SeqCode facilitates naming of South African rhizobia left in limbo

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.

Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3

The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Resource partitioning and amino acid assimilation in a terrestrial geothermal spring

High-temperature geothermal springs host simplified microbial communities; however, the activities of individual microorganisms and their roles in the carbon cycle in nature are not well understood. Here, quantitative stable isotope probing (qSIP) was used to track the assimilation of 13C-acetate and 13C-aspartate into DNA in 74 °C sediments in Gongxiaoshe Hot Spring, Tengchong, China. This revealed a community-wide preference for aspartate and a tight coupling between aspartate incorporation into DNA and the proliferation of aspartate utilizers during labeling. Both 13C incorporation into DNA and changes in the abundance of taxa during incubations indicated strong resource partitioning and a significant phylogenetic signal for aspartate incorporation. Of the active amplicon sequence variants (ASVs) identified by qSIP, most could be matched with genomes from Gongxiaoshe Hot Spring or nearby springs with an average nucleotide similarity of 99.4%. Genomes corresponding to aspartate primary utilizers were smaller, near-universally encoded polar amino acid ABC transporters, and had codon preferences indicative of faster growth rates. The most active ASVs assimilating both substrates were not abundant, suggesting an important role for the rare biosphere in the community response to organic carbon addition. The broad incorporation of aspartate into DNA over acetate by the hot spring community may reflect dynamic cycling of cell lysis products in situ or substrates delivered during monsoon rains and may reflect N limitation.

Robotic-Assisted Surgery Training (RAST): Assessment of Surgeon Console Ergonomic Skills

OBJECTIVE

The aim of this study was to evaluate the responsiveness of postgraduate year (PGY) general surgery residents (GSRs) to surgeon console ergonomics within the robotic-assisted surgery training (RAST) program.

DESIGN

This was a prospective educational study. GSRs were prepared with a pretraining educational video. Faculty provided one-on-one resident hands-on training and testing. Nine proficiency criteria (emergency stop & recover; left side pod adjustments; touchpad controls; footswitch panel; energy control pedals; camera control & focus; arm swap; master & finger clutch; dual console settings control) were assessed with a 5-point Likert-scale. Responsiveness was defined as change in performance over time. The robotic platform was Da Vinci Xi (Intuitive Surgical, Sunnyvale, CA). The Dundee ready educational environment measure (DREEM) inventory was used by GSRs to assess the educational environment.

SETTING

Tertiary care academic teaching institution.

PARTICIPANTS

A total of 22 GSRs: 4 PGY 1, 4 PGY 2, 4 PGY 3, 5 PGY 4, 5 PGY 5.

RESULTS

From June 2022 to March 2023 the hands-on console time decreased at testing when compared to baseline: median 39.0 (range 37-41) vs 20.1 (range 19-22) minutes, respectively. There was no difference in mean hands-on testing scores stratified by PGY: 4.85±0.4 PGY1; 4.98 ± 0.3 PGY2; 4.86 ± 0.4 PGY3, 4.88 ± 0.2 PGY4, and 4.91 ± 0.1 PGY5 (ANOVA test; p = 0.095). The overall DREEM score was 167.1 ± 16.9 with CAC = 0.908 (excellent internal consistency).

CONCLUSIONS

Training in ergonomics on the surgeon console impacted the responsiveness of the GSRs with 51% console time reduction. There were no differences in hands-on testing scores among PGYs. Perception of the educational environment by the GSRs was high.

Complex evolutionary history of photosynthesis in Bradyrhizobium

Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.

