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Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.

Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N 2 O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N 2 O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N 2 O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N 2 O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N 2 O concentration to increase the resolution of these findings., (Copyright © 2022. Published by Elsevier Ltd.)

" Candidatus Accumulibacter" was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as " Candidatus Accumulibacter phosphatis," despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer-scale differentiation into different "types" and "clades"; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, ppk1 , and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with " Candidatus Accumulibacter phosphatis," " Candidatus Accumulibacter delftensis," and " Candidatus Accumulibacter aalborgensis." To compare the species in situ , we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, " Ca . Accumulibacter" species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all " Ca . Accumulibacter" species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. IMPORTANCE " Candidatus Accumulibacter" is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms.

The bacterial genus Tetrasphaera encompasses abundant polyphosphate accumulating organisms (PAOs) that are responsible for enhanced biological phosphorus removal (EBPR) in wastewater treatment plants. Recent analyses of genomes from pure cultures revealed that 16S rRNA genes cannot resolve the lineage, and that Tetrasphaera spp. are from several different genera within the Dermatophilaceae. Here, we examine 14 recently recovered high-quality metagenome-assembled genomes from wastewater treatment plants containing full-length 16S rRNA genes identified as Tetrasphaera, 11 of which belong to the uncultured Tetrasphaera clade 3. We find that this clade represents two distinct genera, named here Ca. Phosphoribacter and Ca. Lutibacillus, and reveal that the widely used model organism Tetrasphaera elongata is less relevant for physiological predictions of this uncultured group. Ca. Phosphoribacter incorporates species diversity unresolved at the 16S rRNA gene level, with the two most abundant and often co-occurring species encoding identical V1-V3 16S rRNA gene amplicon sequence variants but different metabolic capabilities, and possibly, niches. Both Ca. P. hodrii and Ca. P. baldrii were visualised using fluorescence in situ hybridisation (FISH), and PAO capabilities were confirmed with FISH-Raman microspectroscopy and phosphate cycling experiments. Ca. Phosphoribacter represents the most abundant former Tetrasphaera lineage and PAO in EPBR systems in Denmark and globally., (© 2022. The Author(s).)

Objective: During the COVID-19 pandemic, the unemployment rate in the United States peaked at 14.8% in April 2020. We examined patterns in unemployment following this peak in counties with rapid increases in COVID-19 incidence., Method: We used CDC aggregate county data to identify counties with rapid increases in COVID-19 incidence (rapid riser counties) during July 1-October 31, 2020. We used a linear regression model with fixed effect to calculate the change of unemployment rate difference in these counties, stratified by the county's social vulnerability (an indicator compiled by CDC) in the two months before the rapid riser index month compared to the index month plus one month after the index month., Results: Among the 585 (19% of U.S. counties) rapid riser counties identified, the unemployment rate gap between the most and least socially vulnerable counties widened by 0.40 percentage point (p<0.01) after experiencing a rapid rise in COVID-19 incidence. Driving the gap were counties with lower socioeconomic status, with a higher percentage of people in racial and ethnic minority groups, and with limited English proficiency., Conclusion: The widened unemployment gap after COVID-19 incidence rapid rise between the most and least socially vulnerable counties suggests that it may take longer for socially and economically disadvantaged communities to recover. Loss of income and benefits due to unemployment could hinder behaviors that prevent spread of COVID-19 (e.g., seeking healthcare) and could impede response efforts including testing and vaccination. Addressing the social needs within these vulnerable communities could help support public health response measures., Competing Interests: The authors have declared that no competing interests exist.

