staphylococcus and Cutibacterium acnes-with well-documented predispositions for contamination in other clinical settings. Lymph nodes excised from axillary, cervical, and inguinal regions yielded higher positive culture rates than nodes excised from the mediastinum, suggesting proximity to the skin surface may increase contamination risk. Accordingly, cultures from thoracoscopic pulmonary resections displayed contamination rates over 5-fold lower than those from percutaneously accessed lymph nodes. Lymph nodal tissue allocated for culture in the operating room yielded unexpectedly high contamination rates, significantly higher than cultures sent from the frozen section processing area. A significant minority of contamination events were noted in the clinical record and prompted antibiotic therapy on multiple occasions. Collectively, our results illuminate the risk factors contributing to bacterial contamination and argue that routine lymph node bacterial cultures provide minimal clinical benefit for adult patients. This widespread bacterial contamination also warrants cautious implementation of increasingly sensitive molecular microbiology tools for excised tissues.

Pleural and Pericardial Infection Due to Cutibacterium acnes in a Splenectomized Patient: A Case Report of an Underreported Systemic Infection

Infectious pericarditis does not always present with all the classic findings. Some of the traditional signs of fever, pleuritic chest pain, and frictional rub may be missing. This presents a diagnostic challenge, thus clinical suspicion is important. The most common cause of infectious pericarditis is viral. However, bacterial pericarditis may occur with severe complications such as constrictive pericarditis, pericardial effusion, cardiac tamponade, left ventricular pseudoaneurysm, and aortic mycotic aneurysm. The purpose of this presentation is to increase awareness of Cutibacterium acnes (C. acnes) as a cause of bacterial pericarditis. This case report highlights C. acnes as a prevalent cause of both pleural and pericardial infections. The diagnosis can be challenging, considering that this bacterium is difficult to isolate, slow growing, and causes indolent illness. Prolonged incubation time may be required. In addition to the more traditional causes of bacterial pericarditis, namely Staphylococcus and Streptococcus species, C acnes appears to play an important role. It should not be considered a contaminant as it may require further investigation.

Persistent Cutibacterium (Formerly Propionibacterium) acnes Bacteremia and Refractory Endocarditis in a Patient with Retained Implantable Pacemaker Leads

Cutibacterium (formerly Propionibacterium) acnes (C. acnes) is a commensal bacteria commonly found on the human skin and in the mouth. While the virulence of C. acnes is low in humans, it does produce a biofilm and has been identified as an etiologic agent in a growing number of implant-associated infections. C. acnes infections can prove diagnostically challenging as laboratory cultures can often take greater than 5 days to yield positive results, which are then often disregarded as contaminant. Patients with recurrent bacteremia in the setting of implantable devices warrant further studies to evaluate for an associated valvular or lead endocarditis. The patient in this report demonstrates how cardiac device-related endocarditis secondary to C. acnes can be overlooked due to the indolent nature of this pathogen. This patient presented with an implanted cardiac pacemaker device, as well as retained leads from a prior pacemaker. Transesophageal echocardiography was required to confirm the diagnosis in the setting of multiple positive blood cultures and negative transthoracic echocardiograms over a period of 4 years. The purpose of this report is to highlight the difficulties encountered in diagnosing C. acnes endocarditis in a patient with a cardiac implantable electronic device and persistently positive blood cultures.

Cardiac Tamponade Caused by Cutibacterium acnes: An Updated and Comprehensive Review of the Literature

