Sequence types of Staphylococcus epidermidis associated with prosthetic joint infections are not present in the laminar airflow during prosthetic joint surgery

Staphylococcus capitis: insights into epidemiology, virulence, and antimicrobial resistance of a clinically relevant bacterial species

SUMMARYStaphylococcus capitis is divided into two subspecies, S. capitis subsp. ureolyticus (renamed urealyticus in 1992; ATCC 49326) and S. capitis subsp. capitis (ATCC 27840), and fits with the archetype of clinically relevant coagulase-negative staphylococci (CoNS). S. capitis is a commensal bacterium of the skin in humans, which must be considered an opportunistic pathogen of interest particularly as soon as it is identified in a clinically relevant specimen from an immunocompromised patient. Several studies have highlighted the potential determinants underlying S. capitis pathogenicity, resistance profiles, and virulence factors. In addition, mobile genetic element acquisitions and mutations contribute to S. capitis genome adaptation to its environment. Over the past decades, antibiotic resistance has been identified for S. capitis in almost all the families of the currently available antibiotics and is related to the emergence of multidrug-resistant clones of high clinical significance. The present review summarizes the current knowledge concerning the taxonomic position of S. capitis among staphylococci, the involvement of this species in human colonization and diseases, the virulence factors supporting its pathogenicity, and the phenotypic and genomic antimicrobial resistance profiles of this species.

Resistome, mobilome, and virulome explored in clinical isolates derived from acne patients in Egypt: unveiling unique traits of an emerging coagulase-negative Staphylococcus pathogen

Coagulase-negative staphylococci (CoNS) are a group of gram-positive staphylococcal species that naturally inhabit the healthy human skin and mucosa. The clinical impact of CoNS-associated infections has recently been regarded as a challenge for diagnosis and therapeutic options. CoNS-associated infections are primarily caused by bacterial resistance to antibiotics and biofilm formation. As antibiotics are still the most used treatment, this problem will likely persist in the future. The present study aimed to investigate the resistance and virulence of CoNS recovered from various acne lesions and explore their genetic basis. Skin swab samples were collected from participants with acne and healthy skin. All samples underwent conventional culture for the isolation of CoNS, MALDI-TOF confirmation, antibiotic susceptibility, and biofilm formation testing. A total of 85 CoNS isolates were recovered from the samples and preliminarily identified as Staphylococcus epidermidis. Isolates from the acne group (n = 60) showed the highest rates of resistance to penicillin (73%), cefoxitin (63%), clindamycin (53.3%), and erythromycin (48%), followed by levofloxacin (36.7%) and gentamycin (31.7%). The lowest rates of resistance were observed against tetracycline (28.3%), doxycycline (11.7%), and minocycline (8.3%). CoNS isolated from mild, moderate acne and healthy isolates did not show strong biofilm formation, whereas the isolates from the severe cases of the acne group showed strong biofilm formation (76.6%). Four extensively drug-resistant and strong biofilm-forming staphylococcal isolates recovered from patients with severe acne were selected for whole-genome sequencing (WGS), and their genomes were investigated using bioinformatics tools. Three of the sequenced genomes were identified as S. epidermidis; however, isolate 29AM was identified as Staphylococcus warneri, which is a newly emerging pathogen that is not commonly associated with acne and was not detected by MALDI-TOF. All the sequenced strains were multidrug-resistant and carried multiple resistance genes, including blaZ, mecA, tet(K), erm(C), lnuA, vgaA, dfrC, fusB, fosBx1, norA, and vanT, which were found to be located on plasmids and chromosomes. Virulence features were detected in all genomes in the presence of genes involved in adherence and biofilm formation (icaA, icaB, icaC, sdrG, sdrH, atl, ebh, and ebp). Only the S. warneri isolate 29AM contained immune evasion genes (capB, capC, acpXL, and manA), an anti-phagocytosis gene (cdsA), and other unique features. As a result of their potential pathogenicity and antibiotic resistance, CoNS must be monitored as an emerging pathogen associated with acne infections. To the best of our knowledge, this is the first report to isolate, identify, and correlate S. warneri with severe acne infections among Egyptian patients using WGS and bioinformatic analysis.