Functional biology and biotechnology of thermophilic viruses

Viruses have developed sophisticated biochemical and genetic mechanisms to manipulate and exploit their hosts. Enzymes derived from viruses have been essential research tools since the first days of molecular biology. However, most viral enzymes that have been commercialized are derived from a small number of cultivated viruses, which is remarkable considering the extraordinary diversity and abundance of viruses revealed by metagenomic analysis. Given the explosion of new enzymatic reagents derived from thermophilic prokaryotes over the past 40 years, those obtained from thermophilic viruses should be equally potent tools. This review discusses the still-limited state of the art regarding the functional biology and biotechnology of thermophilic viruses with a focus on DNA polymerases, ligases, endolysins, and coat proteins. Functional analysis of DNA polymerases and primase-polymerases from phages infecting Thermus, Aquificaceae, and Nitratiruptor has revealed new clades of enzymes with strong proofreading and reverse transcriptase capabilities. Thermophilic RNA ligase 1 homologs have been characterized from Rhodothermus and Thermus phages, with both commercialized for circularization of single-stranded templates. Endolysins from phages infecting Thermus, Meiothermus, and Geobacillus have shown high stability and unusually broad lytic activity against Gram-negative and Gram-positive bacteria, making them targets for commercialization as antimicrobials. Coat proteins from thermophilic viruses infecting Sulfolobales and Thermus strains have been characterized, with diverse potential applications as molecular shuttles. To gauge the scale of untapped resources for these proteins, we also document over 20,000 genes encoded by uncultivated viral genomes from high-temperature environments that encode DNA polymerase, ligase, endolysin, or coat protein domains.

Rain triggers seasonal stratification in a temperate shelf sea

The North Atlantic Storm Track acts as a conveyor belt for extratropical cyclones that frequently deliver high winds and rainfall to northwest European shelf seas. Storms are primarily considered detrimental to shelf sea stratification due to wind-driven mixing countering thermal buoyancy, but their impact on shelf scale stratification cycles remains poorly understood. Here, we show that storms trigger stratification through enhanced surface buoyancy from rainfall. A multidecadal model confirms that rainfall contributed to triggering seasonal stratification 88% of the time from 1982 to 2015. Stratification could be further modulated by large-scale climate oscillations, such as the Atlantic Multidecadal Variability (AMV), with stratification onset dates being twice as variable during a positive AMV phase than a negative one. Further insights into how changing storm activity will impact shelf seas are discussed beyond the current view of increasing wind-driven mixing, with significant implications for marine productivity and ecosystem function.

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park

Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0-60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.

Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum

The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.

Comparison of continuous versus intermittent enteral feeding in critically ill patients: a systematic review and meta-analysis

Background

The enteral route is commonly utilised to support the nutritional requirements of critically ill patients. However, there is paucity of data guiding clinicians regarding the appropriate method of delivering the prescribed dose. Continuous enteral feeding is commonly used; however, a bolus or intermittent method of administration may provide several advantages such as minimising interruptions. The purpose of this meta-analysis is to compare a continuous versus an intermittent or bolus enteral nutrition administration method.

Methods

A systematic review and meta-analysis were performed with studies identified from the PubMed, EMBASE, Cochrane Library and Web of Science databases. Studies were included if they compared a continuous with either an intermittent or bolus administration method of enteral nutrition in adult patients admitted to the intensive care unit. Study quality was assessed using the PEDro and Newcastle–Ottawa scoring systems. Review Manager was used for performing the random-effects meta-analysis on the outcomes of mortality, constipation, diarrhoea, increased gastric residuals, pneumonia, and bacterial colonisation.

Results

A total of 5546 articles were identified, and 133 were included for full text review. Fourteen were included in the final analysis. There was an increased risk of constipation with patients receiving continuous enteral nutrition (relative risk 2.24, 95% confidence interval 1.01–4.97, p = 0.05). No difference was identified in other outcome measures. No appreciable bias was identified.

Conclusion

The current meta-analysis has not identified any clinically relevant difference in most outcome measures relevant to the care of critically ill patients. However, there is a paucity of high-quality randomised controlled clinical trials to guide this decision. Therefore, clinicians may consider either dosing regimen in the context of the patient’s care requirements.

Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota

BACKGROUND

Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments.

RESULTS

Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages.

CONCLUSIONS

This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( https://seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.

Thoracic ultrasound for TB diagnosis in adults and children

Thoracic ultrasound is an appealing alternative to chest radiography for the diagnosis of TB. Based on research experience conducting thoracic ultrasound for adults and children in South Africa, three key considerations for potential scale-up were identified. First, thoracic ultrasound requires a comprehensive training programme for novice users; artificial intelligence may be used to simplify training and interpretation. Second, a robust ultrasound device is needed with good subpleural resolution and a probe suitable for children. Third, comprehensive scanning of the lungs is time-intensive, and shorter scanning protocols may be more feasible in clinical practice.

