Augmented recovery of microorganisms from swabs by homogenization: a novel standardizable high-throughput approach

Quantitative and qualitative assessment of airborne microorganisms during gross anatomical class and the bacterial and fungal load on formalin-embalmed corpses

Mold growth on body donations remains an underreported yet serious issue in anatomical teaching. Bacterial and fungal growth pose health risks to lecturers and students, alongside with ethical and aesthetic concerns. However, limited information exists on the presence of bacteria and fungi on body donations and their underlying causes. To investigate the potential impact of airborne germs on body donation contamination, we conducted indoor air measurements before, during, and after our anatomical dissection course, with outdoor measurements serving as a control. Tissue samples from the dissected body donations were collected to assess the germ load, with qualitative and quantitative microbiological analyses. Air samples from the dissection hall contained no fungi, but various fungal species were identified in the adjacent stairways and outdoors which implies that fungal occurrence in the dissection hall air was independent of lecturers' and students' presence. Moreover, our results indicate that adequate ventilation filters can effectively reduce indoor fungal germs during courses, while the bacterial load in room air appears to increase, likely due to the presence of lecturers and students. Additionally, the tissue samples revealed no bacterial or fungal germs which implies that our ethanol-formalin-based embalming solution demonstrates an effective long-term antimicrobial preservation of corpses.

The Challenge of Periprosthetic Joint Infection Diagnosis: From Current Methods to Emerging Biomarkers

Due to the increase in the life span and mobility at older ages, the number of implanted prosthetic joints is constantly increasing. However, the number of periprosthetic joint infections (PJIs), one of the most severe complications after total joint arthroplasty, also shows an increasing trend. PJI has an incidence of 1-2% in the case of primary arthroplasties and up to 4% in the case of revision operations. The development of efficient protocols for managing periprosthetic infections can lead to the establishment of preventive measures and effective diagnostic methods based on the results obtained after the laboratory tests. In this review, we will briefly present the current methods used in PJI diagnosis and the current and emerging synovial biomarkers used for the prognosis, prophylaxis, and early diagnosis of periprosthetic infections. We will discuss treatment failure that may result from patient factors, microbiological factors, or factors related to errors during diagnosis.

Pre-processing tissue specimens with a tissue homogenizer: clinical and microbiological evaluation

BACKGROUND

Tissues are valuable specimens in diagnostic microbiology because they are often obtained by invasive methods, and effort should thus be taken to maximize microbiological yield. The objective of this study was to evaluate the added value of using tissue pre-processing (tissue homogenizer instrument gentleMACS Dissociator) in detecting microorganisms responsible for infections.

METHODS

We included 104 randomly collected tissue samples, 41 (39.4 %) bones and 63 (60.6 %) soft tissues, many of those (42/104 (40.4 %)) were of periprosthetic origins. We compared the agreement between pre-processing tissues using tissue homogenizer with routine microbiology diagnostic procedure, and we calculated the performance of these methods when clinical infections were used as reference standard.

RESULTS

There was no significant difference between the two methods (McNemar test, p = 0.3). Among the positive culture using both methods (n = 62), 61 (98.4 %) showed at least one similar microorganism. Exactly similar microorganisms were found in 42/62 (67.7 %) of the samples. From the included tissues, 55/ 104 (52.9 %) were deemed as infected. We found that the sensitivity of homogenized tissue procedure was lower (83.6 %) than when tissue was processed using tissue homogenizer (89.1 %). Sub-analysis on periprosthetic tissues and soft or bone tissues showed comparable results.

CONCLUSIONS

The added value of GentleMACS Dissociator tissue homogenizer is limited in comparison to routine tissue processing.

Targeted Swabbing of Implant-Associated Biofilm Formation-A Staining-Guided Sampling Approach for Optimizing Routine Microbiological Diagnostics

Background: Swabbing of implants removed from potentially infected sites represents a time saving and ubiquitously applicable alternative to sonication approaches. The latter bears an elevated risk of processing related contaminations due to the high number of handling steps. Since biofilms are usually invisible to the naked eye, adequate swabbing relies on the chance of hitting the colonized area on the implant. A targeted directed swabbing approach could overcome this detriment. Method: Three dyes were tested at different concentrations for their toxicity on biofilm-associated cells of S. epidermidis, the species most frequently identified as a causative agent of implant-associated infections. Results: Malachite green (0.2%) delivered the highest bacterial recovery rates combined with the best results in biofilm visualization. Its suitability for diagnostic approaches was demonstrated for smooth and rough implant surfaces. Biofilm-covered areas were successfully visualized. Conclusion: Subsequent targeted swab-sampling resulted in a significantly increased bacterial recovery rate compared to a dye-free “random swabbing” diagnostic approach.

