Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

BACKGROUND

Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood.

RESULTS

Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems.

CONCLUSIONS

Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.

Anatomic and physiologic diagnostic discrepancies in fetuses with single ventricle congenital heart disease in a contemporary cohort

OBJECTIVE

Image quality of fetal echocardiography (FE) has improved in the recent era, but few recent studies have reported the accuracy of FE specifically in single ventricle congenital heart disease (SV). Our study aims to assess the ability of FE to correctly predict postnatal anatomy and physiology in SV in a contemporary cohort.

METHODS

The contemporary, clinical reports of FE with SV performed from 7/2017 to 7/2021 were compared with postnatal echocardiograms in a formal quality assurance program. SV were grouped by anatomic subtype. Diagnostic errors were designated as major if the error would have resulted in significant alteration in fetal counseling or postnatal management. Remaining errors were classified as minor. Physiologic discrepancies, including prostaglandin dependency (PGE-D), atrioventricular valve regurgitation (AVVR), pulmonary venous obstruction, and atrial septal restriction were assessed by review of postnatal course.

RESULTS

A total of 119 subjects were analyzed. SV subtypes in the cohort included hypoplastic left heart syndrome (HLHS) (n=68), tricuspid atresia (n=16), double inlet left ventricle (n=12), unbalanced atrioventricular canal (UAVC) (n=11), heterotaxy (n=9), and other (n=3). The rate of major anatomic and physiologic errors was low (n=6, 5.0%). A higher proportion of minor errors were noted in HLHS and tricuspid atresia but the differences were not statistically significant. Physiologic discrepancies were uncommon, with three major discrepancies including underestimation of degree of venous obstruction in one non-HLHS fetus with total anomalous pulmonary venous return, overestimation of atrial septal restriction in one HLHS fetus, and incorrect prediction of PGE-D with 1 false-negative for pulmonary blood flow. No discrepancy in degree of AVVR or atrial septal restriction affected postnatal care. Minor physiologic discrepancies included two false-positive predictions of PGE-D with 1 false-positive for ductal-dependent systemic flow, and 1 false-positive for pulmonary blood flow.

CONCLUSIONS

In this contemporary review of FE in SV at our center, there was high accuracy in describing anatomic and physiologic findings in fetuses with SV. Major physiologic discrepancies were uncommon but included important cases of false-negative prediction of PGE-dependence and underestimation of obstruction of total anomalous pulmonary venous return. These data can both inform more accurate counseling of families with SV fetuses and guide diagnostic improvement efforts. This article is protected by copyright. All rights reserved.

Radiotherapy for Liver Cancer: An International Multi-Centre Pooled Analysis of 925 Cases

PURPOSE/OBJECTIVE(S)

Primary and secondary liver cancer incidence is growing and has a poor prognosis. The standard use of radiation has been hampered by studies with a wide range of patients, different management protocols and varied outcomes. To overcome this heterogeneity in the literature, larger and higher-level trials are warranted, but, so far, have been difficult to implement. Therefore, pooled analyses may offer the best way to determine the benefit of radiation, identify treatment parameters needed to optimize treatment techniques, and identify patient factors that allow for better patient selection.

MATERIALS/METHODS

Patients with liver cancer treated by radiotherapy at centers in Canada, United States and Australia was pooled. Patient and treatment characteristics were noted, as well as the clinical outcomes of local control within 1 year, recurrence and mortality. Stepwise Cox proportional hazards models were used to identify significant predictors for recurrence and mortality. Patients were stratified by center, and primary versus metastatic disease.

RESULTS

A total of 925 patients were included in this study. Mean age was 67 years, and 45% had a primary diagnosis of hepatocellular carcinoma. 1-year local control rate was 80%. Median survival was 1.8 years (1.9 years for primary liver cancer, and 1.4 years for metastatic liver cancer). Higher total dose and BED was associated with better survival. Median time to recurrence was 1.5 years. Higher total dose was associated with lower risk of recurrence CONCLUSION: As one of the largest pooled analyses in hepatic cancer, this international multi-center study provides pragmatic data on clinical outcomes of patients receiving radiotherapy for liver cancer. This database may assist in better selection of patients for future studies and answer questions such as what is the optimal dose and which patients benefit from treatment.

Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms

Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax, supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.

The temporal burden of preparing catheters for re-use in adults with spinal cord injury: a cross-sectional study

STUDY DESIGN

Cross-sectional OBJECTIVES: Neurogenic lower urinary tract dysfunction is common among people with spinal cord injury (SCI). Although single-use clean intermittent catheterization is recommended to facilitate routine bladder emptying, catheter re-use is common. Barriers associated with the preparation (i.e., cleaning) of catheters for re-use are unknown. This study examined barriers to catheter re-use in adult individuals with SCI by assessing (1) the time needed to clean a catheter, and (2) the perceived difficulty of the catheter cleaning routine.

SETTING

Laboratory METHODS: Twenty individuals with chronic SCI ( ≥ 1 year since injury; Group 1 = 10 with tetraplegia; Group 2 = 10 with paraplegia) completed the study. Using a standardized cleaning procedure (i.e., Milton method), catheter cleaning was timed for each participant. Perceived difficulty was assessed using a 5-point Likert scale. Functional impairment was assessed with the Upper Extremity Motor Score (UEMS).

RESULTS

Significant between-group differences were observed for total cleaning time (Group 1 = 1584.1 ± 179.8 s; Group 2 = 1321.0 ± 93.8 s, p = 0.004) and perceived difficulty [Group 1 = 2.6 (2, 3); Group 2 = 2 (1.7, 2.3), p = 0.028]. Total cleaning time was significantly correlated with UEMS (ρ = -0.709, p ≤ 0.001) and perceived difficulty (ρ = 0.468, p = 0.037). UEMS emerged as an independent predictor of total cleaning time (R² = 0.745, β = -0.833, p ≤ 0.001).

CONCLUSIONS

Preparing catheters for re-use is time-intensive and difficult for people with higher SCI level, severity and more pronounced upper limb motor impairment, which was independently associated with total cleaning time. Performing this routine on a consistent basis would require a substantial time commitment and would have a profoundly negative impact on overall quality of life.

Borgs are giant genetic elements with potential to expand metabolic capacity

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as 'Borgs'. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Bacteriophages (phages) are obligate parasites that use host bacterial translation machinery to produce viral proteins. However, some phages have alternative genetic codes with reassigned stop codons that are predicted to be incompatible with bacterial translation systems. We analysed 9,422 phage genomes and found that stop-codon recoding has evolved in diverse clades of phages that infect bacteria present in both human and animal gut microbiota. Recoded stop codons are particularly over-represented in phage structural and lysis genes. We propose that recoded stop codons might function to prevent premature production of late-stage proteins. Stop-codon recoding has evolved several times in closely related lineages, which suggests that adaptive recoding can occur over very short evolutionary timescales.

Cardiovascular disease risk factors and outcomes of acute myocardial infarction in young adults in two nationwide cohorts in the united states

Funding Acknowledgements

Type of funding sources: None.

Background

Acute myocardial infarction (AMI) can have considerable morbidity and devastating socioeconomic and psychological consequences in young adults. Previous studies reveal that the decline in mortality in AMI has mainly been in the older population while being comparatively less significant in younger patients. This study compares young adults (18 to 44 years) hospitalized with AMI across two nationwide cohorts, 2007 and 2017, in the United States (US). It examines the burden of AMI hospitalizations, the prevalence of comorbidities, and in-hospital outcomes in young adults a decade apart. It highlights the rise in AMI hospitalizations, lack of decrease in mortality, sex-based and racial disparities, the surge in post-MI complications, and the decline in reperfusion interventions in young AMI patients over a decade.

