sccomp: Robust differential composition and variability analysis for single-cell data.

Cellular omics such as single-cell genomics, proteomics, and microbiomics allow the characterization of tissue and microbial community composition, which can be compared between conditions to identify biological drivers. This strategy has been critical to revealing markers of disease progression, such as cancer and pathogen infection. A dedicated statistical method for differential variability analysis is lacking for cellular omics data, and existing methods for differential composition analysis do not model some compositional data properties, suggesting there is room to improve model performance. Here, we introduce sccomp, a method for differential composition and variability analyses that jointly models data count distribution, compositionality, group-specific variability, and proportion mean-variability association, being aware of outliers. sccomp provides a comprehensive analysis framework that offers realistic data simulation and cross-study knowledge transfer. Here, we demonstrate that mean-variability association is ubiquitous across technologies, highlighting the inadequacy of the very popular Dirichlet-multinomial distribution. We show that sccomp accurately fits experimental data, significantly improving performance over state-of-the-art algorithms. Using sccomp, we identified differential constraints and composition in the microenvironment of primary breast cancer.

Women with type 1 diabetes exhibit a progressive increase in gut Saccharomyces cerevisiae in pregnancy associated with evidence of gut inflammation.

AIMS: Studies of the gut microbiome have focused on its bacterial composition. We aimed to characterize the gut fungal microbiome (mycobiome) across pregnancy in women with and without type 1 diabetes. METHODS: Faecal samples (n = 162) were collected from 70 pregnant women (45 with and 25 without type 1 diabetes) across all trimesters. Fungi were analysed by internal transcribed spacer 1 amplicon sequencing. Markers of intestinal inflammation (faecal calprotectin) and intestinal epithelial integrity (serum intestinal fatty acid binding protein; I-FABP), and serum antibodies to Saccharomyces cerevisiae (ASCA) were measured. RESULTS: Women with type 1 diabetes had decreased fungal alpha diversity by the third trimester, associated with an increased abundance of Saccharomyces cerevisiae that was inversely related to the abundance of the anti-inflammatory butyrate-producing bacterium Faecalibacterium prausnitzii. Women with type 1 diabetes had higher concentrations of calprotectin, I-FABP and ASCA. CONCLUSIONS: Women with type 1 diabetes exhibit a shift in the gut mycobiome across pregnancy associated with evidence of gut inflammation and impaired intestinal barrier function. The relevance of these findings to the higher rate of pregnancy complications in type 1 diabetes warrants further study.

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework.

BACKGROUND: The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in the cell-free DNA of human blood and could possibly be harnessed as a new cancer biomarker. However, there has been limited use of rigorous experimental controls to account for contamination, which invariably affects low-biomass microbiome studies. RESULTS: We apply a combination of 16S-rRNA-gene sequencing and droplet digital PCR to determine if the specific detection of cell-free microbial DNA (cfmDNA) is possible in metastatic melanoma patients. Compared to matched stool and saliva samples, the absolute concentration of cfmDNA is low but significantly above the levels detected from negative controls. The microbial community of plasma is strongly influenced by laboratory and reagent contaminants introduced during the DNA extraction and sequencing processes. Through the application of an in silico decontamination strategy including the filtering of amplicon sequence variants (ASVs) with batch dependent abundances and those with a higher prevalence in negative controls, we identify known gut commensal bacteria, such as Faecalibacterium, Bacteroides and Ruminococcus, and also other uncharacterised ASVs. We analyse additional plasma samples, highlighting the potential of this framework to identify differences in cfmDNA between healthy and cancer patients. CONCLUSIONS: Together, these observations indicate that plasma can harbour a low yet detectable level of cfmDNA. The results highlight the importance of accounting for contamination and provide an analytical decontamination framework to allow the accurate detection of cfmDNA for future biomarker studies in cancer and other diseases.

First trimester screening for preterm and term pre-eclampsia by maternal characteristics and biophysical markers in a low-risk population.

