The effect of changing diagnostic method from culture to PCR on the number of episodes of human campylobacteriosis in Denmark: a retrospective study (2015-2022)

IMPORTANCE

This study is important because it shows the potential epidemiological silence associated with the use of culture as the primary diagnostic method for the laboratory identification of human campylobacteriosis. Also, we show how polymerase chain reaction methods are associated with a systematic increase in the number of human campylobacteriosis episodes as reported by routine disease surveillance. These findings are operationally relevant and have public health implications because they tell how crucial it is to consider changes in diagnostic methods, e.g., in the epidemiological analysis of historical data and in the interpretation of future data in light of the past. We also believe that this study highlights how the synergy between microbiology and epidemiology is essential for disease surveillance.

Next Generation Sequencing Outperforms Cultivation-Based Methods for Detection of Bacterial Genera in Bile After Liver Transplantation

BACKGROUND AND AIMS

Bacterial cholangitis is a common complication in patients with ischemic type biliary lesions and/or anastomotic strictures after liver transplantation (LTX). Patients frequently need antibiotics and endoscopic retrograde cholangiography (ERC) to improve the bile flow. Antibiotic treatment is based on findings in standard microbiological cultivation (SMC) of bile. However, the cultivation techniques are limited to a subset of bacteria easy-to-cultivate. Therefore, the aim of our study was to evaluate the value of next generation sequencing as an additional diagnostic tool to SMC in ischemic type biliary lesions and/or anastomotic strictures.

METHODS

We sequenced the V1-V2 region of the 16S rRNA gene in 242 stored bile samples in patients after LTX and compared the results with findings of SMC. SMC was performed in n = 135 (56%) fresh bile samples in addition to NGS. SMC was part of the clinical routine in these patients.

RESULTS

NGS detected bacterial genera in bile samples more often than SMC (P = 5.42 × 10-74). SMC showed insufficient discovery of bacterial genera compared to NGS with better performance in patients receiving antibiotics prior to ERC. SMC missed many bacterial genera detected by NGS.

CONCLUSIONS

NGS was more sensitive in detecting bacteria in bile than SMC, no clinical parameters could be used to improve discovery rates in SMC and many genera were missed by SMC. Therefore, NGS should be used in a combined approach with SMC for improved diagnostics to achieve more specific and targeted antibiotic treatments.

From Submerged Cultures to 3D Cell Culture Models: Evolution of Nasal Epithelial Cells in Asthma Research and Virus Infection

Understanding the response to viral infection in the context of respiratory diseases is of significant importance. Recently, there has been more focus on the role of the nasal epithelium in disease modeling. Here, we provide an overview of different submerged, organotypic 3D and spheroid cell culture models of nasal epithelial cells, which were used to study asthma and allergy with a special focus on virus infection. In detail, this review summarizes the importance, benefits, and disadvantages of patient-derived cell culture models of nasal- and bronchial epithelial cells, including a comparison of these cell culture models and a discussion on why investigators should consider using nasal epithelial cells in their research. Exposure experiments, simple virus transduction analyses as well as genetic studies can be performed in these models, which may provide first insights into the complexity of molecular signatures and may open new doors for drug discovery and biomarker research.

Preservation fluid cultures. Clinical significance in liver transplantation

The aim of this study was to determine the incidence of preservation fluids (PF) bacterial positive cultures, identify the germs involved, determine their correlation with infections in recipients during the postoperative period and compare outcomes in terms of morbidity, hospital stay and both patient and graft survival. We describe incidence and etiology of germs developed in PF cultures in our series and evaluate its impact on recipients. A prospective study in deceased donor liver transplants (LT) recipients was carried out from January 2014 to December 2017. Back table PF cultures were analized considering positive the development of any germs and negative to no signs of growth after 5 days. PF were classified as contamination or pathogens. Targeted antibiotic therapy was administered in the last ones. Recipients were divided in: PF (-) and PF(+). Recipients infections related to positive PF were analyzed. These were identified as "direct correlation" when the same germ grew up in PF. Hospital stay and 30 days follow up were compared. Eighty-eight patients PFs were included, 38% (33) had positive cultures, 28 (85%) of these were considered contamination and only 5 as pathogens. We found no differences in postoperative infections (p 0.840), ICU and total hospital stay (p 0.374 and 0.427) between both groups. Postoperative infections and hospital stay seem not to be infuenced by PF cultures positivity. Treatment of isolated pathogens could have prevented infections, therefore, those groups that perform PF cultures should consider treatment in these cases and conclude prophylaxis when PF is negative or contaminated.