Treatment outcomes and safety in children with rifampicin-resistant TB

BACKGROUND: The treatment of rifampicin-resistant TB (RR-TB) in children is evolving rapidly. As newer regimens are introduced into routine care, it is vital to compare their outcome and safety with well-characterised clinical cohorts treated with historical regimens.METHODS: Study sample comprised a prospective observational cohort of children on routine RR-TB treatment, enrolled from 2011 to 2015 in Cape Town, South Africa. Children were followed for safety, treatment response and outcome.RESULTS: Of 136 children included, 27 (19.9%) were living with HIV and 48 (37.8%) had severe TB. The median time-to-culture conversion in children with bacteriological confirmation (n = 44) was 28.5 days (IQR 14.5-45). Overall, 118/129 (91.5%) had favourable TB treatment outcomes. Of 106 (77.9%) children who received an injectable drug, 9 (8.5%) developed hearing loss and 7/136 (5.1%) developed other Grade 3 or higher adverse events likely related to treatment.CONCLUSIONS: In this cohort with a substantial proportion of children with severe manifestations of TB and with HIV, TB treatment outcomes were excellent. Apart from hearing loss, few children developed severe adverse events related to treatment. This study provides robust reference data for future evaluation of shorter, injectable-sparing regimens.

Bradyrhizobium altum sp. nov., Bradyrhizobium oropedii sp. nov. and Bradyrhizobium acaciae sp. nov. from South Africa show locally restricted and pantropical nodA phylogeographic patterns

Africa is known for its rich legume diversity with a significant number of endemic species originating in South Africa. Many of these legumes associate with rhizobial symbionts of the genus Bradyrhizobium, of which most represent new species. Yet, none of the Bradyrhizobium species from South Africa have been described. In this study, phylogenetic analysis of 16S rRNA gene sequences of fourteen strains isolated in southern Africa from root nodules of diverse legumes (i.e., from the tribes Crotalarieae, Acacieae, Genisteae, Phaseoleae and Cassieae) revealed that they belong to the Bradyrhizobium elkanii supergroup. The taxonomic position and possible novelty of these strains were further interrogated using genealogical concordance of five housekeeping genes (atpD, dnaK, glnII, gyrB and rpoB). These phylogenies consistently recovered four monophyletic groups and one singleton within Bradyrhizobium. Of these groups, two were conspecific with Bradyrhizobium brasilense UFLA 03-321^T and Bradyrhizobium ivorense CI-1B^T, while the remaining three represented novel taxa. Their existence was further supported with genome data, as well as metabolic and physiological traits. Analysis of nodA gene sequences further showed that the evolution of these bacteria likely involved adapting to local legume hosts and environmental conditions through the acquisition, via horizontal gene transfer, of optimal symbiotic loci. We accordingly propose the following names Bradyrhizobium acaciae sp. nov. 10BB^T (SARCC 730^T = LMG 31409^T), Bradyrhizobium oropedii sp. nov. Pear76^T (SARCC 731^T = LMG 31408^T), and Bradyrhizobium altum sp. nov. Pear77^T (SARCC 754^T = LMG 31407^T) to accommodate three novel species, all of which are symbionts of legumes in South Africa.

Diversity of Root Nodule-Associated Bacteria of Diverse Legumes Along an Elevation Gradient in the Kunlun Mountains, China