AIM: To develop a combined predictive model for preterm and term pre-eclampsia (PE) during the first trimester of pregnancy. METHODS: This investigation was a nested case-control study in singleton pregnancies at the Maternal-Fetal Medicine Unit, University of Chile Hospital. A priori risks for preterm and term PE were calculated by multivariate logistic regression analyses. Biophysical markers were log10 -transformed and expressed as multiples of the median. A multivariate logistic regression analysis was used to estimate a combined predictive model of preterm and term PE. Detection rates at different cut-off points were determined by a receiver operator curve analysis of a posteriori risks. RESULTS: First trimester mean arterial pressure and uterine artery Doppler pulsatility index were significantly higher in women who develop PE than in the unaffected group. The detection rate of preterm PE based on maternal characteristics and biophysical markers was 72% at a 10% false-positive rate, corresponding to a cut-off risk of 1 in 50. The detection rate for term PE was 30% at a 10% false-positive rate. CONCLUSION: Preterm PE can be predicted by a combination of maternal characteristics and biophysical markers. However, first trimester screening is less valuable for term PE.

Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga Ulva spp.

Bacterial communities play an essential role for the function of marine macroalgae. Recent work has shown that bacterial communities associated with individual macroalgae possess on a local scale a functional core that is likely derived from diverse members of functional guilds. It is not known whether such functional cores also exist across large spatial scales or between closely related host species. To address this, we studied here the bacterial communities on three species of the green macroalgal genus Ulva from different geographic locations. While the taxonomic composition was too variable to describe a community core, we identified genes that were enriched across all Ulva samples as compared to the communities of the surrounding seawater. Of these core functions, 70% were consistently found and independent of the Ulva species and biogeography, while the remaining functions (~30%) are possibly involved in local or host-specific adaptations. For each host individual, the core functions are provided by bacteria with distinct phylogenetic origin and these bacteria could constitute a global guild of Ulva-associated bacteria. Together, our results demonstrate the presence of a stable core set of functional genes in the bacterial communities associated with closely related host species and across large biogeographies.

Metformin as a prophylactic treatment of gestational diabetes in pregnant patients with pregestational insulin resistance: A randomized study.

AIM: We aimed to assess the use of metformin (MTF) in the prevention of gestational diabetes mellitus (GDM) in patients with pregestational insulin resistance (PIR). METHODS: A double blind, multicenter, randomized trial was carried out in patients with a history of PIR and pregestational MTF treatment. Groups were allocated either to MTF 1700 mg/day or placebo. Patients were recruited between 12+0 and 15+6 gestational weeks, and treatment was extended until week 36. A multiple logistic regression analysis was applied to determine the relation between the use of metformin and the development of GDM. RESULTS: One hundred and forty one patients were randomized (68 patients in the MTF group and 73 in the placebo group). A total of 30 patients withdrew from the study during follow-up. Administration of MTF was not associated with a decrease in the incidence of GDM as compared to placebo (37.5% vs 25.4%, respectively; P = 0.2). Moreover, MTF administration was associated with a significant increase in drug intolerance as compared to placebo (14.3% vs 1.8%, respectively; P = 0.02). CONCLUSION: The use of MTF is not effective in prevention of GDM in populations with PIR. The use of MTF shows a significantly higher frequency of drug intolerance than placebo.

Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA.

Mycobacterium chimaera is an opportunistic environmental mycobacterium belonging to the Mycobacterium avium-M. intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest worldwide spread of a specific M. chimaera clone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays specific for M. chimaera Here, we assessed 354 mycobacterial genome sequences and confirmed that M. chimaera is a phylogenetically coherent group. In silico comparisons indicated six DNA regions present only in M. chimaera We targeted one of these regions and developed a TaqMan quantitative PCR (qPCR) assay for M. chimaera with a detection limit of 100 CFU/ml in whole blood spiked with bacteria. In vitro screening against DNA extracted from 40 other mycobacterial species and 22 bacterial species from 21 diverse genera confirmed the in silico-predicted specificity for M. chimaera Screening 33 water samples from heater-cooler units with this assay highlighted the increased sensitivity of PCR compared to culture, with 15 of 23 culture-negative samples positive by M. chimaera qPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens for M. chimaera.

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra.

