Novel sampling technique maintaining the two-dimensional organization of microbes during cultivation from chronic wounds: The Imprint method

This study aimed to develop and validate "the Imprint method,", a technique for sampling microbes from chronic wounds while preserving their two-dimensional spatial organization. We used nylon filters to sample bacteria and compared with sampling using Eswabs in 12 patients. The Imprint method identified a mean of 0.93 unique species more than Eswab (4.3 ± 2.2 and 3.4 ± 1.4 unique species, respectively; mean ± SD; n = 30). Accuracy between the Eswab and the Imprint method was 93.2% and in cases of disagreement between methods, Imprint had a higher sensitivity in 6/8 of the most prevalent species. In vitro validation confirmed that the Imprint method could transfer bacterial colonies while replicating their two-dimensional organization and the area covered by bacteria on the plate sampled. Clinical testing demonstrated that the imprint method is a rapid and feasible technique that identified more unique bacterial species than Eswab with a good agreement between methods but that Imprint was better at detecting important pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa. The Imprint method is a novel technique that cultures and records the two-dimensional organization of microbes, providing an alternative or supplement to conventional surface culture using Eswab.

Inhibition of Pseudomonas aeruginosa quorum sensing by chemical induction of the MexEF-oprN efflux pump

The cell-to-cell communication system quorum sensing (QS), used by various pathogenic bacteria to synchronize gene expression and increase host invasion potentials, is studied as a potential target for persistent infection control. To search for novel molecules targeting the QS system in the Gram-negative opportunistic pathogen Pseudomonas aeruginosa, a chemical library consisting of 3,280 small compounds from LifeArc was screened. A series of 10 conjugated phenones that have not previously been reported to target bacteria were identified as inhibitors of QS in P. aeruginosa. Two lead compounds (ethylthio enynone and propylthio enynone) were re-synthesized for verification of activity and further elucidation of the mode of action. The isomeric pure Z-ethylthio enynone was used for RNA sequencing, revealing a strong inhibitor of QS-regulated genes, and the QS-regulated virulence factors rhamnolipid and pyocyanin were significantly decreased by treatment with the compounds. A transposon mutagenesis screen performed in a newly constructed lasB-gfp monitor strain identified the target of Z-ethylthio enynone in P. aeruginosa to be the MexEF-OprN efflux pump, which was further established using defined mex knockout mutants. Our data indicate that the QS inhibitory capabilities of Z-ethylthio enynone were caused by the drainage of intracellular signal molecules as a response to chemical-induced stimulation of the MexEF-oprN efflux pump, thereby inhibiting the autogenerated positive feedback and its enhanced signal-molecule synthesis.

Reduced Skin Microbiome Diversity in Infancy Is Associated with Increased Risk of Atopic Dermatitis in High-Risk Children

It is currently unknown whether alterations in the skin microbiome exist before development of atopic dermatitis (AD). In this prospective Danish birth cohort of 300 children, we examined whether skin microbiome alterations during the first 2 months of life were associated with an increased risk of AD in the first 2 years and its severity after adjustment for environmental factors and selected skin chemokine and natural moisturizing factor levels. We found no overall association between the skin microbiome at birth and age 2 months and AD during the first 2 years of life. However, when restricting the analysis to children with at least one parent with atopy, a lower alpha diversity at age 2 months was associated with an increased risk of AD (adjusted hazard ratio = 1.7, 95% confidence interval = 1.1-2.6). We observed a stronger association in children where both parents had atopy (adjusted hazard ratio = 4.4, 95% confidence interval = 1.1-18.2). The putative pathogenic role of changes in the skin microbiome on AD risk remains uncertain but may play a role in those with an atopic predisposition.

A simplified bacterial community found within the epidermis than at the epidermal surface of atopic dermatitis patients and healthy controls

There has been considerable research into the understanding of the healthy skin microbiome. Similarly, there is also a considerable body of research into whether specific microbes contribute to skin disorders, with atopic dermatitis (AD) routinely linked to increased Staphylococcus aureus (S. aureus) colonisation. In this study, the epidermal surface of participants was sampled using swabs, while serial tape-stripping (35 tapes) was performed to sample through the stratum corneum. Samples were taken from AD patients and healthy controls, and the bacterial communities were profiled by metabarcoding the universal V3-V4 16S rRNA region. Results show that the majority of bacterial richness is located within the outermost layers of the stratum corneum, however there were many taxa that were found almost exclusively at the very outermost layer of the epidermis. We therefore hypothesise that tape-stripping can be performed to investigate the 'core microbiome' of participants by removing environmental contaminants. Interestingly, significant community variation between AD patients and healthy controls was only observable at the epidermal surface, yet a number of individual taxa were found to consistently differ with AD status across the entire epidermis (i.e. both the epidermal surface and within the epidermis). Sampling strategy could therefore be tailored dependent on the hypothesis, with sampling for forensic applications best performed using surface swabs and outer tapes, while profiling sub-surface communities may better reflect host genome and immunological status.