Bacteria in root nodules of legumes play important roles in promoting plant growth. In this study, we investigated root nodule-associated bacteria isolated from leguminous plants along an elevation gradient on the northern slope of the Kunlun Mountains, China, using a cultivation approach. In total, 300 isolates were obtained from seven legume species within six ecological zones. Isolates were identified based on 16S rRNA gene phylogenetic analysis and potential rhizobia were further identified using a recA gene phylogeny. Among the isolates, Bacillales (particularly Bacillus) were the dominant isolates from all host legumes and all elevations (63.5%), followed by Rhizobiales (13%) and Pseudomonadales (11.7%). Less than 3% of the isolates belonged to Burkholderiales, Paenibacillales, Enterobacteriales, Actinomycetales, Sphingomonadales, Xanthomonadales, Chitinophagales, Brevibacillales, Staphylococcales, or Mycobacteriales. A few elevation-specific patterns emerged within the Bacillales and Pseudomonadales. For example, isolates related to the psychrotroph Bacillus psychrosaccharolyticus were only isolated from the highest elevation sites (>3,500 m) whereas those related to the mesophile Bacillus endophyticus were only isolated from lowest elevation sites (1,350 m), suggestive of a role of soil temperature in their distribution. Similarly, isolates related to Pseudomonas brassicacearum were the dominant Pseudomonadales isolates, but they were only isolated from middle and low elevations (<3,200 m). A total of 39 isolates belonged to the Rhizobiales, 36 of which were confirmed to the genus level using the recA gene. In all, Rhizobiales isolates were obtained from five different host legumes spanning the entire elevation gradient. Those from the low-elevation Qira Desert-Oasis Transition Zone (1,350-1,960 m) suggested some patterns of host preference. For example, most isolates from Albizia julibrissin formed a monophyletic group related to Rhizobium lemnae and most from Alhagi sparsifolia were closely related to Ensifer kummerowiae. In general, this study shows that most bacteria associated with root nodules of legumes are widely distributed in distinct ecological zones within a single geographic region but suggests that both climate and host interactions may influence their distributions.

High burden of viral respiratory co-infections in a cohort of children with suspected pulmonary tuberculosis

Background

The presentation of pulmonary tuberculosis (PTB) in young children is often clinically indistinguishable from other common respiratory illnesses, which are frequently infections of viral aetiology. As little is known about the role of viruses in children with PTB, we investigated the prevalence of respiratory viruses in children with suspected PTB at presentation and follow-up.

Methods

In an observational cohort study, children < 13 years were routinely investigated for suspected PTB in Cape Town, South Africa between December 2015 and September 2017 and followed up for 24 weeks. Nasopharyngeal aspirates (NPAs) were tested for respiratory viruses using multiplex PCR at enrolment, week 4 and 8.

Results

Seventy-three children were enrolled [median age 22.0 months; (interquartile range 10.0–48.0); 56.2% male and 17.8% HIV-infected. Anti-tuberculosis treatment was initiated in 54.8%; of these 50.0% had bacteriologically confirmed TB. At enrolment, ≥1 virus were detected in 95.9% (70/73) children; most commonly human rhinovirus (HRV) (74.0%). HRV was more frequently detected in TB cases (85%) compared to ill controls (60.6%) (p = 0.02). Multiple viruses were detected in 71.2% of all children; 80% of TB cases and 60.6% of ill controls (p = 0.07). At follow-up, ≥1 respiratory virus was detected in 92.2% (47/51) at week 4, and 94.2% (49/52) at week 8.

Conclusions

We found a high prevalence of viral respiratory co-infections in children investigated for PTB, irrespective of final PTB diagnosis, which remained high during follow up. Future work should include investigating the whole respiratory ecosystem in combination with pathogen- specific immune responses.

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase

Despite the high abundance of Aquificae in many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) of Thermocrinis Octopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional viral species. Despite low overall similarity among viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a PolA-type DNA polymerase polyprotein with likely accessory functions, a DNA Pol III sliding clamp, a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsid, large and small subunits of terminase, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivated Caudovirales. These viruses are predicted to infect Aquificae, as multiple CRISPR spacers matching the viral genomes were identified within the genomes and metagenomic contigs from these bacteria. Based on the predicted atypical bi-directional replication strategy, low sequence similarity to known viral genomes, and unique position in gene-sharing networks, we propose a new putative genus, "Pyrovirus," in the order Caudovirales.