Bacterial pericarditis is a critical diagnosis caused by a wide range of organisms including Streptococcus pneumoniae and other anaerobic organisms like Cutibacterium acnes which has been gaining more importance as a causative organism. Cutibacterium species are Gram-positive microaerophilic rods that constitute part of the normal flora of skin and mucosal membranes. The incidence of pericarditis caused by this organism is underreported as it is often dismissed as a skin flora contaminant. However, if left untreated, Cutibacterium acnes can cause pericarditis with serious complications. In this paper, we present a comprehensive review of the literature regarding pericarditis caused by Cutibacterium acnes along with a case presentation from our institution. In our institution, a 20-year-old man with history of atrial septal defect presented with chest pain radiating to the back along with symptoms of upper respiratory tract infection including headaches and myalgia. Electrocardiogram was remarkable for diffuse low-voltage waves. Echocardiography revealed a large pericardial effusion with tamponade features. Pericardiocentesis drained 1.2 L of milky fluid. Pericardial fluid analysis grew Cutibacterium acnes after being cultured for 8 days. The patient received 3 weeks of IV penicillin followed by 3 weeks of oral amoxicillin along with nonsteroidal anti-inflammatory agents and colchicine with no recurrence. Pericarditis caused by Cutibacterium acnes requires a high clinical suspicion since isolation of this organism can be dismissed as a skin flora contaminant. Literature review reveals that this infection may be underdiagnosed and underreported. Prompt diagnosis may lead to timely initiation of antibiotics which can help prevent devastating complications like constrictive pericarditis. Prospective studies are needed to evaluate the true incidence and prevalence of this disease.

Anaerobic blood culture positivity at a University Hospital in Hungary: A 5-year comparative retrospective study

Anaerobic bacteremia (AB) is usually detected in about 0.5-13% of positive blood cultures. The aim of this study was to determine prevalence of anaerobic bacteremia over a 5-year period (2013-2017), to identify current trends at our University Hospital and to compare the results to those in a similar study (2005-2009) in the same region. During the study period, an average of 23,274 ± 2,756 blood cultures were received per year. Out of the positive blood cultures, 3.3-3.6% (n = 423) yielded anaerobic bacteria, representing 3.5-3.8 anaerobic isolates/1000 blood culture bottles (including both aerobic and anaerobic bottles) per year for hospitalized patients. Mean age of affected patients was 70-73 years (range: 18-102 years) with a male-to-female ratio: 0.60. Most isolated anaerobes were Cutibacterium spp. (54.0 ± 8.5%; n = 247), while among anaerobes other than Cutibacterium spp., Bacteroides and Parabacteroides and Clostridium spp. were the most prevalent. Blood culture time-to-positivity (TTP) for clinically relevant bacteria was 31.4 ± 23.4 h, while for Cutibacterium spp., TTP values were 112.9 ± 37.2 h (p < 0.0001). In conclusion, the prevalence of anaerobic bacteremia should be determined on institutional basis.

Late Spinal Implant Infection caused by Cutibacterium acnes

Cutibacterium spp. have been frequently associated with foreign-body material infections. The vast majority of these infections occur via the exogenous route. Rarely, haematogenous infections occur, possibly seeding from pilosebaceous glands. A late spinal implant-associated infection is presented in this case report, and the possible sources of haematogenous seeding are discussed.

[Febrile myalgia revealing Propionibacterium acnes endocarditis]

INTRODUCTION

Propionibacterium acnes endocarditis is rare and difficult to diagnose. We report a case of Propioniacterium acnes endocarditis revealed by a lower limb fasciitis.

CASE REPORT

A 54-year-old patient presented with recurrent febrile myalgia of the lower limbs, that appeared three years after an aortic surgery (aortic valve sparing reimplentation and ascending aortic prosthesis implantation). Computer tomography showed fasciitis of both legs. Positron emission tomography showed ¹⁸Fluorodeoxyglucose intake of the aortic prosthesis and in muscles of the lower limbs. Ten days after blood sample drawing, cultures showed the presence of Propionibacterium acnes. The aortic prosthesis was surgically removed, whose culture confirmed infection by Propionibacterium acnes. The diagnosis of infective endocarditis revealed by lower limb emboli was made. Evolution was favorable.

CONCLUSION

In patients with vascular prostheses, Propionibacterium acnes infection must be evoked face to an atypical inflammatory process. Very prolonged blood culture incubation is needed to identify the pathogen.

From trash to treasure: detecting unexpected contamination in unmapped NGS data

Background

Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Typically the amount of reads that correctly maps to the reference genome ranges between 70% and 90%, leaving in some cases a consistent fraction of unmapped sequences. This ’misalignment’ can be ascribed to low quality bases or sequence differences between the sample reads and the reference genome. Investigating the source of the unmapped reads is definitely important to better assess the quality of the whole experiment and to check for possible downstream or upstream ’contamination’ from exogenous nucleic acids.