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Northern post-glacial lakes are significant, increasing sources of atmospheric carbon through ebullition (bubbling) of microbially-produced methane (CH 4 ) from sediments. Ebullitive CH 4 flux correlates strongly with temperature, reflecting that solar radiation drives emissions. However, here we show that the slope of the temperature-CH 4 flux relationship differs spatially across two post-glacial lakes in Sweden. We compared these CH 4 emission patterns with sediment microbial (metagenomic and amplicon), isotopic, and geochemical data. The temperature-associated increase in CH 4 emissions was greater in lake middles-where methanogens were more abundant-than edges, and sediment communities were distinct between edges and middles. Microbial abundances, including those of CH 4 -cycling microorganisms and syntrophs, were predictive of porewater CH 4 concentrations. Results suggest that deeper lake regions, which currently emit less CH 4 than shallower edges, could add substantially to CH 4 emissions in a warmer Arctic and that CH 4 emission predictions may be improved by accounting for spatial variations in sediment microbiota., (© 2021. The Author(s).)

Candidatus Microthrix is one of the most common bulking filamentous microorganisms found in activated sludge wastewater treatment plants (WWTPs) across the globe. One species, Ca. M. parvicella, is frequently observed, but global genus diversity, as well as important aspects of its ecology and physiology, are still unknown. Here, we use the MiDAS ecosystem-specific 16S rRNA gene database in combination with amplicon sequencing of Danish and global WWTPs to investigate Ca. Microthrix spp. diversity, distribution, and factors affecting their global presence. Only two species were abundant across the world confirming low diversity of the genus: the dominant Ca. M. parvicella and an unknown species typically present along with Ca. M. parvicella, although usually in lower abundances. Both species were mostly found in Europe at low-to-moderate temperatures and their growth was favored in municipal WWTPs with advanced process designs. As no isolate is available for the novel species, we propose the name " Candidatus Microthrix subdominans." Ten high-quality metagenome-assembled genomes recovered from Danish WWTPs, including 6 representing the novel Ca. M. subdominans, demonstrated high genetic similarity between the two species with a likely preference for lipids, a putative capability to reduce nitrate and nitrite, and the potential to store lipids and poly-P. Ca. M. subdominans had a potentially more versatile metabolism including additional sugar transporters, higher oxygen tolerance, and the potential to use carbon monoxide as energy source. Newly designed fluorescence in situ hybridization probes revealed similar filamentous morphology for both species. Raman microspectroscopy was used to quantify the in situ levels of intracellular poly-P. Despite the observed similarities in their physiology (both by genomes and in situ ), the two species showed different seasonal dynamics in Danish WWTPs through a 13-years survey, possibly indicating occupation of slightly different niches. The genomic information provides the basis for future research into in situ gene expression and regulation, while the new FISH probes provide a useful tool for further characterization in situ . This study is an important step toward understanding the ecology of Ca. Microthrix in WWTPs, which may eventually lead to optimization of control strategies for its growth in this ecosystem., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Nierychlo, Singleton, Petriglieri, Thomsen, Petersen, Peces, Kondrotaite, Dueholm and Nielsen.)

Persons from racial and ethnic minority groups are disproportionately affected by COVID-19, including experiencing increased risk for infection (1), hospitalization (2,3), and death (4,5). Using administrative discharge data, CDC assessed monthly trends in the proportion of hospitalized patients with COVID-19 among racial and ethnic groups in the United States during March-December 2020 by U.S. Census region. Cumulative and monthly age-adjusted COVID-19 proportionate hospitalization ratios (aPHRs) were calculated for racial and ethnic minority patients relative to non-Hispanic White patients. Within each of the four U.S. Census regions, the cumulative aPHR was highest for Hispanic or Latino patients (range = 2.7-3.9). Racial and ethnic disparities in COVID-19 hospitalization were largest during May-July 2020; the peak monthly aPHR among Hispanic or Latino patients was >9.0 in the West and Midwest, >6.0 in the South, and >3.0 in the Northeast. The aPHRs declined for most racial and ethnic groups during July-November 2020 but increased for some racial and ethnic groups in some regions during December. Disparities in COVID-19 hospitalization by race/ethnicity varied by region and became less pronounced over the course of the pandemic, as COVID-19 hospitalizations increased among non-Hispanic White persons. Identification of specific social determinants of health that contribute to geographic and temporal differences in racial and ethnic disparities at the local level can help guide tailored public health prevention strategies and equitable allocation of resources, including COVID-19 vaccination, to address COVID-19-related health disparities and can inform approaches to achieve greater health equity during future public health threats., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