Author Correction: Roadmap for naming uncultivated Archaea and Bacteria

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Paraburkholderia youngii sp. nov. and 'Paraburkholderia atlantica' - Brazilian and Mexican Mimosa-associated rhizobia that were previously known as Paraburkholderia tuberum sv. mimosae

Previous studies have recognized South and Central/Latin American mimosoid legumes in the genera Mimosa, Piptadenia and Calliandra as hosts for various nodulating Paraburkholderia species. Several of these species have been validly named in the last two decades, e.g., P. nodosa, P. phymatum, P. diazotrophica, P. piptadeniae, P. ribeironis, P. sabiae and P. mimosarum. There are still, however, a number of diverse Paraburkholderia strains associated with these legumes that have an unclear taxonomic status. In this study, we focus on 30 of these strains which originate from the root nodules of Brazilian and Mexican Mimosa species. They were initially identified as P. tuberum and subsequently placed into a symbiovar (sv. mimosae) based on their host preferences. A polyphasic approach for the delineation of these strains was used, consisting of genealogical concordance analysis (using atpD, gyrB, acnA, pab and 16S rRNA gene sequences), together with comparisons of Average Nucleotide Identity (ANI), DNA G+C content ratios and phenotypic characteristics with those of the type strains of validly named Paraburkholderia species. Accordingly, these 30 strains were delineated into two distinct groups, of which one is conspecific with 'P. atlantica' CNPSo 3155^T and the other new to Science. We propose the name Paraburkholderia youngii sp. nov. with type strain JPY169^T (= LMG 31411^T; SARCC751^T) for this novel species.

Human papillomavirus vaccine effectiveness within a cervical cancer screening programme: cohort study

OBJECTIVE

To assess the effectiveness of an HPV vaccination programme in reducing the risk of cervical abnormalities identified at subsequent screening.

DESIGN

Retrospective cohort study using administrative health data.

SETTING

General population of Ferrara Province, Italy.

POPULATION

Female residents born in 1986-1993 and participating in the organized cervical screening programme in 2011-2018, who were eligible for HPV vaccination in catch-up cohorts.

METHODS

Logistic regression to evaluate the potential association between abnormal cervical cytology and one, two, three or at least one dose of HPV vaccine.

MAIN OUTCOME MEASURES

Cervical abnormalities, as predicted by low-grade or high-grade cytology, by number of vaccine doses, stratified by age.

RESULTS

The sample consisted of 7785 women (mean age 27.5 years, SD 2.3). Overall, 391 (5.0%) were vaccinated with ≥1 dose and 893 (11.5%) had abnormal cytology. Women receiving at least one vaccine dose were significantly less likely to have an abnormal cytology (adjusted odds ratio 0.52; 95% confidence interval 0.34-0.79). Similar results were observed for women receiving a single dose, for both bivalent and quadrivalent vaccines, and applying buffer periods (excluding cytological outcomes within 1 month, 6 months and 1 year of the first dose).

CONCLUSIONS

In the context of an organised cervical screening programme in Italy, catch-up HPV vaccination almost halved the risk of cytological abnormalities.

TWEETABLE ABSTRACT

Among Ferrara women, vaccination against human papillomavirus halved the risk of screening cervical abnormalities.

The logistical management of tertiary urethral disease in the United Kingdom: Implications from an online audit of male reconstructive urethral surgery

Objective:

To determine those patient groupings, based on volume and risk, whose optimal urethral reconstructive management might be provided by a reorganisation of UK reconstructive surgeons.

Methods:

Between 2010 and 2017, ~689 men/year were enrolled onto an online audit platform collecting data about urethral reconstruction in the UK; this accrual was compared against hospital episode statistics (HES). The available workforce, and where this was based, was collected. Individual and institutional incumbent patient volumes, pathology, surgical complexity and outcomes from treatment were collated to stratify volume/risk groups.

Results:

More than 90% of all HES-recorded data were accrued, being provided by 50 surgeons at 39 operative sites. Most reconstructive surgery was provided at 10 centres performing >20 procedures/year. More than 50% of all interventions were of a high-volume low-risk type. Of activity, 32.3% was intermediate volume or moderate risk, and 12.5% of men presented for lower-volume or higher-risk procedures.

Conclusion:

Correlation of detailed volume/outcome data allows the definition of patient populations presenting for urethral reconstruction. Stratification of each group’s management, to optimise the surgical outcome, may be applied to a hierarchical service delivery model based on the complexity of the patient’s presenting urethral pathology.

