What's Now and What's Next for Surgical Endometriosis Management in the Infertile Patient? An Evidence-Based Review for the General OB/GYN.

Endometriosis is a significant contributor to female infertility, and its complex nature and varied phenotypes lead to questions regarding the value of surgical management. In this manuscript, we summarize current evidence and recommendations regarding surgical treatment for infertility in peritoneal disease, endometriomas, adenomyosis, and deep endometriosis, and highlight recent evidence regarding perinatal outcomes in women with endometriosis. Our purpose is to provide a concise "user's guide" for decisions regarding the surgical management of endometriosis in patients with infertility and generate awareness of recent perinatal outcome data.

Temperature stability and enhanced transport properties by surface modifications of silica nanoparticle tracers for geo-reservoir exploration.

Tracer tests are an important tool for characterizing and monitoring subsurface reservoir properties. However, they are limited both because of the tracer molecules constraining factors such as irreversible adsorption, retention, and degradations, i.e. interaction processes of fluorophore molecule with surrounding media resulting in a large variation in transport properties. Elaborate tests utilizing more than one tracer to distinguish time or location of injection are complex and interpretation is ambiguous because each tracer interacts differently. In this study, we present an approach to increase tracer stability and enhance the transport uniformity of different tracers, thus making tests utilizing multiple tracers simpler and more feasible. We present this concept of tracer multiplicity by encapsulating an anionic, cationic or amphoteric fluorophore inside mesoporous silica nanoparticle carriers coated with a protective titania layer. Upon encapsulation, increased thermal resistance and drastically lowered sorption affinity towards quartz sand was detected in batch and flow-through experiments. An additional advantage of the presented nanoparticle tracers over molecular tracers is their modularity, which is demonstrated by surface modifications and application of additives that greatly reduce sorption and increase recovery rates in the flow experiments. With the here presented concept of tracer multiplicity, we introduce a new approach for colloidal tracer design that has the potential to expand and enhance measurable parameters, measurement accuracy and simplicity of analysis.

Clinical and genomic features of Mycobacterium avium complex: a multi-national European study.

BACKGROUND: The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. METHODS: Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. RESULTS: Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). CONCLUSIONS: This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.

Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing: From Sequence Data to Resistance Profiles.

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) isolates has been shown to provide accurate predictions for resistance and susceptibility for many first- and second-line anti-tuberculosis drugs. However, bioinformatic pipelines and mutation catalogs to predict antimicrobial resistances in MTBC isolates are often customized and detailed protocols are difficult to access. Here, we provide a step-by-step workflow for the processing and interpretation of short-read sequencing data and give an overview of available analysis pipelines.

Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing.

Whole genome sequencing (WGS) is becoming an important diagnostic tool for antimicrobial susceptibility testing of Mycobacterium tuberculosis complex (MTBC) isolates in many countries. WGS protocols usually start with the preparation of a DNA-library: the critical first step in the process. A DNA-library represents the genomic content of a DNA sample and consists of unique short DNA fragments. Although available DNA-library protocols come with manufacturer instructions, details of the entire process, including quality controls, instrument parameters, and run evaluations, often need to be developed and customized by each laboratory to implement WGS technology effectively. Here, we provide a detailed workflow for a DNA-library preparation based on an adapted Illumina protocol optimized for the reduction of reagent costs.

Titania-mediated stabilization of fluorescent dye encapsulation in mesoporous silica nanoparticles.