Objective: Priorities of the Centers for Disease Control and Prevention's 6|18 Initiative include outpatient asthma self-management education (ASME) and home-based asthma visits (home visit) as interventions for children with poorly-controlled asthma. ASME and home visit intervention programs are currently not widely available. This project was to assess the economic sustainability of these programs for state asthma control programs reimbursed by Medicaid., Methods: We used a simulation model based on parameters from the literature and Medicaid claims, controlling for regression to the mean. We modeled scenarios under various selection criteria based on healthcare utilization and age to forecast the return on investment (ROI) using data from New York. The resulting tool is available in Excel or Python., Results: Our model projected health improvement and cost savings for all simulated interventions. Compared against home visits alone, the simulated ASME alone intervention had a higher ROI for all healthcare utilization and age scenarios. Savings were primarily highest in simulated program participants who had two or more asthma-related emergency department visits or one inpatient visit compared to those participants who had one or more asthma-related emergency department visits. Segmenting the selection criteria by age did not significantly change the results., Conclusions: This model forecasts reduced healthcare costs and improved health outcomes as a result of ASME and home visits for children with high urgent healthcare utilization (more than two emergency department visits or one inpatient hospitalization) for asthma. Utilizing specific selection criteria, state based asthma control programs can improve health and reduce healthcare costs.

Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on isolates or enrichment cultures, but these may not reflect the true diversity and in situ activities of the syntrophs predominating in full-scale systems. Here we obtained 182 medium to high quality metagenome-assembled genomes (MAGs) from the microbiome of two full-scale anaerobic digesters. The transcriptomic response of individual MAG was studied after stimulation with low concentrations of acetate, propionate, or butyrate, separately. The most pronounced response to butyrate was observed for two MAGs of the recently described genus Candidatus Phosphitivorax (phylum Desulfobacterota), expressing a butyrate beta-oxidation pathway. For propionate, the largest response was observed for an MAG of a novel genus in the family Pelotomaculaceae, transcribing a methylmalonyl-CoA pathway. All three species were common in anaerobic digesters at Danish wastewater treatment plants as shown by amplicon analysis, and this is the first time their syntrophic features involved in SCFA oxidation were revealed with transcriptomic evidence. Further, they also possessed unique genomic features undescribed in well-characterized syntrophs, including the metabolic pathways for phosphite oxidation, nitrite and sulfate reduction.

High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities. IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird's-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data., (Copyright © 2020 Michaelsen et al.)

Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change 1 . However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health 2,3 . Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.

Objective: The objective of this study was to assess the potential health and budgetary impacts of implementing a pharmacist-involved team-based hypertension management model in the United States., Research Design: In 2017, we evaluated a pharmacist-involved team-based care intervention among 3 targeted groups using a microsimulation model designed to estimate cardiovascular event incidence and associated health care spending in a cross-section of individuals representative of the US population: implementing it among patients with: (1) newly diagnosed hypertension; (2) persistently (≥1 year) uncontrolled blood pressure (BP); or (3) treated, yet persistently uncontrolled BP-and report outcomes over 5 and 20 years. We describe the spending thresholds for each intervention strategy to achieve budget neutrality in 5 years from a payer's perspective., Results: Offering this intervention could prevent 22.9-36.8 million person-years of uncontrolled BP and 77,200-230,900 heart attacks and strokes in 5 years (83.8-174.8 million and 393,200-922,900 in 20 years, respectively). Health and economic benefits strongly favored groups 2 and 3. Assuming an intervention cost of $525 per enrollee, the intervention generates 5-year budgetary cost-savings only for Medicare among groups 2 and 3. To achieve budget neutrality in 5 years across all groups, intervention costs per person need to be around $35 for Medicaid, $180 for private insurance, and $335 for Medicare enrollees., Conclusions: Adopting a pharmacist-involved team-based hypertension model could substantially improve BP control and cardiovascular outcomes in the United States. Net cost-savings among groups 2 and 3 make a compelling case for Medicare, but favorable economics may also be possible for private insurers, particularly if innovations could moderately lower the cost of delivering an effective intervention.