Level of evidence:

Level IV

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

THU0540 A PHASE 2B STUDY OF INTRAVENOUSLY (IV) ADMINISTERED TC 99M TILMANOCEPT TO DETERMINE DIFFERENTIAL UPTAKE, REPRODUCIBILITY OVER TIME AND IMAGE STABILITY IN HEALTHY SUBJECTS AND IN PATIENTS WITH RHEUMATOID ARTHRITIS (RA) ON STABLE TREATMENT

Background:

At present, there are no reliable noninvasive means to directly monitor disease activity in RA patients. Activated macrophages are a critical component of the inflammatory etiology of RA due to their role in prolonged RA joint inflammation and destruction through the release of pro-inflammatory cytokines and chemokines. Tc 99m tilmanocept is a radiopharmaceutical imaging agent that binds with high affinity to the macrophage mannose receptor CD206 that resides on activated macrophages. Previous clinical trials demonstrated safety and tolerability of Tc 99m tilmanocept, as well as a determination of optimal clinical dose and timeframe for RA imaging.

Objectives:

The current phase 2b study aims to evaluate reproducibility and stability of imaging and will assess quantitative Tc 99m tilmanocept uptake cut points that reliably enable discrimination between joints of healthy people and RA patients.

Methods:

The analysis cohort contained 18 healthy controls (HC) clinically free of inflammatory joint disease and 12 subjects with clinically diagnosed RA who are on stable anti-inflammatory and/or anti-rheumatic therapy. Each subject received a 150-mcg dose of tilmanocept radiolabeled with 10 mCi of Tc 99m in a 3mL IV injection. Injection was followed by planar imaging at 60 and 180 minutes for both HC and RA subjects on study Day 0 and repeated in RA subjects on Day 8. Images were quantitatively assessed to detect localization within synovial spaces of bilateral hands and wrists by determining average pixel intensity in each region of interest relative to average pixel intensity in a joint-specific reference region.

Results:

Data obtained from the interim analysis support the hypothesis that Tc 99m tilmanocept imaging can provide robust quantitative imaging in HC and RA subjects. Repeat images within and between days demonstrate root mean squared differences that are approximately 10% or less of the observed localization of Tc 99m tilmanocept. Qualitatively, images of HC indicated no disease-related site-specific localization, whereas localization is present in RA subjects at levels expected given the difference in macrophage number and density in different pathotypes of RA. Notably, images from patients with active RA exhibit the same localization patterns on images taken in a test-retest fashion on the same day as well as in subjects with images acquired on Day 0 and Day 8 (see Figure 1). These results show low imaging readout variability, enabling reliable quantification of joints with RA-involved macrophage-mediated inflammation. Analysis of the HC and RA images was used to determine initial quantitative “cut-points” to differentiate between joints with and without the inflammation typically seen in RA.

Figure 1.

Tilmanocept consistently localizes in areas of macrophage-driven inflammation, demonstrating low variability. RA patients exhibit reproducible localization over a 1-week period. Typical of healthy subjects, no evidence of inflammation-related Tc 99m tilmanocept uptake was observed in the healthy control. Images on the right show same patient imaged on 2 different days.

Conclusion:

Tc 99m tilmanocept imaging of the joints in healthy subjects as well as in patients with active RA under stable treatment is reproducible and stable over time. The results confirmed that the signal in joints of healthy subjects and RA patients can be quantified and used to establish cut points to distinguish inflamed and non-inflamed joints on a joint-by-joint basis. These results provide the foundation for a noninvasive, objective method to monitor activity in macrophage-driven inflammation in joints of patients with RA.

Disclosure of Interests:

Ayah Hussein Employee of: Currently employed by Navidea Biopharmaceuticals, David Ralph Consultant of: Previous consultant for Navidea Biopharmaceuticals, Employee of: Currently employed by Navidea Biopharmaceuticals, Beth Potter Employee of: Currently employed by Navidea Biopharmaceuticals, Bonnie Abbruzzese Employee of: Currently employed by Navidea Biopharmaceuticals, Rachael Hershey Employee of: Currently employed by Navidea Biopharmaceuticals, Katherine Repp Employee of: Previously employed by Navidea Biopharmaceuticals, Haya Shakhtra Employee of: Currently employed by Navidea Biopharmaceuticals, Mehak Goel Employee of: Currently employed by Navidea Biopharmaceuticals, Madison Palmer Employee of: Currently employed by Navidea Biopharmaceuticals, Allison Kissling Employee of: Previously employed by Navidea Biopharmaceuticals, Carley Hartings Employee of: Previously employed by Navidea Biopharmaceuticals, Michael Blue Employee of: Currently employed by Navidea Biopharmaceuticals, Michael Rosol Employee of: Currently employed by Navidea Biopharmaceuticals

All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy

In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95-96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria. As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.