Purpose

Coronary heart disease prevalence is challenging to ascertain in younger adults because of limited data and frequent silent clinical presentations. AMI and its complications can cause considerable morbidity, psychological trauma, and socioeconomic burden in the young.

Methods

We identified hospitalizations for AMI in young adults in 2007 and 2017 using the weighted data from the National Inpatient Sample (NIS), which covers 20% of stratified data of all non-federal community hospitals in the US. We compared the following data between the two cohorts: admission rates, sociodemographic features, in-hospital morbidity, complications, mortality, rate of coronary interventions, and healthcare utilization between the two cohorts. We used Pearson’s Chi-square test and Mann-Whitney U test to compare categorical and continuous variables, respectively. We also applied multivariable regression analyses to assess and compare the risk of cardiovascular complications and in-hospital mortality while controlling for confounders, including age, sex, race, median household income quartile, primary insurance enrolment, and pre-existing comorbidities.

Results

AMI’s incidence was higher in males in both the cohorts, although with a decline (71.1% vs 66.1%), whereas it rose from 28.9% to 33.9% in females. Hypertension (47.8% vs 60.7%), smoking (49.7% vs 55.8%), obesity (14.8% vs 26.8%), and diabetes mellitus (22.0% vs 25.6%) increased in the 2017 cohort (Table 1). We found no significant difference in all-cause mortality (aOR = 1.01 (0.93-1.10), p=0.749). Post-AMI complications, cardiogenic shock (aOR = 1.16 (1.06-1.27), p=0.001), and fatal arrhythmias increased. Reperfusion interventions decreased in the 2017 cohort (PCI; aOR=0.95 (0.91-0.98), p<0.001; CABG; aOR=0.66 (0.61-0.71), p<0.001) (Table 2).

Conclusion

Our study highlights the rise in AMI hospitalizations, plateauing of mortality, gender disparity, the surge in post-MI complications, and a reassuring decline in the requirement of reperfusion interventions in young AMI patients over a decade.

Species- and site-specific genome editing in complex bacterial communities

Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.

Closely related Lak megaphages replicate in the microbiomes of diverse animals

Lak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.

Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus

Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.

Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes

Thiocyanate (SCN^–) contamination threatens aquatic ecosystems and pollutes vital freshwater supplies. SCN^–-degrading microbial consortia are commercially adapted for remediation, but the impact of organic amendments on selection within SCN^–-degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN^– could be reproducibly selected for based on SCN^– loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN^–-contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN^–-degrading consortium. Five experiments were conducted over 790 days, and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to break down SCN^– using a novel thiocyanate desulfurase, oxidize resulting reduced sulfur, degrade product cyanate to ammonia and CO₂ via cyanate hydratase, and fix CO₂ via the Calvin–Benson–Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN^– at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.

Pulmonary artery injury in left atrial appendage closure device implantation: a systematic review of a potentially fatal complication

Background

Pulmonary artery (PA) injury is a rarely reported complication following percutaneous left atrial appendage closure (LAAC). This study aims to systematically review all reported cases of PA injury associated with LAAC.

Methods

PubMed/Medline, SCOPUS, EMBASE, Google Scholar and the MAUDE databases were searched to find studies reporting PA injury during or after LAAC with the Amplatzer Amulet (AA), Amplatzer Cardiac Plug (ACP) or Watchman device through October 2019. Categorical data were reported in terms of numbers and/or percentages (%).

Results

We found 13 cases (mean age 71.4 yrs) with reported PA injury associated with LAAC. Of these, 9 were case reports, 3 were reported in observational studies, and 1 was in the MAUDE database. Most cases (n=8) were reported in Europe followed by Australia (n=2) and Asia (n=2). The indication for device implantation in all patients was a high bleeding risk with anticoagulation for atrial fibrillation. Five cases were reported with the ACP (1/5 patients died), 5 with AA (2/5 patients died), and 3 with the Watchman (1/2 patients died). Acute and late presentations following implantation were reported for all three devices. 69.2% of cases (9/13) occurred acutely (during or within 24 hours of intervention). Of these, 3/9 occurred during device implantation. 2/4 of the delayed cases occurred >2 weeks following implantation. The mortality rate for acute and delayed cases was 22% (2/9 patients) and 50% (2/4 patients), respectively. A majority of the cases were attributable to barb/strut/hook injury of the PA. PA injury was associated with a mortality rate of approximately 31%. All surviving patients were managed with surgical intervention.