The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature. The SMC clade rose to community dominance within permafrost, with a peak metagenome-based relative abundance of ∼60%. It was also physiologically active in the upper seasonally-thawed soil. Beyond Stordalen Mire, analysis of 16S rRNA gene surveys indicated a global distribution of this clade, predominantly in anaerobic, carbon-rich and cold environments. These findings establish the SMCs as four novel phenotypically and ecologically distinct species within a single novel genus, distinct from C. exile clade at the phylum level. The SMCs are thus part of a novel cold-habitat phylum for an understudied, globally-distributed superphylum encompassing the Caldiserica. We propose the names Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., Ca. Cryosericum gen. nov., Ca. Cryosericum septentrionale sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., and Ca. C. terrychapinii sp. nov., (Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.)

The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ 13 C-CH 4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.

As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.

Objective: To identify the extent to which the Homeland Security Exercise and Evaluation Program's (HSEEP) After Action Report/Improvement Plan (AAR/IP) template was followed by public health entities and facilitated the identification of detailed corrective actions and continuous improvement., Design: Data were drawn from the US H1N1 Public Health Emergency Response (PHER) federal grant awardees (n = 62). After action report/improvement plan text was examined to identify the presence of AAR/IP HSEEP elements and characterized as "minimally complete," "partially complete," or "complete." Corrective actions (CA) and recommendations within the IP focusing on performance deficits were coded as specific, measurable, and time-bound, and whether they were associated with a problem that met root cause criteria and whether the CA/recommendation was intended to address or fix the root cause., Main Outcome Measures: A total of 2619 CA/recommendations were identified. More than half (n = 1480, 57%) addressed root causes. Corrective actions/recommendations associated with complete AARs more frequently addressed root cause (58% vs 51%, χ = 9.1, P < 0.003) and were more specific (34% vs 23%, χ = 32.3, P < 0.0001), measurable (30% vs 18%, χ = 37.9, P < 0.0001), and time-bound (38% vs 15%, χ = 115.5, P < 0.0001) than partially complete AARs. The same pattern was not observed with completeness of IPs. Corrective actions and recommendations were similarly specific and measurable. Recommendations significantly addressed root cause more than CAs., Conclusions: Our analysis indicates a possible lack of awardee distinction between CA and recommendations in AARs. As HSEEP adapts to align with the 2011 National Preparedness Goal and National Preparedness System, future HSEEP documents should emphasize the importance of root cause analysis as a required element within AAR documents and templates in the exercise and real incident environment, as well as the need for specific and measurable CAs.

Background: Public health officials must frequently demonstrate the quality and value of public health services, especially during challenging fiscal climates. One of the ways that public health quality and accountability have been demonstrated is through the use of accreditation and standard setting initiatives., Objective: The objective of this analysis was to identify existing alignment opportunities between standards established by the Public Health Accreditation Board (PHAB) and the Centers for Disease Control and Prevention's (CDC's) public health preparedness (PHP) capabilities in order to optimize and leverage the connections for state and local public health professionals., Design: During March-May 2012, a PHAB/PHP crosswalk was developed by a research team from the CDC's Office for State, Tribal, Local and Territorial Support and Office of Public Health Preparedness and Response's Division of State and Local Readiness to examine the intersection of the PHP capabilities and the PHAB standards. The PHAB/PHP crosswalk used the CDC Public Health Preparedness Capabilities: National Standards for State and Local Planning (PHP Capabilities) and the PHAB Standards and Measures, Version 1.0 (PHAB Standards) as its source documents. To help illustrate the results of the crosswalk, alignment was also depicted through a network graph to transform the results into a visual depiction of the linkages between PHP capabilities and PHAB standards., Results: The most direct links to emergency preparedness were found in PHAB Domains 2 and 5. Opportunities for improved alignment were found throughout the standard documents, particularly in PHAB Domains 3, 8, and 11. The most direct links to accreditation were found in PHP capabilities 1, 2, 3, and 4., Conclusions: The results highlight the synergy between the infrastructure and foundational elements represented by accreditation and targeted programmatic activities supported by preparedness funding.