Microbial yield from infectious tissues pretreated by various methods: an invitro study

Background

This study aimed to evaluate the effects of different pretreatment methods on the microbial yield from infectious tissues.

Methods

Strains of Staphylococcus aureus (SA), Escherichia coli (EC) and Candida albicans (CA) were used to construct single-surface, full-surface, and internal infection models in sterile pork tissue. Manual milling (MM), mechanical homogenization (MH), sonificated (SF), dithiothreitol (DTT), and direct culture (DC) were used to pretreat these tissues, the microbial yield from different pretreatment methods were recorded and compared. Moreover, periprosthetic tissues collected intraoperatively from periprosthetic joint infection (PJI) patients were used as a verification.

Results

The study showed that the microbial yield from MH pretreatment was significantly higher than that of MM (P < 0.01) and SF pretreatment method (P < 0.01). Furthermore, in the internal infection model, the microbial yield from MH group was also significantly higher than that of SF (P < 0.01), DTT (P < 0.01), and DC group (P < 0.01). Moreover, the number of bacterial colonies obtained from periprosthetic tissues pretreated by MH was significantly higher than pretreated by other pretreatment methods (P = 0.004).

Conclusions

The effects of MH and DTT in microbial yield were significantly higher than that of DC, SF and MM, and these methods can be used to process multiple tissue samples at the same time, which might further improve the diagnostic sensitivity of infectious disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12891-021-04071-5.

On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results

Diagnostic testing in the infectious disease laboratory facilitates decision-making by physicians at the bedside as well as epidemiological assessments and surveillance at study level. Problems may arise if test results are uncritically considered as being the same as the unknown true value. To allow a better understanding, the influence of external factors on the interpretation of test results is introduced with the example of prevalence, followed by the presentation of strengths and weaknesses of important techniques in the infectious disease laboratory like microscopy, cultural diagnostics, serology, mass spectrometry, nucleic acid amplification and hypothesis-free metagenomic sequencing with focus on basic, high-technology and potential future approaches. Special problems like multiplex testing as well as uncertainty of test evaluations, if no gold standard is available, are also stressed with a final glimpse on emerging future technologies for the infectious disease laboratory. In the conclusions, suitability for point-of-care-testing and field laboratory applications is summarized. The aim is to illustrate the limitations of diagnostic accuracy to both clinicians and study planners and to stress the importance of close cooperation with experts in laboratory disciplines so as to avoid potentially critical misunderstandings due to inappropriate interpretation of diagnostic test results.

Evaluation of Sample Preparation Methods for Fast Proteotyping of Microorganisms by Tandem Mass Spectrometry

Tandem mass spectrometry-based proteotyping allows characterizing microorganisms in terms of taxonomy and is becoming an important tool for investigating microbial diversity from several ecosystems. Fast and automatable sample preparation for obtaining peptide pools amenable to tandem mass spectrometry is necessary for enabling proteotyping as a high-throughput method. First, the protocol to increase the yield of lysis of several representative bacterial and eukaryotic microorganisms was optimized by using a long and drastic bead-beating setting with 0.1 mm silica beads, 0.1 and 0.5 mm glass beads, in presence of detergents. Then, three different methods to obtain greater digestion yield from these extracts were tested and optimized for improve efficiency and reduce application time: denaturing electrophoresis of proteins and in-gel proteolysis, suspension-trapping filter-based approach (S-Trap) and, solid-phase-enhanced sample preparation named SP3. The latter method outperforms the other two in terms of speed and delivers also more peptides and proteins than with the in-gel proteolysis (2.2 fold for both) and S-trap approaches (1.3 and 1.2 fold, respectively). Thus, SP3 directly improves tandem mass spectrometry proteotyping.