Conclusion

PA injury is an infrequently reported complication following LAAC and is associated with high mortality. Cases can present acutely (intra-procedurally or within 24 hours) or delayed (>24 hours post-implantation). A majority of cases are due to direct injury of the PA by the struts/hooks/barbs of the device. Practitioners should be cognizant of this life-threatening complication, which requires a high index of suspicion for diagnosis and can occur weeks after device implantation.

Funding Acknowledgement

Type of funding source: None

Rates and causes of readmissions following index admissions for Takotsubo syndrome-a meta-analysis of 118,941 index hospitalizations

Background

Rising trends in takotsubo syndrome (TTS)-related complications warrant data to identify the rate, causes and predictors of readmission on a large scale. We conducted the first-ever meta-analysis to evaluate the pooled rate of short-term and long-term readmissions after index TTS admissions.

Methods

PubMed/Medline, EMBASE and SCOPUS databases were systematically reviewed to find studies through October 2019 reporting rates and causes of readmission following index TTS admissions. Random effects models were used to estimate pooled rates and causes of readmissions and I2 statistics were used to report inter-study heterogeneity.

Results

A total of 16 cohorts with 118,941 TTS index admissions (mean age 65–75 yrs; female >85%, median follow-up 272.5 days) revealed a 16.6% [95% CI-13.2%-20.3%, I2=99%] pooled rate of readmission. Short-term and long-term pooled readmission rates are displayed in Fig.1. The readmission rate was higher in cohorts with young patients (<70 vs. >70 yrs), smaller sample size (n<100 vs. n>100) and single-centres vs. multicentres. Studies published from the USA (16.4% vs. 14.9%) had a higher readmission rate as compared to Italy. The most frequent causes were cardiac (40.6%), respiratory (15.7%) and renal (7.0%). Among readmissions with cardiac diagnoses, heart failure was most common (40.1%).

Conclusions

This global meta-analysis revealed that the pooled rate of readmission following index TTS admissions was ∼17% and causes were mainly cardiac or respiratory.

Funding Acknowledgement

Type of funding source: None

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets-from soil and seawater microbiomes-to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon's abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.IMPORTANCE One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism's activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of community interactions but often fail to link the two. Quantitative stable isotope probing (qSIP) is a method that can link the identity and functional activity of specific microbes within a naturally occurring community. Here, we explore how the resolution of density gradient fractionation affects the error and precision of qSIP results, how they may be improved via additional experimental replication, and discuss cost-benefit balanced scenarios for SIP experimental design.

Clades of huge phages from across Earth's ecosystems

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B₁₂ synthesis, but not of vitamin-B₇ , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B₁ synthesis transcripts. Furthermore, ambient vitamin-B₁ concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature.

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0–50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes. The PT modification genes and an adjacent putative restriction enzyme (RE) operon likely form a restriction modification (RM) system for defence from foreign DNA. PacBio sequencing showed >98% methylation at two motifs, and inferred PT guanine modification of 19% of possible TGCA sites. Metagenomic recruitment also reveals the putative virus region and PT modification and RE genes are present in 18-26%, 9-14% and <1.5% of natural populations at 150 m with ≥85% identity to strain SPOT01. The presence of multiple probable RM systems in a highly streamlined genome suggests a surprising importance for defence from foreign DNA for dilute populations that infrequently encounter viruses or other cells. This new strain provides new insights into the ecology, including viral interactions, of this important group of marine microbes.