Mesoporous silica nanoparticles hosting guest molecules are a versatile tool with applications in various fields such as life and environmental sciences. Current commonly applied pore blocking strategies are not universally applicable and are often not robust enough to withstand harsh ambient conditions (e.g. geothermal). In this work, a titania layer is utilized as a robust pore blocker, with a test-case where it is used for the encapsulation of fluorescent dyes. The layer is formed by a hydrolysis process of a titania precursor in an adapted microemulsion system and demonstrates effective protection of both the dye payload and the silica core from disintegration under otherwise damaging external conditions. The produced dye-MSN@TiO2 particles are characterized by means of electron microscopy, elemental mapping, ζ-potential, X-ray diffraction (XRD), nitrogen adsorption, Thermogravimetric analysis (TGA), fluorescence and absorbance spectroscopy and Fourier Transform Infrared Spectroscopy - Total Attenuated Reflectance (FT-IR ATR). Finally, the performance of the titania-encapsulated MSNs is demonstrated in long-term aqueous stability and in flow-through experiments, where owing to improved dispersion encapsulated dye results in improved flow properties compared to free dye properties. This behavior exemplifies the potential advantage of carrier-borne marker molecules over free dye molecules in applications where accessibility or targeting are a factor, thus this encapsulation method increases the variety of fields of application.

Effectiveness of Manual Hysteroscopic Tissue Removal Device for Intrauterine Polyps in Infertile Women in Both Operating and Office Settings.

Background: Mechanical hysteroscopic tissue removal (mHTR) systems are widely used for removing intrauterine pathology. Given the startup and procedural costs for electrically powered mechanical units, disposable manual mHTR systems have been developed. Methods: With little published, we describe its effectiveness for hysteroscopic intrauterine polypectomy. Results: One-hundred fifty-seven infertile women underwent hysteroscopic polypectomy with the manual mHTR device. Complete removal was accomplished in all but three cases, with blood loss being <10 mL and all specimens deemed sufficient for histopathologic diagnosis. Conclusions: These results suggest that the disposable manual mHTR system is effective in removing endometrial polyps. Head-to-head comparisons with other alternative technologies are needed.

Challenging the gold standard: the limitations of molecular assays for detection of Mycobacterium tuberculosis heteroresistance.

OBJECTIVES: Heteroresistant infections are defined as infections in which a mixture of drug-resistant and drug-susceptible populations are present. In Mycobacterium tuberculosis (M. tb), heteroresistance poses a challenge in diagnosis and has been linked with poor treatment outcomes. We compared the analytical sensitivity of molecular methods, such as GeneXpert and whole genome sequencing (WGS) in detecting heteroresistance when compared with the 'gold standard' phenotypic assay: the agar proportion method (APM). METHODS: Using two rounds of proficiency surveys with defined monoresistant BCG strains and mixtures of susceptible/resistant M. tb, we determined the limit of detection (LOD) of known resistance associated mutations. RESULTS: The LOD for rifampin-R (RIF-R) detection was 1% using APM, 60% using GeneXpert MTB/RIF, 10% using GeneXpert MTB/RIF Ultra and 10% using WGS. While WGS could detect mutations beyond those associated with RIF resistance, the LOD for these other mutations was also 10%. Additionally, we observed instances where laboratories did not report resistance in the majority population, yet the mutations were present in the raw sequence data. CONCLUSION: The gold standard APM detects minority resistant populations at a lower proportion than molecular tests. Mycobacterium bovis BCG strains with defined resistance and extracted DNA from M. tb provided concordant results and can serve in quality control of laboratories offering molecular testing for resistance. Further research is required to determine whether the higher LOD of molecular tests is associated with negative treatment outcomes.

Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS.

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml-1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.

Case Report: Fetoscopic Laparoschisis (FETO-LAP)-A New Therapeutic Route to Explore for Fetuses with Severe Diaphragmatic Hernias.