Current and potential approaches on assessing airflow and particle dispersion in healthcare facilities: a systematic review

An indoor environment in a hospital building requires a high indoor air quality (IAQ) to overcome patients' risks of getting wound infections without interrupting the recovery process. However, several problems arose in obtaining a satisfactory IAQ, such as poor ventilation design strategies, insufficient air exchange, improper medical equipment placement and high door opening frequency. This paper presents an overview of various methods used for assessing the IAQ in hospital facilities, especially in an operating room, isolation room, anteroom, postoperative room, inpatient room and dentistry room. This review shows that both experimental and numerical methods demonstrated their advantages in the IAQ assessment. It was revealed that both airflow and particle tracking models could result in different particle dispersion predictions. The model selection should depend on the compatibility of the simulated result with the experimental measurement data. The primary and secondary forces affecting the characteristics of particle dispersion were also discussed in detail. The main contributing forces to the trajectory characteristics of a particle could be attributed to the gravitational force and drag force regardless of particle size. Meanwhile, the additional forces could be considered when there involves temperature gradient, intense light source, submicron particle, etc. The particle size concerned in a healthcare facility should be less than 20 μm as this particle size range showed a closer relationship with the virus load and a higher tendency to remain airborne. Also, further research opportunities that reflect a more realistic approach and improvement in the current assessment approach were proposed.

Interference and co-existence of staphylococci and Cutibacterium acnes within the healthy human skin microbiome

Human skin is populated by trillions of microbes collectively called the skin microbiome. Staphylococcus epidermidis and Cutibacterium acnes are among the most abundant members of this ecosystem, with described roles in skin health and disease. However, knowledge regarding the health beneficial effects of these ubiquitous skin residents is still limited. Here, we profiled the staphylococcal and C. acnes landscape across four different skin sites of 30 individuals (120 skin samples) using amplicon-based next-generation sequencing. Relative abundance profiles obtained indicated the existence of phylotype-specific co-existence and exclusion scenarios. Co-culture experiments with 557 staphylococcal strains identified 30 strains exhibiting anti-C. acnes activities. Notably, staphylococcal strains were found to selectively exclude acne-associated C. acnes and co-exist with healthy skin-associated phylotypes, through regulation of the antimicrobial activity. Overall, these findings highlight the importance of skin-resident staphylococci and suggest that selective microbial interference is a contributor to healthy skin homeostasis.

The dynamic interaction between the common resident skin microbes Staphylococcus epidermidis and Cutibacterium acnes is uncovered, showing that S. epidermidis can selectively exclude acne-associated C. acnes strains from the human skin.

Genomic investigation of clinically significant coagulase-negative staphylococci

Introduction. Coagulase-negative staphylococci have been recognized both as emerging pathogens and contaminants of clinical samples. High-resolution genomic investigation may provide insights into their clinical significance.Aims. To review the literature regarding coagulase-negative staphylococcal infection and the utility of genomic methods to aid diagnosis and management, and to identify promising areas for future research.Methodology. We searched Google Scholar with the terms (Staphylococcus) AND (sequencing OR (infection)). We prioritized papers that addressed coagulase-negative staphylococci, genomic analysis, or infection.Results. A number of studies have investigated specimen-related, phenotypic and genetic factors associated with colonization, infection and virulence, but diagnosis remains problematic.Conclusion. Genomic investigation provides insights into the genetic diversity and natural history of colonization and infection. Such information allows the development of new methodologies to identify and compare relatedness and predict antimicrobial resistance. Future clinical studies that employ suitable sampling frames coupled with the application of high-resolution whole-genome sequencing may aid the development of more discriminatory diagnostic approaches to coagulase-staphylococcal infection.

Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections

Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily as causing bloodstream infections in neonatal intensive care units (NICUs), but has also recently been described in prosthetic joint infections (PJIs). The multidrug-resistant S. capitis subsp. urealyticus clone NRCS-A, comprising three sublineages, is prevalent in NICUs across the world, but its impact on other patient groups such as those suffering from PJIs or among adults planned for arthroplasty is unknown. Genome sequencing and subsequent analysis were performed on a Swedish collection of PJI isolates (n = 21), nasal commensals from patients planned to undergo arthroplasty (n = 20), NICU blood isolates (n = 9), operating theatre air isolates (n = 4), and reference strains (n = 2), in conjunction with an international strain collection (n = 248). The NRCS-A Outbreak sublineage containing the composite type V SCCmec-SCCcad/ars/cop element was present in PJIs across three Swedish hospitals. However, it was not found among nasal carrier strains, where the less virulent S. capitis subsp. capitis was most prevalent. The presence of the NRCS-A Outbreak clone in adult patients with PJIs demonstrates that dissemination occurs beyond NICUs. As this clone has several properties which facilitate invasive infections in patients with medical implants or immunosuppression, such as biofilm forming ability and multidrug resistance including heterogeneous glycopeptide-intermediate susceptibility, further research is needed to understand the reservoirs and distribution of this hospital-associated pathogen.

Thyroid radiation shields: A potential source of intraoperative infection

Introduction

Thyroid radiation shields are often uncovered by the surgical gown and may represent a preventable source of wound contamination. The aims of this study are to define the common pathogens found on thyroid radiation shields and evaluate the effectiveness of a simple cleaning method.

Methods

Samples were obtained from 29 community thyroid shields collected from the operating theatres of 3 teaching hospitals. Each shield was swabbed under strict sterile technique using a separate swab for each of 4 designated zones. After sampling, shields were cleaned with a readily available disinfectant and sampling was repeated after 5 min. All swabs were cultured in ambient air at 37 °C on 5% sheeps blood agar for 48 hrs and subsequent growth was identified by a MALDI-TOF Walkaway mass spectrometer.

Results

Before cleaning, 100% of thyroid shields (29/29) and 68% of shield zones (79/116) grew at least 1 type of bacteria. Coagulase negative staphylococci, including S. epidermidis, S. capitis, S. cohnii, S. haemolyticus and S. hominis, were most commonly isolated. Enterobacteriaceae and S. aureus were also cultured. After cleaning, culturable contamination was reduced by 86.3% and 64.5%, respectively (p < 0.001).

Conclusion

The most common pathogens associated with SSIs can be isolated on thyroid radiation shields. Appropriate cleaning of thyroid shields with readily available disinfectant can significantly reduce the bacterial burden as detectable by culture. Hospitals should facilitate staff education and reinforce their policies on cleaning these shields which may often be overlooked.

Genotypic and phenotypic changes of Staphylococcus epidermidis during relapse episodes in prosthetic joint infections

Staphylococcus epidermidis is a coagulase-negative bacterium capable of causing recurrent relapses in prosthetic joint infection (PJI). The aim of this study was to determine if Staphylococcus epidermidis isolates from patients with recurrent relapses of prosthetic joint infection (PJI) changed genotypically (pulsed-field gel electrophoresis (PFGE) pattern analysis and genes involved in biofilm formation) and phenotypically (antimicrobial resistance, biofilm formation) during the different episodes. Four patients with PJI recurrent relapses were evaluated clinically and microbiologically. Genotypic and phenotypic characteristics of 31 S. epidermidis isolates were determined. In all cases, PJI was treated with antimicrobial therapy and resection of the prosthesis without reimplantation. Months later, all patients had a relapse episode and treated with rifampin plus vancomycin and surgical debridement. Changes in the antibiotics resistance profile in isolates from patients 1 and 2 were observed in the two episodes. Patient 1 had four clones A, B, C, and D that were distributed differentially in the two episodes. Similarly, patients 2 and 3 had two clones and subclones (E-E1 and F-F1, respectively), and patient 4 had only the clone G in both episodes. The clone F formed small-colony variants (SCVs). High level of biofilm formation was found in all clones, except for clones D and G. Clones/subclones showed a genotypic variation in icaA, sdrF, bap, sesI, and embp genes. The principal coordinate analysis showed that all clones/subclones were different. These results showed that the initial infective clone of S. epidermidis from PJI, changed genotypically and phenotypically after a second relapse as a response to the treatment.