High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants

In this report, we explored the benefits of cyclic ion mobility (cIM) mass spectrometry in the analysis of isomeric post-transcriptional modifications of RNA. Standard methyl-cytidine samples were initially utilized to test the ability to correctly distinguish different structures sharing the same elemental composition and thus molecular mass. Analyzed individually, the analytes displayed characteristic arrival times (tD ) determined by the different positions of the modifying methyl groups onto the common cytidine scaffold. Analyzed in mixture, the widths of the respective signals resulted in significant overlap that initially prevented their resolution on the tD scale. The separation of the four isomers was achieved by increasing the number of passes through the cIM device, which enabled to fully differentiate the characteristic ion mobility behaviors associated with very subtle structural variations. The placement of the cIM device between the mass-selective quadrupole and the time-of-flight analyzer allowed us to perform gas-phase activation of each of these ion populations, which had been first isolated according to a common mass-to-charge ratio and then separated on the basis of different ion mobility behaviors. The observed fragmentation patterns confirmed the structures of the various isomers thus substantiating the benefits of complementing unique tD information with specific fragmentation data to reach more stringent analyte identification. These capabilities were further tested by analyzing natural mono-nucleotide mixtures obtained by exonuclease digestion of total RNA extracts. In particular, the combination of cIM separation and post-mobility dissociation allowed us to establish the composition of methyl-cytidine and methyl-adenine components present in the entire transcriptome of HeLa cells. For this reason, we expect that this technique will benefit not only epitranscriptomic studies requiring the determination of identity and expression levels of RNA modifications, but also metabolomics investigations involving the analysis of natural extracts that may possibly contain subsets of isomeric/isobaric species.

Acceptability of a first-line anti-tuberculosis formulation for children: qualitative data from the SHINE trial

SETTING: We conducted a qualitative exploration into the palatability and acceptability of a novel fixed-dose combination (FDC) anti-tuberculosis drug. This study was nested in the SHINE (Shorter treatment for minimal TB in children) trial, which compares the safety and efficacy of treating non-severe drug-susceptible tuberculosis (TB) with a 6 vs. 4 months anti-tuberculosis regimen in children aged 0-16 years. Participants were recruited in Cape Town, South Africa.OBJECTIVE: To describe the palatability and acceptability of a FDC of rifampicin, isoniazid and pyrazinamide among South African children and their caregivers in the SHINE trial.METHODS: We conducted 20 clinic observations of treatment administration, during which we conducted 16 semi-structured interviews with children and their caregivers. Data were organised thematically to report on experiences with administering and ingesting the FDC.RESULTS: Children and caregivers' experiences varied from delight to disgust. In general, participants said that the FDC compared favourably to other formulations. Pragmatic challenges such as dissolving the FDC and the time required to administer the FDC impeded caregivers' ability to integrate treatment into their daily routines. Drug manipulation was common among caregivers to improve TB treatment administration.CONCLUSION: This novel FDC appears acceptable for children, albeit with practical challenges to administration. Scale-up of FDC use should include supplementary intervention components to support caregivers.

Successful development of methodology for detection of hapten-specific contact hypersensitivity (CHS) memory in swine

Hapten contact hypersensitivity (CHS) elicits a well-documented inflammation response that can be used to illustrate training of immune cells through hapten-specific CHS memory. The education of hapten-specific memory T cells has been well-established, recent research in mice has expanded the “adaptive” characteristic of a memory response from solely a function of the adaptive immune system, to innate cells as well. To test whether similar responses are seen in a non-rodent model, we used hapten-specific CHS to measure the ear inflammation response of outbred pigs to dinitrofluorobenzene (DNFB), oxazolone (OXA), or vehicle controls. We adapted mouse innate memory literature protocols to the domestic pig model. Animals were challenged up to 32 days post initial sensitization exposure to the hapten, and specific ear swelling responses to this challenge were significant for 7, 21, and 32 days post-sensitization. We established hapten-specific CHS memory exists in a non-rodent model. We also developed a successful protocol for demonstrating these CHS responses in a porcine system.

Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus

The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.

The synergistic effect of concatenation in phylogenomics: the case in Pantoea

With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.

Genome-informed Bradyrhizobium taxonomy: where to from here?

Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels.

An inverse free electron laser acceleration-driven Compton scattering X-ray source

The generation of X-rays and γ-rays based on synchrotron radiation from free electrons, emitted in magnet arrays such as undulators, forms the basis of much of modern X-ray science. This approach has the drawback of requiring very high energy, up to the multi-GeV-scale, electron beams, to obtain the required photon energy. Due to the limit in accelerating gradients in conventional particle accelerators, reaching high energy typically demands use of instruments exceeding 100’s of meters in length. Compact, less costly, monochromatic X-ray sources based on very high field acceleration and very short period undulators, however, may enable diverse, paradigm-changing X-ray applications ranging from novel X-ray therapy techniques to active interrogation of sensitive materials, by making them accessible in energy reach, cost and size. Such compactness and enhanced energy reach may be obtained by an all-optical approach, which employs a laser-driven high gradient accelerator based on inverse free electron laser (IFEL), followed by a collision point for inverse Compton scattering (ICS), a scheme where a laser is used to provide undulator fields. We present an experimental proof-of-principle of this approach, where a TW-class CO₂ laser pulse is split in two, with half used to accelerate a high quality electron beam up to 84 MeV through the IFEL interaction, and the other half acts as an electromagnetic undulator to generate up to 13 keV X-rays via ICS. These results demonstrate the feasibility of this scheme, which can be joined with other techniques such as laser recirculation to yield very compact photon sources, with both high peak and average brilliance, and with energies extending from the keV to MeV scale. Further, use of the IFEL acceleration with the ICS interaction produces a train of high intensity X-ray pulses, thus enabling a unique tool synchronized with a laser pulse for ultra-fast strobe, pump-probe experimental scenarios.

Do stroke patients screened as lower-nutritional-risk still receive dietitian assessment if indicated? A retrospective evaluation of two dietetic models of care for adult stroke patients

BACKGROUND

Dietetic models of care at Logan Hospital changed from all patients with a confirmed stroke receiving dietitian assessment (Old pathway) to only those patients screened as high-nutritional-risk (Modified pathway). However, it was unknown whether all low-nutritional-risk patients who were indicated for dietitian assessment for nutrition support actually received assessment. This pre-post retrospective study evaluated whether the Old pathway and the Modified pathway were equally effective in identifying low-nutritional-risk stroke patients who were indicated for dietitian assessment and compared the time spent providing Dietetic care.

METHODS

For both pathways, medical charts were reviewed for low-nutritional-risk patients admitted between December 2012 and November 2017 with a confirmed stroke, who were given a standard food and fluid diet code and scored MST < 2 (Malnutrition Screening Tool) on admission. Data collected included demographics, anthropometrics, malnutrition assessment, dietetic intervention and time spent caring for patients. Malnutrition-related clinical indicators were used to classify patients as either Dietitian Assessment for Nutrition Support Indicated or Not Indicated.

RESULTS

Low-nutritional-risk patients were similar on the Old (n = 180) and Modified (n = 206) pathways [mean (SD) 66 (13) years, 63% male, 4% malnutrition]. Those classified as Dietitian Assessment for Nutrition Support Indicated (n = 61 of 180) were older, had a longer length of stay (P < 0.05), and were all identified by the Dietitian on both pathways. Ten minutes less dietetic time per patient was required on the Modified pathway (P < 0.001).

CONCLUSIONS

The Modified Nutrition Stroke pathway performed more efficiently than the Old pathway and was equally effective at ensuring that stroke patients who were determined as being low-nutritional-risk received dietitian assessment during admission if indicated.