Pumping) and Skimming on the Microbial Profile of Human Milk Using Culture Techniques and Metataxonomic Analysis

Human milk microbiota is a unique bacterial community playing a relevant role in infant health, but its composition depends on different factors (woman health, lactation stage, and geographical lactation). However, information is lacking regarding some other factors that may affect the bacterial community of human milk. In this study we aimed to study the impact of the sample collection method and the skimming procedure using culture-dependent and culture-independent techniques to study the human milk microbial profile. One set of milk samples was provided by women (n = 10) in two consecutive days; half of the samples were collected the first day by manual expression and the other half on the second day by pumping. The rest of the participants (n = 17) provided milk samples that were fractionated by centrifugation; the bacterial profiles of whole milk and skimmed milk were compared by culture techniques in 10 milk samples, while those of whole milk, fat and skimmed milk were subjected to metataxonomic analysis in seven samples. Globally, the results obtained revealed high interindividual variability but that neither the use of single-use sterile devices to collect the sample nor the skimming procedure have a significant impact of the microbial profile of human samples.

False Negative Results in Bartonellosis Diagnosis

We report a fatal case of Bartonella henselae bacteremic patient. He had negative serology and PCRs from whole blood and liquid culture; only ftsZ nested PCR was positive from the blood liquid culture. The isolate had positive PCRs. When considered, bartonellosis diagnosis can be still challenging because of technical limitations.

Platelet Rich Plasma Enhancement of Skin Regeneration in an ex-vivo Human Experimental Model

This study reports on the development of an original, ex-vivo wounded skin culture protocol using autologous Platelet Rich Plasma (PRP) and enriched Dulbecco's Modified Eagle's Medium (DMEM). Human skin samples obtained from specimens harvested during reduction mammoplasty procedures, were injured in their central portion—to create a standard wound—and cultured under three different conditions:

– enriched DMEM with saline solution in the central wound (control)

– enriched DMEM with the same medium in the central wound

– enriched DMEM plus 2.5% autologous PRP, with the same PRP added medium in the central wound.

Morphological analysis was carried out at 0 h (T₀) and on days 1, 3, 5 and 10 (T₁-T₃-T₅-T₁₀) using Hematoxylin and Eosin; Masson's trichrome staining; Weigert staining and Ki-67 staining to identify the skin histological features in the different experimental conditions. The combination of DMEM and PRP allowed a favorable modulation of the epithelial cells and fibroblasts proliferation, and a relevant anti-inflammatory action. PRP also demonstrated an inhibitory effect on both the collagen and elastic fibers' de-structuration and a favorable modulation of the re-organization of these fibers. The step by step histological and immune-histo-chemical regenerative effects of PRP on human skin wound repair and regeneration process was observed over a period of 10 days.

Specialized Living Wound Dressing Based on the Self-Assembly Approach of Tissue Engineering

There is a high incidence of failure and recurrence for chronic skin wounds following conventional therapies. To promote healing, the use of skin substitutes containing living cells as wound dressings has been proposed. The aim of this study was to produce a scaffold-free cell-based bilayered tissue-engineered skin substitute (TES) containing living fibroblasts and keratinocytes suitable for use as wound dressing, while considering production time, handling effort during the manufacturing process, and stability of the final product. The self-assembly method, which relies on the ability of mesenchymal cells to secrete and organize connective tissue sheet sustaining keratinocyte growth, was used to produce TESs. Three fibroblast-seeding densities were tested to produce tissue sheets. At day 17, keratinocytes were added onto 1 or 3 (reference method) stacked tissue sheets. Four days later, TESs were subjected either to 4, 10, or 17 days of culture at the air–liquid interface (A/L). All resulting TESs were comparable in terms of their histological aspect, protein expression profile and contractile behavior in vitro. However, signs of extracellular matrix (ECM) digestion that progressed over culture time were noted in TESs produced with only one fibroblast-derived tissue sheet. With lower fibroblast density, the ECM of TESs was almost completely digested after 10 days A/L and lost histological integrity after grafting in athymic mice. Increasing the fibroblast seeding density 5 to 10 times solved this problem. We conclude that the proposed method allows for a 25-day production of a living TES, which retains its histological characteristics in vitro for at least two weeks.

High frequency of Mycoplasma pneumoniae among patients with atypical pneumonia in Tehran, Iran

Introduction

Mycoplasma pneumoniae is a major cause of atypical community-acquired pneumonia (CAP) with a prevalence range of 15-20% and up to 40% in adults and children, respectively. In Iran, the recorded frequency ranges between 1-6.15%. We aimed to investigate the frequency of M. pneumoniae among patients with atypical pneumonia acquired from the community.