Results

Here we propose DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. DecontaMiner builds an offline HTML page containing summary statistics and plots. The latter are obtained using the state-of-the-art D3 javascript libraries. DecontaMiner has been mainly used to detect contamination in human RNA-Seq data. The software is freely available at http://www-labgtp.na.icar.cnr.it/decontaminer.

Conclusions

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2684-x) contains supplementary material, which is available to authorized users.

Clinical impact of extended blood culture examination: Too much of a good thing

Blood culture is the most critical examination for diagnosing bacterial infections. The longer the blood culture incubation period, the higher the chances of identifying bacterial strains. However, unnecessary extension of the incubation period can burden the capacity of the instrument and merely result in the detection of contaminant bacteria having no clinical significance. This study aimed to optimize the blood culture incubation period using the currently available continuous-monitoring automated blood culture instrument. This was a 2-year retrospective study performed at Osaka University Hospital (January 1, 2016 to December 31, 2017). The BD BACTEC™ FX blood culture system (Becton Dickinson, Sparks, MD, USA) and BD BACTEC™ Plus series blood culture bottles were used. All blood cultures were incubated for more than 12 consecutive days. We reviewed the clinical data of cases that tested positive between 6 and 12 days of incubation. During the study period, 14,822 sets of blood culture were drawn. Of 1751 sets testing positive, 95.7% (1665 sets) became positive within 5 days of incubation. The overall contamination rate (false positives) after 6 days of incubation was 80.2% (69/86 sets). Based on the positive blood culture results, antimicrobials were changed in 7.0% (6/86) of the sets, and a diagnosis of infectious disease was made in only one case. There was no death associated with the extended blood culture results. In conclusion, the clinical impact of extended blood culture incubation for 6 days or more was limited, and a routine extension of the incubation period might be unnecessary.

Silent Native-valve Endocarditis Caused by Propionibacterium acnes

We describe a rare case of Propionibacterium acnes native-valve endocarditis that silently progressed in a 67-year-old man with hybrid dialysis. The patient was scheduled for kidney transplantation, and pre-operative investigation incidentally detected a vegetative structure at his native mitral valve that had increased in size. He underwent cardiac surgery and P. acnes was detected in cultures of a resected cardiac valve specimen and blood. This case highlights that P. acnes can silently cause infective endocarditis in a native-valve, and that physicians should consider the possibility of infection when P. acnes is isolated in blood cultures.

Constrictive pericarditis caused by Cutibacterium (Propionibacterium) acnes: A case report and review of literature

Constrictive and effusive-constrictive pericarditis are rare cardiac disorders. Only rarely are the conditions caused by purulent infection, and even more infrequently by anaerobe bacteria. We describe a case of constrictive – and effusive-constrictive pericarditis due to Cutibacterium (formerly Propionibacterium) acnes in a 75-year old, immunocompetent and previously healthy patient without any predisposition. The patient was successfully treated with subtotal pericardiectomy and beta-lactam antibacterials. C. acnes was the only infectious agent recovered from samples of cultured pericardial tissue.

C. acnes is a microaerophilic, Gram-positive anaerobic bacillus that is a part of the normal flora. In symptomatic patients, however, positive samples should be considered as clinically relevant and not dismissed as contamination. Due to the low virulence, the capability of adherence and biofilm formation of C. acnes, diagnosing C. acnes constrictive pericarditis may be difficult. In the context of compatible symptoms, the incubation time of clinical samples should be prolonged or supplemented by polymerase chain reaction techniques. Parenteral beta-lactam antibacterials are considered the drugs of choice.

Severe constrictive and effusive-constrictive pericarditis caused by C. acnes is rare, but can be seen even in otherwise healthy patients. Prolonged incubation time and polymerase chain reaction techniques may be required in order to confirm diagnosis.