Introduction: In the event of a major chemical, biological, radiological, nuclear, or explosive (CBRNE) attack or a natural disaster, large quantities of pharmaceuticals and medical supplies may be required with little or no warning. Pharmaceutical surge capacity for immediate response, before Strategic National Stockpile (SNS) supplies become available, remains a significant gap in emergency preparedness. To date, limited attempts have been made to assess collective regional hospital pharmaceutical response capabilities. In this project, we characterized the level of hospital pharmaceutical response preparedness in a major metropolitan region., Methods: The Johns Hopkins Office of Critical Event Preparedness and Response (CEPAR) convened a collaborative partnership to assess hospital pharmaceutical response capabilities. A survey was developed to characterize pharmaceutical response preparedness to CBRNE threats., Results: All 22 acute care hospitals in the Maryland region were sent pharmaceutical response surveys, and responses were received from 86% (19/22). Within the past year, 84% (16/19) of hospitals had implemented an exercise with pharmacy participation. More than half of the hospitals expect to receive assistance from the SNS in 48 hours or less. Seventy-four percent (14/19) of the hospitals reported an additional dedicated reserve supply for biological events, 74% (14/19) for chemical events, and 58% (11/19) for radiological events., Conclusion: Many hospitals in this metropolitan region have taken important steps toward enhancing pharmaceutical preparedness. However, hospitals generally remain underprepared for CBRNE threats and collectively have limited supplies of antibiotics to provide prophylaxis or treatment for hospital staff, their families, and patients in the event of a significant biological incident.

Granulicatella species, formerly known as nutritionally variant streptococci, cause a variety of infections, primarily endocarditis. We report the first culture-proven case of a Granulicatella species causing septic arthritis. A 68-year-old female presented with knee pain and swelling. She was initially evaluated with arthrocentesis and arthroscopy, but no organism was identified. Her pain improved after a brief course of antibiotics but recurred 3 months later. She underwent repeat arthrocentesis, with direct inoculation of synovial fluid into blood culture bottles. Granulicatella adiacens was recovered from both bottles. She was treated with cefazolin for 4 weeks combined with gentamicin for the first 2 weeks. Her knee pain and swelling resolved without evidence of recurrence. Granulicatella should be considered in cases of septic arthritis with initially negative synovial fluid cultures. Inoculation of blood cultures bottles with synovial fluid may increase the diagnostic yield for these species.

Pirprofen (600 mg, 800 mg) and aspirin (3,600 mg) were compared in 30 outpatients (33-67 yr old) with definite or classical rheumatoid arthritis. After 10 wk of treatment with either pirprofen dose, the number of painful joints, grip strength, and the duration of morning stiffness improved significantly. Only the number of painful joints improved significantly with aspirin. The erythrocyte sedimentation rate decreased with aspirin and 600 mg pirprofen but increased (significantly) with 800 mg pirprofen. The differences in improvement between the 3 treatment groups were not statistically significant. Gastrointestinal disturbances were the most frequently reported side-effects in each treatment group. Central nervous system effects and tinnitus were reported by more patients in the aspirin group than in either of the pirprofen groups.