BACKGROUND: The purpose of this report is to describe the seminal case of a near-term human fetus with a life-threatening left diaphragmatic hernia that underwent fetoscopic tracheal occlusion (FETO) combined with fetoscopic partial removal of herniated bowel from the fetal chest by fetoscopic laparoschisis (FETO-LAP). CASE SUMMARY: A life-threatening left diaphragmatic hernia (liver-up; o/e LHR of ≤25%; MRI lung volume ≤ 20%) was observed in a human fetus at 34 weeks of gestation. After counselling the mother about the high risks of postnatal demise if left untreated, the expected limitations of fetoscopic tracheal occlusion (FETO), and the previously untested option of combining FETO with fetoscopic laparoschisis, i.e., partial removal of the herniated bowel from the fetal chest (FETO-LAP), she consented to the latter novel treatment approach. FETO-LAP was performed at 36 + 5 weeks of gestation under general maternofetal anesthesia. Mother and fetus tolerated the procedure well. The neonate was delivered and the balloon removed on placental support at 37 + 2 weeks of gestation. On ECMO, a rapid increase in tidal volume was seen over the next eight days. Unfortunately, after this period, blood clots obstructed the ECMO circuit and the neonate passed away. DISCUSSION: This seminal case shows that in a fetus with severe left diaphragmatic hernia, partial removal of the herniated organs from the fetal chest is not only possible by minimally invasive fetoscopic techniques but also well tolerated. As the effect of FETO alone is limited in saving severely affected fetuses, combining FETO with fetoscopic laparoschisis (FETO-LAP) offers a new therapeutic route with multiple, potentially life-saving implications.

Microbial signatures in amniotic fluid at preterm birth and association with bronchopulmonary dysplasia.

BACKGROUND: Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. METHODS: AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. RESULTS: The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. CONCLUSIONS: Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD.

Blind spot in endocarditis guidelines: Mycobacterium chimaera prosthetic valve endocarditis after cardiac surgery-a case series.

Background: The recently published 2023 Duke-ISCVID Criteria for Infective Endocarditis for the first time consider mycobacteria (esp. Mycobacterium chimaera) as 'typical' microorganisms for prosthetic valve endocarditis (major criteria). This reflects the ongoing worldwide outbreak of M. chimaera prosthetic valve endocarditis. Case summary: Our case series demonstrates a diagnostic pathway for mycobacterial endocarditis. Symptoms are unspecific, and standard microbiological testing does not result in identification of the causative agent (see Graphical Abstract); therefore patients require special microbiological and imaging diagnostics. One patient with early diagnosis and stringent antibiotic and surgical therapy survived. Two patients with disseminated infection at the time point of diagnosis had fatal outcomes. Discussion: The diagnostic approach in our small retrospective case series is in line with the new modified Duke criteria and underlines the diagnostic gap in the previous definitions. Outcome of M. chimaera prosthetic valve endocarditis is related to timely diagnosis and anti-mycobacterial as well as surgical treatment. Non-tuberculous mycobacteria should be given more attention in future endocarditis guidelines.

Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region.

Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.

Multi-Dimensional Machine Learning Analysis of Polyaniline Films Using Stitched Hyperspectral ToF-SIMS Data.

The self-organizing map with relational perspective mapping (SOM-RPM) is an unsupervised machine learning method that can be used to visualize and interpret high-dimensional hyperspectral data. We have previously used SOM-RPM for the analysis of time-of-flight secondary ion mass spectrometry (ToF-SIMS) hyperspectral images and three-dimensional (3D) depth profiles. This provides insightful visualization of features and trends of 3D depth profile data, using a slice-by-slice view, which can be useful for highlighting structural flaws including molecular characteristics and transport of contaminants to a buried interface and characterization of spectra. Here, we apply SOM-RPM to stitched ToF-SIMS data sets, whereby the stitched data are used to train the same model to provide a direct comparison in both 2D and 3D. We conduct an analysis of spin-coated polyaniline (PANI) films on indium tin oxide-coated glass slides that were subjected to heat treatment under atmospheric conditions to model PANI as a conformal aerospace industry coating. Replicates were shown to be precisely equivalent, both spatially and by composition, indicating a clear threshold for annealing of the film. Quantitative assessment was performed on the chemical breakdown trends accompanying annealing based on peak ratios, while spectral analysis alone shows only very subtle differences which are difficult to evaluate quantitatively. The SOM-RPM method considers data sets in their totality and highlights subtle differences between samples often simply differences in peak intensity ratios.