Surgical site infections and the microbiome: An updated perspective

OBJECTIVE

To address 3 questions: What are the origins of bacteria causing surgical site infections (SSIs)? Is there evidence that the offending bacteria are present at the incision site when surgery begins? What are the estimates of the proportion of SSIs that can be prevented with perioperative control of the microbiome?

DESIGN

Review of the literature, examining recognized sources of bacteria causing surgical site infections.

METHODS

Specifically, I examined the impact of improved control of the microbiome of the skin and nares on reducing SSIs. The initial effort was to examine the reduction of SSIs linked solely to preoperative skin preparation regimens and to either topical nasal antibiotics or pre- and postoperative nasal antiseptic regimens. To corroborate the concept of the importance of the microbiome, a review of studies showing the relationship of SSIs and marker organisms (eg, Propionobacterium acnes) present at the incision sites was performed. The relationships of SSIs to the microbiome of the skin and nares were summarized.

RESULTS

Depending on key assumptions, ∼70%-95% of all SSIs arise from the microbiome of the patients' skin or nares. Data from the studies of marker organisms suggest that the infecting bacteria are present at the incision site at the time of surgery.

CONCLUSIONS

Almost all SSIs arise from the patient's microbiome. The occurrence of SSIs can be viewed as a perioperative failure to control the microbiome.

Patient and surgical factors affecting procedure duration and revision risk due to deep infection in primary total knee arthroplasty

BACKGROUND

The aim of this study was to assess which patient and procedure factors affected both the risk of infection as well as procedure duration. Additionally, to assess if procedure duration affected the revision risk due to deep infection in total knee arthroplasty (TKA) patients and in a subgroup of low-risk patients.

METHODS

28,262 primary TKA with 311 revisions due to deep infection were included from the Norwegian Arthroplasty Register (NAR) and analysed from primary surgery from 2005 until 31st December 2015 with a 1 and 4 year follow up. The risk of revision due to deep infection was calculated in a multivariable Cox regression model including patient and procedure related risk factors, assessing Hazard Ratio (HR) with 95% confidence interval (CI).

RESULTS

Multivariate analysis showed statistically significant associations with revision due to deep infection and increased procedure duration for male patients, ASA3+ (American Society of Anesthesiologists) and perioperative complications. Procedure duration ≥110 min (75 percentile) had a higher risk of deep infection compared to duration <75 min (25 percentile), in the unadjusted analysis (HR = 1.8, 95% CI 1.3-2.5, p = 0.001) and in the adjusted analysis (HR = 1.5, 95% CI 1.0-2.1, p = 0.03). For low-risk patients, procedure duration did not increase the risk of infection.

CONCLUSION

Male patients, ASA 3+ patients and perioperative complications were risk factors both for longer procedure duration and for deep infection revisions. Patients with a high degree of comorbidity, defined as ASA3+, are at risk of infection with longer procedure durations. The occurrence of perioperative complications potentially leading to a more complex and lengthy procedure was associated with a higher risk of infection. Long procedure duration in itself seems to have minor impact on infection since we found no association in the low-risk patient.

Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins

Purpose

The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.

Methodology

Phylogenetic relationships between 25 S. pettenkoferi isolates collected from blood cultures and intra-operative air sampling were determined by repetitive-sequence-based PCR typing and analysis of ~157 000 SNPs identified in the core genome after WGS. Antibiotic susceptibility testing and tests for biofilm production (microtitre plate assay) were performed.