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplankton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spearman>0.65) and became stronger (0.61 vs 0.58, t-test: P<0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho=0.49 vs 0.27; these results are consistent with strain-specific interactions. Mantel correlations suggested >1 μm (attached/large) prokaryotes are a major myovirus source. Consideration of microdiversity improved observation of apparent host and virus networks, and provided insights into the ecological and evolutionary factors influencing the success of lineages, with important implications to ecosystem resilience and microbial function.

Innate and humoral recognition of the products of cell death: differential antigenicity and immunogenicity in lupus

While apoptotic debris is believed to constitute the original antigenic insult in lupus (which is characterized by a time-dependent diversification of autoreactivity), whether such debris and autoantibodies specifically recognizing its constituents mediate differential effects on innate and humoral responses in lupus-prone mice is currently unknown. Apoptotic blebs (as opposed to cellular lysate) enhanced preferentially the maturation of dendritic cells (DCs) from bone marrow precursors drawn from lupus-prone mice. Murine, somatically mutated, apoptotic cell-reactive immunoglobulin (Ig)G monoclonal antibodies demonstrated enhanced recognition of DCs and also displayed a prominent lupus strain-specific bias in mediating DC maturation. Further, immunization of such antibodies specifically in lupus-prone mice resulted in widespread humoral autoreactivity; hypergammaglobulinaemia (a hallmark of systemic autoimmunity) was observed, accompanied by enhanced antibody titres to cellular moieties. Induced antibodies recognized antigens distinct from those recognized by the antibodies employed for immunization; in particular, nephritis-associated anti-double stranded (ds) DNA antibodies and neonatal lupus-associated anti-Ro60 antibodies were elicited by a non-dsDNA, non-Ro60 reactive antibody, and Sm was a favoured target. Further, only in lupus-prone mice did such immunization enhance the kinetics of humoral anti-self responses, resulting in the advanced onset of glomerulosclerosis. These studies reveal that preferential innate and humoral recognition of the products of cell death in a lupus milieu influence the indices associated with autoimmune pathology.

Evaluation of supraspinatus strengthening exercises based on fiber bundle architectural changes

Supraspinatus strengthening is an integral part of rehabilitation programs. However, there is disparity regarding the best exercise. Thus, we investigated the effects of supraspinatus strengthening exercises on muscle fiber bundle architecture using real-time ultrasound. Participants were randomized into full-can (FC; n = 12), empty-can (EC; n = 11,) and prone horizontal abduction (PHA; n = 11) groups and performed three sessions/week for 8 weeks. Each session involved four sets of exercise for weeks 1-4 and six sets for weeks 5-8 with eight repetitions/set. Images of supraspinatus were captured in 0° (relaxed) and 60° (contracted) glenohumeral abduction. Fiber bundle length (FBL), pennation angle, and muscle thickness were measured at beginning, mid, and end of training. Maximum isometric abduction strength was measured in full-can, empty-can, and prone horizontal abduction positions using a hand-held dynamometer. FBL decreased after 4 weeks in FC [relaxed: Δ = -0.54 cm, P = 0.001, d = 0.92; contracted: Δ = -0.27 cm, P = 0.008, d = 0.27] and EC [relaxed: Δ = -0.59 cm, P = 0.008, d = 0.86; contracted: Δ = -0.36 cm, P = 0.013, d = 0.59], but not in PHA [relaxed: Δ = -0.11, P = 0.121, d = 0.31; contracted: Δ = -0.06 cm, P = 0.486, d = 0.13]. Strength increased significantly from week 4-8 only in PHA (Δ = +0.96 kg, P = 0.004, d = 0.47) when tested in prone horizontal abduction position. Maintenance of FBL with increased strength indicates prone horizontal abduction may be a better exercise to strengthen supraspinatus.