Disease is increasingly viewed as a major factor impacting the health of both natural and cultured populations of marine organisms, including macroalgae. The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However, how pathogens cause the disease and how the entire macro algal-associated community is involved in the process is unclear. Here, we perform a metagenomic analysis of microbial communities associated with diseased and healthy D. pulchra across multiple bleaching events. Analysis of reconstructed 16S rRNA gene sequences showed that bacteria belonging to the families Rhodobacteraceae, Saprospiraceae and Flavobacteriaceae, including bacteria previously implicated in algal bleaching, to be enriched in diseased D. pulchra. Genes with predicted functions related to chemotaxis, motility, oxidative stress response, vitamin biosynthesis and nutrient acquisition were also prevalent in microbiomes of bleached algae, which may have a role in pathogenicity. Reconstruction of genomes that were abundant on bleached samples revealed that no single organism contains all bleaching-enriched functional genes. This observation indicates that potential virulence traits are distributed across multiple bacteria and that the disease in D. pulchra may result from a consortium of opportunistic pathogens, analogous to dysbiotic or polymicrobial diseases.

Second-Trimester Anterior Cervical Angle in a Low-Risk Population as a Marker for Spontaneous Preterm Delivery.

OBJECTIVE: The aim of this article is to assess the use of the anterior cervical angle (ACA) as a predictor of spontaneous preterm delivery (sPTD) at 20+0-24+6 weeks of gestation in an unselected population. METHODS: We conducted a nested case-control study that included 93 women who later delivered spontaneously <34 weeks of gestation and 225 controls. The ACA was assessed retrospectively on all selected images using ImageJ® software. The concordance correlation coefficient was determined for the assessment of interobserver variability. Continuous variables were adjusted by maternal characteristics and expressed as the z-score or multiples of the expected normal median (MoM) of the unaffected group. Logistic regression analysis was used to evaluate whether any maternal characteristics and ultrasound variables were significantly associated with sPTD <34 weeks. RESULTS: ACA z-score values were significantly greater in women who later delivered <34 weeks compared to controls (ACA z-score = 1.32 ± 0.57 vs. -0.09 ± 0.35; p = 0.035). The best prediction of sPTD <34 weeks was provided by a model that combined cervical length (CL) MoM, ACA z-score and maternal characteristics. For a fixed false-positive rate of 10%, the detection rate for this model was 37.6%. CONCLUSION: A model combining maternal history, CL and ACA at 20+0-24+6 weeks of gestation can predict approximately 40% of the severe preterm births.

Multiple opportunistic pathogens can cause a bleaching disease in the red seaweed Delisea pulchra.

While macroalgae (or seaweeds) are increasingly recognized to suffer from disease, in most cases the causative agents are unknown. The model macroalga Delisea pulchra is susceptible to a bleaching disease and previous work has identified two epiphytic bacteria, belonging to the Roseobacter clade, that cause bleaching under laboratory conditions. However, recent environmental surveys have shown that these in vitro pathogens are not abundant in naturally bleached D. pulchra, suggesting the presence of other pathogens capable of causing this algal disease. To test this hypothesis, we cultured bacteria that were abundant on bleached tissue across multiple disease events and assessed their ability to cause bleaching disease. We identified the new pathogens Alteromonas sp. BL110, Aquimarina sp. AD1 and BL5 and Agarivorans sp BL7 that are phylogenetically diverse, distinct from the previous two pathogens and can also be found in low abundance in healthy individuals. Moreover, we found that bacterial communities of diseased individuals that were infected with these pathogens were less diverse and more divergent from each other than those of healthy algae. This study demonstrates that multiple and opportunistic pathogens can cause the same disease outcome for D. pulchra and we postulate that such pathogens are more common in marine systems than previously anticipated.

Partitioning of functional and taxonomic diversity in surface-associated microbial communities.

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity.

Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community.

In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga's chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.

Assessment of Protein:Creatinine Ratio versus 24-Hour Urine Protein in the Diagnosis of Preeclampsia.