Results

Repetitive-sequence-based PCR as well as WGS data demonstrated the close relatedness of clinically significant blood culture isolates to probable contaminants, as well as to environmental isolates. Antibiotic-susceptibility testing demonstrated a low level of antimicrobial resistance. The mecA gene was present in two cefoxitin-resistant isolates. No isolates were found to produce biofilm.

Conclusion

Close genomic relatedness of S. pettenkoferi isolates from different geographical locations and origins were found within clades, but with substantial genomic difference between the two major clades. The ecological niche of S. pettenkoferi remains unconfirmed, but the presence of S. pettenkoferi in the air of the operating field favours the suggestion of a role in skin flora. Identification of S. pettenkoferi in clinical samples should, in a majority of cases, most likely be regarded as a probable contamination, and its role as a possible pathogen in immunocompromised hosts remains to be clarified.

Staphylococcus capitis isolated from prosthetic joint infections

Further knowledge about the clinical and microbiological characteristics of prosthetic joint infections (PJIs) caused by different coagulase-negative staphylococci (CoNS) may facilitate interpretation of microbiological findings and improve treatment algorithms. Staphylococcus capitis is a CoNS with documented potential for both human disease and nosocomial spread. As data on orthopaedic infections are scarce, our aim was to describe the clinical and microbiological characteristics of PJIs caused by S. capitis. This retrospective cohort study included three centres and 21 patients with significant growth of S. capitis during revision surgery for PJI between 2005 and 2014. Clinical data were extracted and further microbiological characterisation of the S. capitis isolates was performed. Multidrug-resistant (≥3 antibiotic groups) S. capitis was detected in 28.6 % of isolates, methicillin resistance in 38.1 % and fluoroquinolone resistance in 14.3 %; no isolates were rifampin-resistant. Heterogeneous glycopeptide-intermediate resistance was detected in 38.1 %. Biofilm-forming ability was common. All episodes were either early post-interventional or chronic, and there were no haematogenous infections. Ten patients experienced monomicrobial infections. Among patients available for evaluation, 86 % of chronic infections and 70 % of early post-interventional infections achieved clinical cure; 90 % of monomicrobial infections remained infection-free. Genetic fingerprinting with repetitive sequence-based polymerase chain reaction (rep-PCR; DiversiLab®) displayed clustering of isolates, suggesting that nosocomial spread might be present. Staphylococcus capitis has the potential to cause PJIs, with infection most likely being contracted during surgery or in the early postoperative period. As S. capitis might be an emerging nosocomial pathogen, surveillance of the prevalence of PJIs caused by S. capitis could be recommended.

Microbiological Diagnosis of Implant-Related Infections: Scientific Evidence and Cost/Benefit Analysis of Routine Antibiofilm Processing

Prosthetic joint infection is one of the most severe complication following joint arthroplasty, producing a significant worsening of patient's quality of life. Management of PJIs requires extended courses of antimicrobial therapy, multiple surgical interventions and prolonged hospital stay, with a consequent economic burden, which is thought to markedly increase in the next years due to the expected burden in total joint arthroplasties. The present review summarizes the present knowledge on microbiological diagnosis of prosthetic joint infections, focusing on aethiological agents and discussing pros and cons of the available strategies for their diagnosis.Intra-operative clinical diagnosis and pathogen identification is considered the diagnostic benchmark, however the presence of bacterial biofilm makes pathogen detection with traditional microbiological techniques highly ineffective. Diagnosis of PJIs is a rather complex challenge for orthopedics and requires a strict collaboration between different specialists: orthopaedics, infectivologists, microbiologists, pathologists and radiologists. Diagnostic criteria have been described by national and international association and scientific societies. Clinicians should be trained on how to use it, but more importantly they should know potential and limitation of the available tests in order to use them appropriately.