Defining the temporal relationship between the skin microbiome, immune response and skin barrier function during flare and resolution of atopic dermatitis: protocol of a Danish intervention study

INTRODUCTION

Lesional skin of atopic dermatitis (AD) is often colonised by Staphylococcus aureus and the bacterial abundance increases during a flare. However, the role of S. aureus and the skin microbiome in the pathogenesis of AD, including its influence on the dysfunctional skin barrier and immune response, remains to be elucidated. In this study, the temporal relationship between alterations in the skin barrier function, inflammation and microbiome is examined in adults with AD.

METHODS AND ANALYSIS

This clinical study consists of 81 adult patients with AD, as defined by the Hanifin and Rajka criteria, and 41 age and sex-matched controls. The objectives are to examine alterations in the skin microbiome, skin barrier and immune response during (1) an untreated AD flare, (2) an AD flare treated with topical corticosteroids (TCS), (3) an AD flare treated with systemic dicloxacillin/placebo and TCS or (4) cutaneous exposure to either autologous S. aureus, staphylococcal enterotoxin B or a vehicle. Skin biopsies, tape strips, skin and nasal swabs are collected and analysed using RNA sequencing, multiplex immunoassays, liquid chromatography-mass spectrometry and 16S rDNA. Blood samples are analysed for filaggrin gene mutations and leucocyte gene expression.

ETHICS AND DISSEMINATION

The scientific Ethical Committee of the Capital Region in Denmark (phases I and II: H-20011047, phases III and IV: H-21079287), the local data protection agency (phases I and II: P-2020-165, phases III and IV: P-2022-250) and the Danish Medicines Agency (phases III and IV: EudraCT 2021-006883-25, ClinicalTrials.gov: NCT05578482) have approved the studies. Participants will give written informed consent prior to study initiation. The study is conducted in accordance with the Helsinki Declaration. Outcomes will be presented at national and international conferences and in international peer-reviewed publications.

TRIAL REGISTRATION NUMBER

NCT05578482, EudraCT 2021-006883-2.

Involvement of Bacteria in the Pathological Changes Before Achilles Tendon Rupture: A Case Series Investigating 16S rDNA in 20 Consecutive Ruptures

Background

The source of the pathological changes that occur before an acute Achilles tendon rupture (ATR) is not fully understood. Bacterial DNA has previously been detected in samples from ruptured Achilles tendons, suggesting a pathogenic role of bacteria in ATR.

Purpose/Hypothesis

The purpose of this study was to investigate if DNA from bacteria was present in acutely ruptured Achilles tendons. We hypothesized that 20% to 30% of the samples from the rupture site and no samples from healthy tissue would be positive for bacterial DNA.

Study Design

Case series; Level of evidence, 4.

Methods

This study included 20 consecutive patients scheduled for surgical repair of an acute ATR. Tendon biopsy specimens were taken from the rupture site and from the healthy tendon tissue proximal to the rupture to act as a control. Samples were blinded to the technician and analyzed using polymerase chain reaction targeted to the bacterial 16S rDNA gene and Sanger sequencing to identify the bacterial species present. McNemar test for paired proportions was performed to test for statistically significant differences in the number of samples positive for bacterial DNA between the ruptured and control regions of the Achilles tendon.

Results

Of the 20 patients, 1 (5%) had a positive sample with bacterial DNA from the ruptured part of the Achilles tendon. The same patient also had a positive control sample, although with different bacterial DNA. An additional patient had a positive control sample. There was no statistically significant difference in the number of bacterial DNA-positive samples between the ruptured and control regions of the Achilles tendon. The bacteria found (Staphylococcus sp, Micrococcus sp, and Staphylococcus epidermidis) were normal commensal organisms on the human skin.

Conclusion

Bacterial DNA was infrequent in tissue from ruptured Achilles tendons and, if identified, likely was a result of contamination. This suggests that bacteria are not involved in the pathological changes occurring before rupture of the Achilles tendon.

Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms

Microbial biofilms are involved in a number of infections that cannot be cured, as microbes in biofilms resist host immune defenses and antibiotic therapies. With no strict biofilm-antibiotic in the current pipelines, there is an unmet need for drug candidates that enable the current antibiotics to eradicate bacteria in biofilms. We used high-throughput screening to identify chemical compounds that reduce the intracellular c-di-GMP content in Pseudomonas aeruginosa. This led to the identification of a small molecule that efficiently depletes P. aeruginosa for c-di-GMP, inhibits biofilm formation, and disperses established biofilm. A combination of our lead compound with standard of care antibiotics showed improved eradication of an implant-associated infection established in mice. Genetic analyses provided evidence that the anti-biofilm compound stimulates the activity of the c-di-GMP phosphodiesterase BifA in P. aeruginosa. Our work constitutes a proof of concept for c-di-GMP phosphodiesterase-activating drugs administered in combination with antibiotics as a viable treatment strategy for otherwise recalcitrant infections.

Comparison of near-background concentrations of Argon-37 and Xenon-133 in the atmosphere

Radioisotopes of the noble gases xenon and argon can be important indicators of underground nuclear explosions. The Comprehensive Nuclear-Test-Ban Treaty (CTBT) includes monitoring capabilities to identify potential nuclear explosions conducted in violation of the CTBT. This monitoring currently focuses on measurement of the xenon isotopes ^131mXe, ¹³³Xe, ^133mXe, and ¹³⁵Xe. However, it is predicted that within 100 days of an underground nuclear explosion (UNE) ³⁷Ar would be released to the atmosphere at higher concentrations than xenon and with a higher signal to background ratio, depending on the radioxenon background levels. Therefore, inclusion of ³⁷Ar measurement capabilities at atmospheric International Monitoring System (IMS) stations may represent an improvement in the capability to detect a nuclear explosion. At an IMS station location, an understanding of the expected range of background ³⁷Ar activity concentrations is critical to determining what levels would constitute an elevated concentration. This work describes our analysis of atmospheric samples for ³⁷Ar to evaluate the range of background concentrations. Samples were collected at multiple locations withing the United States, with approximately half coming from a sampler co-located with an IMS xenon monitoring station (RN75). The range of ³⁷Ar concentrations measured in atmospheric air samples was relatively narrow; for samples considered detectable, the minimum and maximum measured concentrations were 0.56 and 2.3 mBq/m³, respectively. Comparison of ³⁷Ar and ¹³³Xe concentrations measured at the IMS station indicated some correlation between the measured concentrations. The results presented here demonstrate the capability to detect background concentrations of ³⁷Ar in atmospheric air and provide a basis for potential implementation of ³⁷Ar monitoring at IMS stations.

Background concentrations of Argon-39 in shallow soil gas

While radioisotopes of noble gases are known to be indicators of underground nuclear explosions (UNE), McIntyre et al. (2017) was the first to report the presence of ³⁹Ar in shallow soil gas in association with a decades old UNE. While this finding hinted at the potential application of ³⁹Ar to be used as an indicator of a UNE, doing so would also require an understanding of the natural concentrations of ³⁹Ar present in soil gas. Without knowing the expected range and variability of naturally occurring concentrations of ³⁹Ar, it is difficult to determine what measured concentrations would be indicative of an elevated concentration. This paper presents results from 16 soil gas samples and three atmospheric air samples collected from various locations across the western United States. Shallow soil gas samples were collected into self-contained underwater breathing apparatus (SCUBA) tanks using a custom-built soil gas sampling system and then processed and analyzed for ³⁹Ar. The measured concentrations of ³⁹Ar varied from atmospheric air concentrations to about 3.5 times atmospheric air concentrations (58 mBq/m³). The results presented here represent the first measurements of natural background ³⁹Ar concentrations in shallow soil gas. This data will be necessary if ³⁹Ar is to be used as an indicator of UNE.

Bacterial aggregate size determines phagocytosis efficiency of polymorphonuclear leukocytes

The ability of bacteria to aggregate and form biofilms impairs phagocytosis by polymorphonuclear leukocytes (PMNs). The aim of this study was to examine if the size of aggregates is critical for successful phagocytosis and how bacterial biofilms evade phagocytosis. We investigated the live interaction between PMNs and Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and Staphylococcus epidermidis using confocal scanning laser microscopy. Aggregate size significantly affected phagocytosis outcome and larger aggregates were less likely to be phagocytized. Aggregates of S. epidermidis were also less likely to be phagocytized than equally-sized aggregates of the other three species. We found that only aggregates of approx. 5 μm diameter or smaller were consistently phagocytosed. We demonstrate that planktonic and aggregated cells of all four species significantly reduced the viability of PMNs after 4 h of incubation. Our results indicate that larger bacterial aggregates are less likely to be phagocytosed by PMNs and we propose that, if the aggregates become too large, circulating PMNs may not be able to phagocytose them quickly enough, which may lead to chronic infection.