Utility of strain typing of Propionibacterium acnes in central nervous system and prosthetic joint infections to differentiate contamination from infection: a retrospective cohort

The study aimed to retrospectively assess if strain typing of Propionibacterium acnes could help to distinguish between infection and contamination in isolates recovered from the central nervous system (CNS) and prosthetic joints (PJs). This was a retrospective cohort of all Propionibacterium species isolates from the Barnes-Jewish Hospital (St Louis, MO, USA) clinical microbiology laboratory from 2011 to 2014. Available frozen isolates were recovered, and strain type (IA-1, IA-2, IB, II, III, or nontypeable class A or B) was determined via polymerase chain reaction (PCR)-based methods. For CNS isolates, P. acnes was considered pathogenic if treating physicians administered ≥7 days of directed antibiotic therapy against P. acnes. During the study period, Propionibacterium species was isolated from clinical cultures 411 times. 152 isolates were available for analysis. Of the 152 isolates, 140 were confirmed to be P. acnes, 61 of which were from the CNS (45 contaminants, 16 infections). Strain type IA-1 was more common (50.0%, 8 out of 16) among CNS infections than among contaminants (22.2%, 10 out of 45). For PJ isolates 61.3% (19 out of 31) met the criteria for infection. The predominant strain type for CNS infection was IA-1 and for PJ isolates, IB. Strain type IA-1 was isolated more often in patients with CNS infections, which may indicate a predilection of this strain type to cause CNS infection. Future research should prospectively evaluate strain typing as a means of assisting in the diagnosis of CNS infections and confirm our findings.

Clinical characteristics and antimicrobial susceptibilities of anaerobic bacteremia in an acute care hospital

This study investigated the clinical features of anaerobic bacteraemia in an acute-care hospital, and evaluated the antimicrobial susceptibility of these isolates to commonly available antibiotics. Microbiological and epidemiological data from 2009 to 2011were extracted from the laboratory information system and electronic medical records. One hundred and eleven unique patient episodes consisting of 116 anaerobic isolates were selected for clinical review and antibiotic susceptibility testing. Susceptibilities to amoxicillin-clavulanate, clindamycin, imipenem, metronidazole, moxifloxacin, penicillin and piperacillin-tazobactam were performed using Etest strips with categorical interpretations according to current CLSI breakpoints. Metronidazole-resistant and carbapenem-resistant anaerobic Gram-negative bacilli were screened for the nim and cfiA genes. Clinical data was obtained retrospectively from electronic medical records. During the 3 year period, Bacteroides fragilis group (41%), Clostridium species (14%), Propionibacterium species (9%) and Fusobacterium species (6%) were the most commonly isolated anaerobes. Patients with anaerobic bacteraemia that were included in the study were predominantly above 60 years of age, with community-acquired infections. The most commonly used empiric antibiotic therapies were beta-lactam/beta-lactamase inhibitor combinations (44%) and metronidazole (10%). The crude mortality was 25%, and appropriate initial antibiotic therapy was not significantly associated with improved survival. Intra-abdominal infections (39%) and soft-tissue infections (33%) accounted for nearly three-quarters of all bacteraemia. Antibiotics with the best anaerobic activity were imipenem, piperacillin-tazobactam, amoxicillin-clavulanate and metronidazole, with in-vitro susceptibility rates of 95%, 95%, 94% and 92% respectively. Susceptibilities to penicillin (31%), clindamycin (60%) and moxifloxacin (84%) were more variable. Two multidrug-resistant isolates of Bacteroides species were positive for nim and cfiA genes respectively, while another two imipenem-resistant Fusobacterium species were negative for cfiA genes. This study demonstrated that anaerobic bacteraemia in our patient population was predominantly associated with intra-abdominal and soft-tissue infections. Overall antibiotic resistance was high for penicillin and clindamycin, and the presence of emerging resistance to carbapenems and metronidazole warrants further monitoring.