Methods

Over a period of 5 months between January and June 2017, 520 patients with suspected CAP, who had been to the hospital outpatient clinics of Tehran University, were enrolled in this study. Throat swab specimens were obtained from 110 outpatients who presented with symptoms of atypical pneumonia. M. pneumoniae was identified via culture and biochemical tests, such as fermentation of glucose and arginine, hemolysis, and hemadsorption. For confirmation, PCR was performed to amplify the gene fragment coding for p1 adhesin.

Results

The major and minor clinical signs of the patients were dyspnea (67.3%) and nausea (15.5%), respectively. Out of 110 specimens, 25 (22.7%) and 29 (26.4%) isolates were identified to be M. pneumoniae via culture and molecular assay, respectively. Comparing the results of the two methods, the PCR showed better sensitivity and rapidity for the detection of M. pneumoniae. There was a high congruence between culture and the PCR assay; kappa level was 'almost perfect' (κ=0.90).

Conclusion

This is the first report of high frequency of M. pneumoniae in our region. This finding can serve as baseline information for further investigation and confirmation of the potential epidemics of M. pneumoniae pneumonia in our community.

The value of corneoscleral rim cultures in keratoplasty: a systematic review and cost-effectiveness analysis

PURPOSE

This study evaluated the performance of donor corneoscleral rim cultures for predicting infection after corneal transplantation, and determines if there is a correlation between positive corneoscleral rim cultures and postkeratoplasty infection.

DESIGN AND DATA SOURCES

This was a systematic review, prognostic accuracy analysis, and cost-effectiveness analysis. Databases searched were: Medline (Ovid), Embase (Ovid), CINAHL, Cochrane Library, Web of Science, and BioSis Previews. Grey literature was also explored.

MATERIALS AND METHODS

A systematic review was conducted to locate published and unpublished studies. All studies examining corneal button contamination and its association with endophthalmitis and keratitis posttransplantation were included. Extracted data were used to calculate sensitivity, specificity, positive predictive value, and negative predictive value. Cost data from the London Laboratory Services Group in London, ON were used to calculate the cost-effectiveness of culturing donor rim cultures.

RESULTS

Of 7,870 grafts, 954 had a positive rim culture (12.1%), with 12 patients going on to develop keratitis or endophthalmitis (1.3%). The prevalence of keratitis and endophthalmitis in this study was 0.15%, and the positive predictive value 1.5%. Of the 12 infections, nine were fungal and three bacterial. The estimated cost of a positive and negative test result was CAD$45.99 and $14.15, respectively. The cost to run all 7,870 tests was estimated to be $141,735.86, with an incremental cost-effectiveness ratio of $40,215.70.

CONCLUSION

There was a significant divergence between bacterial and fungal rim-culture results. Bacterial cultures predicted clinical infection poorly, did not change management, and were expensive. Fungal cultures predicted clinical infection in over 10% of patients, had the potential to change management, and were 40% less expensive than full rim culturing (bacterial and fungal tests). Fungal rim cultures may be considered in areas where fungal infection rates are high.

In Vivo Evaluation and Imaging of a Bilayered Self-Assembled Skin Substitute Using a Decellularized Dermal Matrix Grafted on Mice

As time to final coverage is the essence for better survival outcome in severely burned patients, we have continuously strived to reduce the duration for the preparation of our bilayered self-assembled skin substitutes (SASS). These SASS produced in vitro by the self-assembly approach have a structure and functionality very similar to native skin. Recently, we have shown that a decellularized dermal matrix preproduced by the self-assembly approach could be used as a template to further obtain self-assembled skin substitute using a decellularized dermal template (SASS-DM) in vitro. Thus, the production period with patient cells was then reduced to about 1 month. Herein, preclinical animal experiments have been performed to confirm the integration and evolution of such a graft and compare the maturation of SASS and SASS-DM in vivo. Both tissues, reconstructed from adult or newborn cells, were grafted on athymic mice. Green fluorescent protein-transfected keratinocytes were also used to follow grafted tissues weekly for 6 weeks using an in vivo imaging system (IVIS). Cell architecture and differentiation were studied with histological and immunofluorescence analyses at each time point. Graft integration, macroscopic evolution, histological analyses, and expression of skin differentiation markers were similar between both skin substitutes reconstructed from either newborn or adult cells, and IVIS observations confirmed the efficient engraftment of SASS-DM. In conclusion, our in vivo graft experiments on a mouse model demonstrated that the SASS-DM had equivalent macroscopic, histological, and differentiation evolution over a 6-week period, when compared with the SASS. The tissue-engineered SASS-DM could improve clinical availability and advantageously shorten the time necessary for the definitive wound coverage of severely burned patients.