Migration of noble gas tracers at the site of an underground nuclear explosion at the Nevada National Security Site

As part of an underground gas migration study, two radioactive noble gases (³⁷Ar and ¹²⁷Xe) and two stable tracer gases (SF₆ and PFDMCH) were injected into a historic nuclear explosion test chimney and allowed to migrate naturally. The purpose of this experiment was to provide a bounding case (natural transport) for the flow of radioactive noble gases following an underground nuclear explosion. To accomplish this, soil gas samples were collected from a series of boreholes and a range of depths from the shallow subsurface (3 m) to deeper levels (~160 m) over a period of eleven months. These samples have provided insights into the development and evolution of the subsurface plume and constrained the relative migration rates of the radioactive and stable gas species in the case when the driving pressure from the cavity is low. Analysis of the samples concluded that the stable tracer SF₆ was consistently enriched in the subsurface samples relative to the radiotracer ¹²⁷Xe, but the ratios of SF₆ and ³⁷Ar remained similar throughout the samples.

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches

OBJECTIVES

Rigorous visual evidence on whether or not biofilms are involved in diabetic foot osteomyelitis (DFO) is lacking. We employed a suite of molecular and microscopic approaches to investigate the microbiome, and phenotypic state of microorganisms involved in DFO.

METHODS

In 20 consecutive subjects with suspected DFO, we collected intraoperative bone specimens. To explore the microbial diversity present in infected bone we performed next generation DNA sequencing. We used scanning electron microscopy (SEM) and peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) with confocal microscopy to visualize and confirm the presence of biofilms.

RESULTS

In 19 of 20 (95%) studied patients presenting with DFO, it was associated with an infected diabetic foot ulcer. By DNA sequencing of infected bone, Corynebacterium sp. was the most commonly identified microorganism, followed by Finegoldia sp., Staphylococcus sp., Streptococcus sp., Porphyromonas sp., and Anaerococcus sp. Six of 20 bone samples (30%) contained only one or two pathogens, while the remaining 14 (70%) had polymicrobial communities. Using a combination of SEM and PNA-FISH, we identified microbial aggregates in biofilms in 16 (80%) bone specimens and found that they were typically coccoid or rod-shaped aggregates.

CONCLUSIONS

The presence of biofilms in DFO may explain why non-surgical treatment of DFO, relying on systemic antibiotic therapy, may not resolve some chronic infections caused by biofilm-producing strains.

Measurements of Argon-39 at the U20az underground nuclear explosion site

Pacific Northwest National Laboratory reports on the detection of ³⁹Ar at the location of an underground nuclear explosion on the Nevada Nuclear Security Site. The presence of ³⁹Ar was not anticipated at the outset of the experimental campaign but results from this work demonstrated that it is present, along with ³⁷Ar and ⁸⁵Kr in the subsurface at the site of an underground nuclear explosion. Our analysis showed that by using state-of-the-art technology optimized for radioargon measurements, it was difficult to distinguish ³⁹Ar from the fission product ⁸⁵Kr. Proportional counters are currently used for high-sensitivity measurement of ³⁷Ar and ³⁹Ar. Physical and chemical separation processes are used to separate argon from air or soil gas, yielding pure argon with contaminant gases reduced to the parts-per-million level or below. However, even with purification at these levels, the beta decay signature of ⁸⁵Kr can be mistaken for that of ³⁹Ar, and the presence of either isotope increases the measurement background level for the measurement of ³⁷Ar. Measured values for the ³⁹Ar measured at the site ranged from 36,000 milli- Becquerel/standard-cubic-meter-of-air (mBq/SCM) for shallow bore holes to 997,000 mBq/SCM from the rubble chimney from the underground nuclear explosion.

Demonstration of combined zero-valent iron and electrical resistance heating for in situ trichloroethene remediation

The effectiveness of in situ treatment using zero-valent iron (ZVI) for nonaqueous phase or significant sediment-associated contaminant mass can be limited by relatively low rates of mass transfer to bring contaminants in contact with the reactive media. For a field test in a trichloroethene (TCE) source area, combining moderate-temperature subsurface electrical resistance heating with in situ ZVI treatment was shown to accelerate TCE treatment by a factor of about 4 based on organic daughter products and a factor about 8 based on chloride concentrations. A mass-discharge-based analysis was used to evaluate reaction, dissolution, and volatilization processes at ambient groundwater temperature (~10 °C) and as temperature was increased up to about 50 °C. Increased reaction and contaminant dissolution were observed with increased temperature, but vapor- or aqueous-phase migration of TCE out of the treatment zone was minimal during the test because reactions maintained low aqueous-phase TCE concentrations.