BACKGROUND/AIMS: Current evidence has tried to extrapolate the use of the protein:creatinine ratio (PCR) in a single urine sample as a rapid diagnostic tool for preeclampsia (PE). The present study addresses the effectiveness of the PCR in the differential diagnosis of the pregnancy hypertensive disorder (PHD). METHODS: This is a prospective study conducted on patients admitted during 1 year with a diagnosis of PHD. These pregnant women were assessed for the correlation between the 24-hour test and the PCR to detect significant proteinuria. A ROC curve was made to determine the PCR cutoff value that would offer the best positive predictive value (PPV) as an early predictor of global and severe PE. RESULTS: A total of 72 patients with 24-hour proteinuria and PCR were studied (49 with PE). A significant correlation between the quick and the deferred sampling was observed (r = 0.60; p < 0.001). The ROC analysis showed a PCR of 0.36 as the best cutoff value for the diagnosis of global PE (PPV 96.4%; false-positive rate 4.4%; AUC 0.8802) and a cutoff value of 4.58 (sensitivity: 100%; PPV 87.5%; false-positive rate 3.5%; AUC 0.9805) as the best cutoff for the diagnosis of severe proteinuria. CONCLUSIONS: PCR proved to be an effective test for the differential diagnosis of PHS.

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens.

Microorganisms are increasingly being recognized as the causative agents in the diseases of marine higher organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a common, temperate red macroalga, which suffers from a bleaching disease. Two bacterial strains, Nautella italica R11 and Phaeobacter gallaeciensis LSS9, have been shown in vitro to cause bleaching symptoms, but previous work has failed to detect them during a natural bleaching event. To provide a link between in vitro observations and natural occurrences of the disease, we employ here deep-sequencing of the 16S rRNA gene to comprehensively analyze the community composition of healthy and diseased D. pulchra samples from two separate locations. We observed operational taxonomic units (OTUs) with 100% identity and coverage to the 16S RNA gene sequence of both in vitro pathogens, but only the OTU with similarity to strain LSS9 showed a statistically significant higher abundance in diseased samples. Our analysis also reveals the existence of other bacterial groups within the families Rhodobacteraceae and Flavobacteriaceae that strongly contribute to difference between diseased and healthy samples and thus these groups potentially contain novel macroalgal pathogens and/or saprophytes. Together our results provide evidence for the ecological relevance of one kind of in vitro pathogen, but also highlight the possibility that multiple opportunistic pathogens are involved in the bleaching disease of D. pulchra.

Assessment of pregestational insulin resistance as a risk factor of preeclampsia.

AIM: To assess the impact that pregestational insulin resistance (PIR) has as a risk factor for preeclampsia (PE). METHODS: Nested case-control study that included patients with PIR and a control group that was randomly selected from pregnancies admitted to the Fetal Medicine Unit between January 2005 and May 2011. Clinical and hemodynamic variables were analyzed by a multiple logistic regression analysis. RESULTS: Of the 13,124 patients admitted during the study period, 119 had a diagnosis of PIR (0.9%). Patients with PIR were older and had a higher body mass index (BMI). PIR was also related to a significantly higher frequency of chronic hypertension (CrHT; 10.1 vs. 2.2%, p < 0.05) and hypothyroidism (5.0 vs. 1.6%, p < 0.05) than in the control group. Moreover, women with PIR were more likely to develop PE (8.4 vs. 4.2%, p < 0.05) and gestational diabetes mellitus (9.2 vs. 2.9%) than the control group. Multivariate analysis showed that maternal age, CrHT and altered uterine artery Doppler sonography during the first and second trimesters were good predictors of PE and that PIR was not. CONCLUSION: Although PIR correlates with PE, conditions related to the latter (CrHT, higher maternal age and increased BMI) may be predominant as risk factors for PE.

First-trimester adiponectin and subsequent development of preeclampsia or fetal growth restriction.