Comparison of Mycobacterium tuberculosis complex Yield and Contamination Rates using Lowenstein-Jensen with and without Antibiotics in Western Kenya

BACKGROUND

While molecular methods have been recently endorsed for diagnosis of tuberculosis (TB), mycobacterial culture remains the gold standard. Lowenstein-Jensen (LJ) is often used for the cultivation of Mycobacterium tuberculosis complex (MTBC); however contamination often renders a subset of cultures useless. We compared the MTBC yield and contamination rate of processed sputum inoculated on LJ with antibiotics (LJ PACT) to LJ without antibiotics (LJ).

METHODOLOGY

Sputum samples were obtained from people living with HIV enrolled in a TB screening study in western Kenya, processed using NALC/NaOH-Na citrate, then inoculated on LJ PACT and LJ media. Cultures were evaluated weekly with growth identified as acid-fast bacilli by Ziehl-Neelsen bright-field microscopy. MTBC and nontuberculous mycobacteria (NTM) were identified by immunochromatographic and line probe assays.

RESULTS

A total of 700 sputum samples were cultured on both LJ PACT and LJ between March and June 2012. Of those cultured on LJ PACT, 29 (4.1%) grew MTBC, 613 (87.6%) were negative, 12 (1.7%) grew NTM, and 46 (6.6%) were contaminated; on LJ, 28 (4%) grew MTBC, 553 (79%) were negative, 9 (1.3%) grew NTM, and 110 (15.7%) were contaminated. The difference in contamination on LJ PACT and LJ was statistically significant (p<0.0001), while the difference in MTBC growth was not (p=0.566).

The effect of ascorbic acid and fluid flow stimulation on the mechanical properties of a tissue engineered pelvic floor repair material

Synthetic non-degradable meshes used in pelvic floor surgery can cause serious complications such as tissue erosion. A repair material composed of an autologous oral fibroblast seeded degradable polylactic acid scaffold may be a viable alternative. The aims of this study were to investigate the effects of media supplementation with additives (ascorbic acid-2-phosphate, glycolic acid and 17-β-oestradiol) on the mechanical properties of these scaffolds. Oral fibroblasts were isolated from buccal mucosa. The effects of the three additives were initially compared in two-dimensional culture to select the most promising collagen stimulating additive. Sterile electrospun scaffolds were seeded with 500,000 oral fibroblasts and fixed in 6-well plates and subjected to ascorbic acid-2-phosphate (the best performing additive) and/or mechanical stimulation. Mechanical stimulation by fluid shear stress was induced by rocking scaffolds on a platform shaker for 1 h/day for 10 of 14 days of culture. In two-dimensional culture, ascorbic acid-2-phosphate (concentrations from 0.02 mM to 0.04 M) and glycolic acid (10 µM) led to significantly greater total collagen production, but ascorbic acid-2-phosphate at 0.03 mM produced the greatest stimulation (of the order of >100%). In three-dimensional culture, mechanical stimulation alone gave non-significant increases in stiffness and strength. Ascorbic acid-2-phosphate (0.03 mM) significantly increased collagen production in the order 280% in both static and mechanically stimulated scaffolds (p < 0.0001). There was no additional effect of mechanical stimulation. Dense collagen I fibres were observed with ascorbic acid-2-phosphate supplementation. Uniaxial tensiometry showed that strength (p < 0.01) and stiffness (p <0.05) both improved significantly. A combination of ascorbic acid-2-phosphate and mechanical stimulation led to further non-signficant increases in strength and stiffness. In conclusion, a pelvic floor repair material with improved mechanical properties can be developed by supplementing culture media with ascorbic acid-2-phosphate to increase collagen I production. Future studies will assess the change in mechanical properties after implantation in an animal model.

Review: Experimental models for Barrett's esophagus and esophageal adenocarcinoma

Several different cell culture systems and laboratory animal models have been used over the years to study Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Most of the existing models have key differences with the human esophagus and complex pathogenesis of disease. None of the models offers an ideal system for the complex study of environmental exposure, genetic risk, and prevention strategies. In fact, different model systems may be required to answer different specific research questions about the pathogenesis of BE and EAC. Given the high mortality associated with EAC and the fact that current screening strategies miss most cases of EAC, advances in basic and translational science related to esophageal injury, repair, and carcinogenesis are clearly needed. This review describes several of the existing and potential model systems for BE and EAC with their benefits and disadvantages.