Elucidation of the potential disease-promoting influence of IgM apoptotic cell-reactive antibodies in lupus

The undigested remnants of apoptosis are believed to stimulate the generation of autoantibodies in lupus. The biological properties of initiator, disease-specific IgM antibodies that specifically recognize apoptotic cells, readily detected in the sera of lupus patients, remain unclear. Apoptotic cell-reactive IgM monoclonal antibodies (generated from lupus-prone mice), as opposed to control IgM, preferentially stimulated maturation of bone marrow-derived dendritic cells (BMDCs) derived from such mice, relative to BMDCs derived from healthy mice. An influence of both antibody specificity and cell genotype was also apparent in the secretion of signature inflammatory cytokines. Immunization of such antibodies in lupus-prone animals induced increases in total serum IgG levels, with the elicited antibodies also preferentially recognizing moieties on dying cells. An expanded specificity was apparent both upon Western blot on cellular lysate and from the enhanced recognition of dsDNA, Ro60, RNP68 and Sm; the antibody most efficient in mediating autoreactive diversity, while being germline encoded, also induced the highest degree of phenotypic changes on BMDCs. Apoptotic cell-reactive IgM antibodies may therefore be potentially capable of influencing the course of systemic autoimmune disease by affecting both innate and adaptive immunity.

Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data

BACKGROUND

The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome.

RESULTS

Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment.

CONCLUSIONS

Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.

Beta diversity of marine bacteria depends on temporal scale

Factors controlling the spatial distribution of bacterial diversity have been intensely studied, whereas less is known about temporal changes. To address this, we tested whether the mechanisms that underlie bacterial temporal beta-diversity vary across different scales in three marine microbial communities. While seasonal turnover was detected, at least 73% of the community variation occurred at intra-seasonal temporal scales, suggesting that episodic events are important in structuring marine microbial communities. In addition, turnover at different temporal scales appeared to be driven by different factors. Intra-seasonal turnover was significantly correlated to environmental variables such as phosphate and silicate concentrations, while seasonal and interannual turnover were related to nitrate concentration and temporal distance. We observed a strong link between the magnitude of environmental variation and bacterial beta-diversity in different communities. Analogous to spatial biogeography, we found different rates of community changes across temporal scales.

Sternal tuberculosis

Extra-pulmonary tuberculosis constitutes 15-20% of total tuberculosis (TB) case load in immuno-competent patients. Affliction of the skeletal system is rare with still rarer presentation of sternal osteomyelitis even in endemic countries. A patient with primary sternal TB presenting with multiple cutaneous sinuses over the anterior chest wall is being reported. A high element of suspicion is needed more so in resource limited setting for early diagnosis and treatment.

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0-5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus-bacteria relationships were more cross-linked than protist-bacteria relationships, suggestive of increased taxonomic specificity in virus-bacteria relationships. We also found that 80% of bacterial-protist and 74% of bacterial-viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance.

Comparative Analysis of Birth Weight in a Hospital Over a Decade: Low Birth Weight Still a Major Problem

Introduction: The objective of this study was to compare the magnitude of birth weight and proportion of low birth weight in a hospital over a decade. Materials and Methods: A descriptive study was undertaken in a public funded hospital catering to rural and urban population of northern India. Pertinent information was collected for all intramural singleton births using structured proforma for a sample period in a calendar year. For comparison purpose birth data was extracted from log books for the corresponding period of previous decade also. Data management was done using MS excel sheet and analysis carried out by computing descriptive statistics using software statistical package. Results: The mean (2568 + 596.7 gm) & median (2600 gm) birthweight recorded for 2011 was low in-comparison to 2657 + 581.7gm (2750 gm) for 2001. The prevalence of low birth weight (LBW) was 36.1% (2011) in comparison to 30.5% (2001) and the state of deterioration was found to be statistically significant (p<0.001). Higher proportion of LBW birth was observed amongst un-booked ANC, pre-term, anemic mothers and whose residence was from outside the district of location of study institute (<0.001). Statistically significant (<0.001) and higher perinatal mortality was noticed in LBW neonates. Rising level of maternal education was protective against LBW. Mothers with their first pregnancy gave higher proportion of LBW births in comparison to mothers with higher gravida status (<0.001). DOI: http://dx.doi.org/10.3126/jnps.v33i1.6176 J Nepal Paediatr Soc. 2013;33(1):15-20.