Prospective Analysis of a Sterile, Semi-automated Tissue Biopsy Homogenization Method in the Diagnosis of Prosthetic Joint Infections

BACKGROUND/AIM

Prosthetic joint infection (PJI) remains a serious complication of total joint arthroplasty. To effectively treat PJI, it is essential to identify the microorganism causing it and be able to combine correct surgical and anti-infective treatments. This cannot always be achieved with the currently employed diagnostic methods. The aim of this study was to evaluate a semi-automated tissue biopsy bead milling method (Ultra-TurrAX, Axonlab AG; Reichenbach, Germany) based on the hypothesis that the results are more sensitive for microbe detection and less prone to contamination.

MATERIALS AND METHODS

We included 35 consecutive patients undergoing 38 hip or knee arthroplasty revisions in this study. In addition to manually processed biopsies, we processed tissue specimens harvested intraoperatively using a semi-automated method. The sensitivity and specificity of both methods were calculated using MSIS criteria and sonication results as gold standards.

RESULTS

For total hip arthroplasty samples were evaluated separately based on MSIS criteria as the reference standard, Ultra-TurrAX processing yielded 81% (62-100%) sensitivity and 100% specificity. Using sonication as the gold standard, a sensitivity of 80% (60-100%) and specificity of 80% (45-100%) were calculated. In total knee arthroplasty, Ultra-TurrAX processing yielded 27% (1-54%) sensitivity and 57% (20-94%) specificity when using MSIS criteria as the gold standard. Using sonication as the gold standard, a sensitivity of 60% (17-100%) and specificity of 77% (54-100%) were calculated.

CONCLUSION

This is the first study to analyze bead mill processing in total hip and knee arthroplasty revisions in a consecutive patient series. The method's sensitivity was comparable to and its specificity superior to regular sample processing results reported in the literature with respect to hip arthroplasties and to both hip and knee arthroplasties collectively. With respect to total knee arthroplasties, the method fared worse in our collective, most likely due to the small number of patients in the sample. Integrating the method into the clinical workflow allowed for speedier and more efficient sample handling and processing. The theoretical advantage of a lower risk of contamination because of fewer manual processing steps is, in our opinion, valid.

Predictors of colonization with Staphylococcus species among patients scheduled for cardiac and orthopedic interventions at tertiary care hospitals in north-eastern Germany-a prevalence screening study

As methicillin-resistant Staphylococcus aureus (MRSA) colonization and infection in humans are a global challenge. In Mecklenburg and Western Pomerania (Germany) 1,517 patients who underwent surgical interventions were systematically screened for MRSA and MSSA colonization on the day of hospital admission and discharge. Demographic data, risk factors and colonization status of the (i) nose, (ii) throat, (iii) groin, and (iv) thorax or site of surgical intervention were determined. Of the 1,433 patients who were included for further evaluation, 331 (23.1%) were colonized with MSSA, while only 17 (1.2%) were MRSA carriers on the day of hospital admission. A combination of nose, throat and groin swabs returned a detection rate of 98.3% for MSSA/MRSA. Trauma patients had lower prevalence of MRSA/MSSA (OR 0.524, 95% CI: 0.37-0.75; p < 0.001) than patients with intended orthopedic interventions. Males showed significantly higher nasal S. aureus carrier rates than females (odds ratio (OR) = 1.478; 95% CI: 1.14-1.92; p = 0.003). Nasal S. aureus colonization was less frequent among male smokers as compared to non-smokers (chi² = 16.801; phi = 0.154; p < 0.001). Age, gender and smoking had a significant influence on S. aureus colonization. Combining at least three different swabbing sites should be considered for standard screening procedure to determine S. aureus colonization at patients scheduled for cardiac or orthopedic interventions at tertiary care hospitals.

Evaluation of Liquid-Based Swab Transport Systems against the New Approved CLSI M40-A2 Standard

Following revised information pertaining to newer swab types and testing protocols in the new CLSI M40-A2 standard, we evaluated three liquid swab transport systems for the recovery of aerobic, anaerobic, and fastidious organisms at room temperature and at 4°C. All tested liquid swab transport systems were fully compliant with the M40-A2 standard, with acceptable performance at both temperatures after the full specified holding period, using both qualitative (roll-plate) and quantitative (swab elution) methods.