Quantification of the antibody response to Propionibacterium acnes in a patient with prosthetic valve endocarditis: - a case report

Background

The isolation of Propionibacterium acnes in blood cultures is often considered a contaminant. On rare occasions, P. acnes can cause severe infections, including endocarditis and intravascular prosthesis-associated infections. To evaluate the discrimination between a contaminant and a clinically relevant infection we used an Ouchterlony test system to quantify the antibody response to P. acnes in a patient with a proven P. acnes endocarditis.

Case presentation

We report on a 64-year-old Caucasian man who developed P. acnes endocarditis four years following a composite valve-graft conduit replacement of the aortic root. Bacterial growth in blood cultures was detected after an incubation period of 6 days. However, the antibody titer to P. acnes was 1:8 at the time of diagnosis and declined slowly thereafter over 2½ years. The patient’s response to the antibiotic treatment was excellent, and no surgical re-intervention was necessary.

Conclusion

The working hypothesis of infective endocarditis can be substantiated by serologic testing, which, if positive, provides one additional minor criterion. Moreover, quantification of the antibody response to P. acnes, though not specific, may assist in the differentiation between contaminants and an infection. This quantification may have implications for the patient management, e.g. indication for and choice of the antibiotic therapy.

Cardiovascular Implantable Electronic Device Infections due to Propionibacterium Species

INTRODUCTION

Propionibacterium species are part of the normal skin flora and often considered contaminants when identified in cultures. However, they can cause life-threatening infections, including prosthetic cardiovascular device infections. Clinical presentation and management of cardiovascular implantable electronic device (CIED) infection due to Propionibacterium species has not been well described.

METHODS

Retrospective review of all cases of CIED infection due to Propionibacterium species admitted to Mayo Clinic between January 1, 1990 and December 31, 2014. Patient charts were reviewed for clinical, microbiological, and imaging data. Descriptive analysis was performed.

RESULTS

We identified 14 patients with CIED infection due to Propionibacterium species, accounting for 2.3% of all CIED infections. Patients were predominantly male (n = 12, 86%). The median age at admission was 58.5 years (range 22-83). Twelve patients had implantable cardioverter defibrillators (ICDs) and two had permanent pacemaker systems. Twelve patients had generator pocket infection (86%). Two patients met clinical criteria for CIED-related infective endocarditis. Median time between last device manipulation and infection was 9 months (range 1-98). All patients were treated with complete device removal and antibiotic therapy. Six-month follow-up data were available for 10 patients (71%), with no relapses documented.

CONCLUSION

CIED infections due to Propionibacterium species accounted for 2.3% of all device infections over a 25-year period. The most common infectious syndrome was generator pocket infection with delayed onset. There was an unanticipated predominance of ICDs in this cohort. Cure was achieved in all cases with complete device removal and antibiotic therapy.

Identification of low abundance microbiome in clinical samples using whole genome sequencing

Identifying the microbiome composition from primary tissues directly affords an opportunity to study the causative relationships between the host microbiome and disease. However, this is challenging due the low abundance of microbial DNA relative to the host. We present a systematic evaluation of microbiome profiling directly from endoscopic biopsies by whole genome sequencing. We compared our methods with other approaches on datasets with previously identified microbial composition. We applied this approach to identify the microbiome from 27 stomach biopsies, and validated the presence of Helicobacter pylori by quantitative PCR. Finally, we profiled the microbial composition in The Cancer Genome Atlas gastric adenocarcinoma cohort.

Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen

Propionibacterium acnes is known primarily as a skin commensal. However, it can present as an opportunistic pathogen via bacterial seeding to cause invasive infections such as implant-associated infections. These infections have gained more attention due to improved diagnostic procedures, such as sonication of explanted foreign materials and prolonged cultivation time of up to 14 days for periprosthetic biopsy specimens, and improved molecular methods, such as broad-range 16S rRNA gene PCR. Implant-associated infections caused by P. acnes are most often described for shoulder prosthetic joint infections as well as cerebrovascular shunt infections, fibrosis of breast implants, and infections of cardiovascular devices. P. acnes causes disease through a number of virulence factors, such as biofilm formation. P. acnes is highly susceptible to a wide range of antibiotics, including beta-lactams, quinolones, clindamycin, and rifampin, although resistance to clindamycin is increasing. Treatment requires a combination of surgery and a prolonged antibiotic treatment regimen to successfully eliminate the remaining bacteria. Most authors suggest a course of 3 to 6 months of antibiotic treatment, including 2 to 6 weeks of intravenous treatment with a beta-lactam. While recently reported data showed a good efficacy of rifampin against P. acnes biofilms, prospective, randomized, controlled studies are needed to confirm evidence for combination treatment with rifampin, as has been performed for staphylococcal implant-associated infections.