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience

Observation of short-term temporal variation in bacterial and viral communities is important for understanding patterns of aquatic microbial diversity. We collected surface seawater once daily for 38 consecutive days with seven more samples interspersed over 40 more days at one location ∼2 km from Santa Catalina Island, California. Bacterial communities were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and viral communities were analyzed by terminal restriction fragment length polymorphism (TRFLP) of the conserved T4-like myoviral gene encoding the major capsid protein (g23). Common bacterial and viral taxa were consistently dominant, and relatively few displayed dramatic increases/decreases or 'boom/bust' patterns that might be expected from dynamic predator-prey interactions. Association network analysis showed most significant covariations (associations) occurred among bacterial taxa or among viral taxa and there were several modular (highly-interconnected) associations (P≤0.005). Associations observed between bacteria and viruses (P≤0.005) occurred with a median time lag of 2 days. Regression of all pairwise Bray-Curtis similarities between samples indicated a rate of bacterial community change that slows from 2.1%-0.18% per day over a week to 2 months; the rate stays around 0.4% per day for viruses. Our interpretation is that, over the scale of days, individual bacterial and viral OTUs can be dynamic and patterned; resulting in statistical associations regarded as potential ecological interactions. However, over the scale of weeks, average bacterial community variation is slower, suggesting that there is strong community-level ecological resilience, that is, a tendency to converge towards a 'mean' microbial community set by longer-term controlling factors.

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.

Population ecology of nitrifying archaea and bacteria in the Southern California Bight

Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia-oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time - a consistent feature of marine Crenarchaeota- however, average values were similar at different depths and ranged from 2.20 to 2.76 x 10(4) amoA copies ml(-1). Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r(2) = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) amoA genes at 150 m; these AOA groups were found to strongly co-vary in time (r(2) = 0.70, P < 0.001) whereas AOA : beta-AOB ratios ranged from 13 to 5630. Increases in the AOA : beta-AOB ratio correlated with the accumulation of nitrite (r(2) = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.

Evolution of interventions for complex coronary lesions

The exponential growth of percutaneous coronary intervention (PCI) has in large part been due to expansion of the indications to include the procedure in patients with extensive coronary disease, multiple risk factors, older age and comorbidities. Improvement in PCI equipment, development of new interventional techniques, and availability of myocardial and systemic support techniques have all contributed to this growth. With these advances, patients once considered high risk for PCI are no longer considered high risk. This article reviews the complex coronary lesions challenges, various interventional and pharmacologic strategies for optimal results and novel technology.

Preliminary survey of leptospirosis amongst febrile patients from urban slums of East Delhi

AIM

To determine the possibility of leptospirosis among patients from urban slums presenting with febrile illness during monsoon and post-monsoon season.

METHODS

Evidence of leptospirosis in 180 patients with febrile illness was determined by looking for presence of immunoglobulin M (IgM) antibodies by leptospiral IgM enzyme linked immunosorbent assay (ELISA). The test was carried out on 160 Widal test negative and 20 Widal test positive sera received from febrile patients during June to September 2001.

RESULTS

Twenty-seven out of 180 (15%) sera were positive for leptospiral IgM antibodies.

CONCLUSIONS

This preliminary survey indicates that leptospirosis could be an important cause of febrile illness in patients from urban slums during monsoon and post-monsoon season.

Outcome in children receiving continuous venovenous hemofiltration

OBJECTIVE

Continuous venovenous hemofiltration (CVVH) alone or with dialysis (D) has become an important supportive therapy for critically ill children with acute renal failure. Previous reports of pediatric patient outcome either mix CVVH/D with other renal replacement modalities or do not examine severity of illness. The current study examines only outcomes of children receiving CVVH/D using Pediatric Risk of Mortality (PRISM) scores to control for severity of illness.