BACKGROUND/AIMS: The evidence regarding the utility of assessing first-trimester adiponectin (ApN) serum levels in early prediction of preeclampsia (PE) and fetal growth restriction (FGR) is contradictory. This study aims to determine the role of maternal serum ApN levels as an early predictor of PE and FGR. METHODS: A prospective case-control study among a pregnant population who attended their 11- to 14-week ultrasound scan at the University of Chile's Clinical Hospital's Fetal Medicine Unit. We included patients who developed PE or FGR (10 cases per group) and 35 healthy controls. We determined ApN levels in blood samples from these 55 patients using a commercial ELISA kit and assessed the relationship of ApN levels with variables like development of PE, FGR, weight at birth and maternal BMI. RESULTS: There were no significant differences among first-trimester ApN serum levels in the groups. Average concentrations were 8, 6.8 and 10.8 ng/ml for the control, PE and FGR groups, respectively. CONCLUSION: In our study, maternal serum ApN levels were not useful in predicting subsequent development of PE and FGR. However, maternal serum ApN concentration adjusted by BMI was significantly higher during the first trimester in women who later developed FGR.

Hepatitis aguda poralfa-metildopa durante el embarazo / Acute hepatitis due to alpha-methyldopa in pregnancy

La alfa-metildopa (AMD) es un fármaco de uso común durante en el tratamiento del síndrome hipertensivo crónico del embarazo. La hepatotoxicidad de este medicamento está descrita en forma excepcional en las gestantes. Se presenta el primer caso clínico reportado en Chile de hepatitis secundaria al uso de AMD durante el segundo trimestre del embarazo. Se propone una aproximación a su diagnóstico y tratamiento (AU)

Alpha-methyldopa (AMD) is a centrally-acting antihypertensive drug frequently used for the treatment of chronic hypertension during pregnancy. Acute hepatitis in pregnancy due to AMD is rare. We present the first case reported in Chile of AMD-induced hepatitis in the second trimester of pregnancy. An approach to the diagnosis and treatment of this entity is proposed (AU)

Muerte fetal: experiencia de 10 años en el Hospital Clínico de la Universidad de Chile / Fetal demise: a 10-year experience in Hospital Clínico of the University of Chile

Objetivo: Conocer la tasa de mortalidad fetal intermedia (TMFI) y tardía (TMFT) en la población gestante atendida en un período de 10 años en el Hospital Clínico de la Universidad de Chile. Material y métodos: Estudio descriptivo donde se analizaron los datos de la muertes fetales ocurridas a partir de las 22 semanas o 500 g de peso entre 1994 y 2004. Resultados: La TMFI fue de 1,43/1000 nacidos vivos (NV) y la TMFT fue de 4,28/1000 NV. Las principales etiologías asociadas según su prevalencia fueron: enfermedad materna, patología de anexos ovulares, malformaciones congénitas e hipoxia (el 39, el 36, el 19 y el 10%, respectivamente). Conclusión: La TMFT en este estudio es similar a la nacional (4,3/1000 NV

Objetive: To know Fetal Mortality Rate during ten years in the Hospital Clínico Universidad de Chile. Material and methods: Intermedial and Late Fetal Mortality Rate (IFMR­LFMR) for Hospital Clínico Universidad de Chile for the period between 1994 to 2004 were analyzed. The information was obtained from clinical date. Results: IFMR: 1,43/1000, LFMR 4,28/1000. Causes of intrauterine fetal death were: maternal diseases (39%), placental and funicular accident (36%), structural abnormality (19%) and hypoxia (10%). Conclusion: LFMR in this study is the same that the Chilean reality (4,3/1000) (AU)

[Recurrent Impetigo Herpetiformis: successfully managed with ciclosporine. Report of one case]. / Impétigo herpetiforme recurrente: manejo exitoso con ciclosporina.

Impetigo Herpetiformis is a high-risk gestational skin disease that represents a risk for both the mother and offspring. Its management is based on multisystemic support and maternal steroid therapy. When these measures are insufficient to control the disease, the association of ciclosporine to the treatment has been proposed. We report a 24 year-old woman with a 16 weeks pregnancy, that presented with Impetigo Herpetiformis. The disease was refractory to the use of steroids, the patient had a metabolic decompensation and a dehydration with electrolyte imbalance. Therefore, treatment with ciclosporine was initiated and a rapid regression of the lesions was observed. Gestation was maintained, with a good perinatal outcome.