Microbiota and the gut-liver axis: Bacterial translocation, inflammation and infection in cirrhosis

Liver disease is associated with qualitative and quantitative changes in the intestinal microbiota. In cirrhotic patients the alteration in gut microbiota is characterized by an overgrowth of potentially pathogenic bacteria (i.e., gram negative species) and a decrease in autochthonous familiae. Here we summarize the available literature on the risk of gut dysbiosis in liver cirrhosis and its clinical consequences. We therefore described the features of the complex interaction between gut microbiota and cirrhotic host, the so called “gut-liver axis”, with a particular attention to the acquired risk of bacterial translocation, systemic inflammation and the relationship with systemic infections in the cirrhotic patient. Such knowledge might help to develop novel and innovative strategies for the prevention and therapy of gut dysbiosis and its complication in liver cirrhosis.

Pacemaker endocarditis caused by Propionibacterium acnes in an adult patient with Ebstein's anomaly: a report of a rare case

We report a rare case of a Brazilian adult woman with Ebstein's Anomaly who presented with pacemaker endocarditis caused by Propionibacterium acnes. Ebstein's Anomaly is a rare congenital malformation of the heart. Infective endocarditis is defined as an infection of heart valves, of the mural endocardium, of a septal defect, or of a cardiac electronic implantable device. Propionibacterium acnes is a skin commensal bacterium, that is usually considered as a contaminant, but can, on rare occasions, cause serious infections including endocarditis of prosthetic valves, native valves and cardiac electronic implantable devices. Diagnosis was made after nearly two years of investigation by identification of the organism by the MALDI-TOF technique and transoesophageal echocardiogram. The patient was successfully treated with daptomycin and device removal. She remains free of endocarditis after 32 months of follow-up.

Antimicrobial susceptibility of clinical isolates of anaerobic bacteria in Ontario, 2010-2011

The local epidemiology of antimicrobial susceptibility patterns in anaerobic bacteria is important in guiding the empiric treatment of infections. However, susceptibility data are very limited on anaerobic organisms, particularly among non-Bacteroides organisms. To determine susceptibility profiles of clinically-significant anaerobic bacteria in Ontario Canada, anaerobic isolates from sterile sites submitted to Public Health Ontario Laboratory (PHOL) for identification and susceptibility testing were included in this study. Using the E-test method, isolates were tested for various antimicrobials including, penicillin, cefoxitin, clindamycin, meropenem, piperacillin-tazobactam and metronidazole. The MIC results were interpreted based on guidelines published by Clinical and Laboratory Standards Institute. Of 2527 anaerobic isolates submitted to PHOL, 1412 were either from sterile sites or bronchial lavage, and underwent susceptibility testing. Among Bacteroides fragilis, 98.2%, 24.7%, 1.6%, and 1.2% were resistant to penicillin, clindamycin, piperacillin-tazobactam, and metronidazole, respectively. Clostridium perfringens was universally susceptible to penicillin, piperacillin-tazobactam, and meropenem, whereas 14.2% of other Clostridium spp. were resistant to penicillin. Among Gram-positive anaerobes, Actinomyces spp., Parvimonas micra and Propionibacterium spp. were universally susceptible to β-lactams. Eggerthella spp., Collinsella spp., and Eubacterium spp. showed variable resistance to penicillin. Among Gram-negative anaerobes, Fusobacterium spp., Prevotella spp., and Veillonella spp. showed high resistance to penicillin but were universally susceptible to meropenem and piperacillin-tazobactam. The detection of metronidazole resistant B. fragilis is concerning as occurrence of these isolates is extremely rare. These data highlight the importance of ongoing surveillance to provide clinically relevant information to clinicians for empiric management of infections caused by anaerobic organisms.