PATIENTS

Twenty-one patients (mean age: 8.8 +/- 6.3 years; mean weight: 28.3 +/- 20.8 kg) received 22 courses of CVVH/D.

OUTCOMES

Nine (42.8%) of 21 patients survived. Nine (75%) of 12 deaths occurred within 25 days of pediatric intensive care unit (PICU) admission. Mean PRISM score at PICU admission and CVVH initiation were 13.1 +/- 5.8 and 15.4 +/- 8.9, respectively. Mean patient weight, age, PRISM score at PICU admission and at CVVH/D initiation, maximum pressor number, estimated glomerular filtration rate at CVVH/D initiation and change in mean airway pressure did not differ between survivors and nonsurvivors. The degree of fluid overload at CVVH/D initiation was significantly lower in survivors (16.4% +/- 13.8%) compared with nonsurvivors (34.0% +/- 21.0%), even when controlled for severity of illness by PRISM score. Mean cost of providing CVVH/D accounted for only 1% of total PICU cost per patient.

CONCLUSIONS

The pattern of early multiorgan system failure and death, minimal relative cost of CVVH/D provision, and potential for improved outcome with initiation of CVVH/D at lesser degrees of fluid overload are factors that may support early initiation of CVVH/D in critically ill children with acute renal failure.

Multiple aortic thrombi associated with protein C and S deficiency

We describe a woman with an unusual case of thromboembolism of the mesenteric artery in whom multiple thrombi were subsequently found in the aorta and right heart chambers on transesophageal echocardiography. Further evaluation revealed a deficiency of protein C and S plasma proteins, inhibitors of the clotting system. The patient was treated successfully with systemic anticoagulation. Aortic thrombus is common in the setting of underlying atherosclerosis. However, the association of aortic thrombus with a deficiency of protein C and S is rare. To our knowledge, this is the first reported case of mural thrombus of the thoracic aorta associated with combined protein C and S deficiency. Our report underscores the important role of transesophageal echocardiography in the evaluation of patients with arterial thromboembolism.

Factors affecting longevity of homograft valves used in right ventricular outflow tract reconstruction for congenital heart disease

BACKGROUND

Few studies have explored the long-term function of cryopreserved homograft valves used for reconstruction of the right ventricular tract (RVOT) in patients with congenital heart disease.

METHODS AND RESULTS

Among 205 patients receiving cryopreserved homografts for reconstruction of the RVOT between November 1985 and April 1999, the outcome of 220 homografts in 183 operative survivors was analyzed. There were 150 pulmonary and 70 aortic homografts used. Median age at implantation was 4.4 years (mean 6.9+/-7.6 years, range 3 days to 48 years). End points included (1) patient survival, (2) homograft failure (valve explant or late death), and (3) homograft dysfunction (homograft insufficiency or homograft stenosis). Survival was 88% at 10 years. Freedom from homograft failure was 74+/-4% at 5 years and 54+/-7% at 10 years. Univariable analysis identified younger age, longer donor warm ischemic time, valve Z: value <2, and previous procedure as risk factors for homograft failure and dysfunction. Aortic homograft type and extracardiac operative technique predicted homograft failure but not dysfunction. For patients </=1 year of age, valve type did not predict failure or dysfunction. Multivariable analysis identified younger age and longer donor warm ischemic time as risk factors for homograft failure and dysfunction, whereas, Z: value <2 and aortic valve type predicted homograft valve failure.

CONCLUSIONS

Homograft valves used for RVOT reconstruction provide effective intermediate palliation with excellent late survival. Factors that adversely affect graft longevity include younger age, longer donor warm ischemic time, smaller homograft size, use of aortic homograft in the older patient, and extracardiac operative technique.