Altered profile of human gut microbiome is associated with cirrhosis and its complications

BACKGROUND & AIMS

The gut microbiome is altered in cirrhosis; however its evolution with disease progression is only partly understood. We aimed to study changes in the microbiome over cirrhosis severity, its stability over time and its longitudinal alterations with decompensation.

METHODS

Controls and age-matched cirrhotics (compensated/decompensated/hospitalized) were included. Their stool microbiota was quantified using multi-tagged pyrosequencing. The ratio of autochthonous to non-autochthonous taxa was calculated as the cirrhosis dysbiosis ratio (CDR); a low number indicating dysbiosis. Firstly, the microbiome was compared between controls and cirrhotic sub-groups. Secondly, for stability assessment, stool collected twice within 6months in compensated outpatients was analyzed. Thirdly, changes after decompensation were assessed using (a) longitudinal comparison in patients before/after hepatic encephalopathy development (HE), (b) longitudinal cohort of hospitalized infected cirrhotics MELD-matched to uninfected cirrhotics followed for 30days.

RESULTS

244 subjects [219 cirrhotics (121 compensated outpatients, 54 decompensated outpatients, 44 inpatients) and 25 age-matched controls] were included. CDR was highest in controls (2.05) followed by compensated (0.89), decompensated (0.66), and inpatients (0.32, p<0.0001) and negatively correlated with endotoxin. Microbiota and CDR remained unchanged in stable outpatient cirrhotics (0.91 vs. 0.86, p=0.45). In patients studied before/after HE development, dysbiosis occurred post-HE (CDR: 1.2 to 0.42, p=0.03). In the longitudinal matched-cohort, microbiota were significantly different between infected/uninfected cirrhotics at baseline and a low CDR was associated with death and organ failures within 30days.

CONCLUSIONS

Progressive changes in the gut microbiome accompany cirrhosis and become more severe in the setting of decompensation. The cirrhosis dysbiosis ratio may be a useful quantitative index to describe microbiome alterations accompanying cirrhosis progression.

Propionibacterium acnes prosthetic valve endocarditis with abscess formation: a case report

BACKGROUND

Endocarditis due to Propionibacterium acnes is a rare disease. Scant data on treatment of these infections is available and is based on case reports only. If the disease is complicated by abscess formation, surgical intervention combined with an antibiotic therapy might improve clinical outcome. In some cases, cardiac surgeons are reluctant to perform surgery, since they consider the intervention as high risk. Therefore, a conservative therapy is required, with little, if any evidence to choose the optimal antibiotic. We report the first case of a successfully treated patient with P. acnes prosthetic valve endocarditis without surgery.

CASE PRESENTATION

We report the case of a 29-year-old patient with a prosthetic valve endocarditis and composite graft infection with abscess formation of the left ventricular outflow tract due to P. acnes. Since cardiac surgery was considered as high risk, the patient was treated intravenously with ceftriaxone 2 g qd and rifampin 600 mg bid for 7 weeks and was switched to an oral therapy with levofloxacin 500 mg bid and rifampin 600 mg bid for an additional 6 months. Two sets of blood cultures collected six weeks after completion of treatment remained negative. The patient is considered to be cured based on absence of clinical signs and symptoms, normal laboratory parameters, negative radiology scans and negative blood cultures, determined at site visits over two years after completion of treatment.

CONCLUSION

To our knowledge, this is the first successfully managed patient with P. acnes prosthetic valve endocarditis with abscess formation of the left ventricular outflow tract who was treated with antibiotics alone without a surgical intervention. A six month treatment with a rifampin and levofloxacin combination was chosen, based on the excellent activity against stationary-phase and adherent bacteria.

De Novo meningitis caused by Propionibacterium acnes in a patient with metastatic melanoma

Propionibacterium acnes is a known cause of postneurosurgical meningitis; however, it is rarely implicated in de novo meningitis. Herein we report a case of a 49-year-old male with de novo meningitis caused by P. acnes with metastatic melanoma as the only identified risk factor for his infection.

Multiple splenic nodules with fever: a case of splenic abscess due to Propionibacterium acnes

A 64-year-old man with a history of chronic lymphocytic leukemia (CLL) presented in the hematology department due to remarkable leukocytosis and progressing anemia. Ultrasound confirmed splenomegaly and plain computed tomography revealed multiple hypoattenuating areas in the large spleen. Following a clinical diagnosis of relapse of CLL, he underwent treatment with fludarabine, cyclophosphamide, and rituximab (FC-R). After five cycles of FC-R treatment, his leukocyte count and hemoglobin level were normalized, and the size of the spleen also decreased. He began to have intermittent high fever (38 °C), however, approximately 6 months after the initiation of FC-R treatment. The results of an interferon-gamma release assay were positive. (18)F-fluoro-2-deoxy-D-glucose positron emission tomography showed multiple areas of high-uptake in the spleen, which was unclear in other radiologic modalities. We performed a splenectomy for the high fever and to confirm the diagnosis. Tissue cultures of the infarcted area of spleen were positive for Propionibacterium acnes. After splenectomy, the patient's condition improved and there were no further episodes of fever. Until recently, three cases of splenic abscess caused by Propionibacterium acnes were reported. Here we present a fourth case of splenic abscess due to Propionibacterium acnes and review the literature.

Optimization of microbial screening for cord blood

BACKGROUND

Collection and processing of cord blood (CB) is associated with significant risk of contamination; hence standards mandate microbial screening of the final product. The sensitivity of current methods to evaluate the microbial content of CB is unknown, given the small volume tested and reduced sensitivity of pediatric bottles. Hence, this study was undertaken to evaluate an optimal microbial screening method.

STUDY DESIGN AND METHODS

CB was collected using a closed system then spiked with organisms at 1 or 10 colony-forming units (CFUs)/mL. Samples were screened using culture bottles (BacT/ALERT, bioMérieux; and BACTEC, Becton Dickinson). Several methods were evaluated with different combinations of inoculated bottles (adult vs. pediatric), sample types (plasma discard, red blood cell [RBC] discard, or final product), and sample volumes.

RESULTS

Of 94 cord blood units (CBUs) spiked with organisms before screening, 81% tested positive for contamination overall. Screening of CB in pediatric bottles resulted in equivalent detection rates on the BacT/ALERT and BACTEC systems (33% at 1 CFU/mL and 73% at 10 CFUs/mL, respectively). However, the pediatric bottle screen only detected 15% of obligate anaerobes. A combined fraction method showed superior detection (71%) compared to the plasma fraction (27%) and resulted in optimal anaerobic detection.

CONCLUSIONS

This study demonstrates that the optimal microbial screening method for CB includes testing a combination of discard fractions (plasma and RBCs) in addition to final product using an automated culture system. Inoculating a small sample of final product in a pediatric bottle is suboptimal for microbial detection and may lead to distribution of contaminated CB for transplantation.

A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an Urban Landscape

Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.

Facial nerve palsy caused by parotid gland abscess

Objectives:

We present the first report of methicillin-resistant Staphylococcus aureus and Propionibacterium acnes parotid abscesses complicated by facial nerve palsy. Facial nerve palsy secondary to parotid gland abscess is rare, with only eight previously reported cases.

Method:

Case reports and literature review concerning parotid abscess and facial nerve palsy presentation and management.

Case reports:

Within two months, two female patients presented with parotid gland abscess complicated by unilateral facial paralysis. Both were treated with intravenous antibiotics and surgery. In the first case, methicillin-resistant Staphylococcus aureus was cultivated, in the other, Propionibacterium acnes was found. In the first case, facial nerve function did not recover.

Conclusion:

Parotid gland abscess can lead to facial paralysis. Both methicillin-resistant Staphylococcus aureus and Propionibacterium acnes may be involved. Ultrasonography or computed tomography is recommended to exclude a parotid abscess in patients presenting with suppurative parotitis.