Marine sulfated glycans inhibit the interaction of heparin with S-protein of SARS-CoV-2 Omicron XBB variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide COVID-19 pandemic, leading to 6.8 million deaths. Numerous variants have emerged since its outbreak, resulting in its significantly enhanced ability to spread among humans. As with many other viruses, SARS‑CoV‑2 utilizes heparan sulfate (HS) glycosaminoglycan (GAG) on the surface of host cells to facilitate viral attachment and initiate cellular entry through the ACE2 receptor. Therefore, interfering with virion-HS interactions represents a promising target to develop broad-spectrum antiviral therapeutics. Sulfated glycans derived from marine organisms have been proven to be exceptional reservoirs of naturally existing HS mimetics, which exhibit remarkable therapeutic properties encompassing antiviral/microbial, antitumor, anticoagulant, and anti-inflammatory activities. In the current study, the interactions between the receptor-binding domain (RBD) of S-protein of SARS-CoV-2 (both WT and XBB.1.5 variants) and heparin were applied to assess the inhibitory activity of 10 marine-sourced glycans including three sulfated fucans, three fucosylated chondroitin sulfates and two fucoidans derived from sea cucumbers, sea urchin and seaweed Saccharina japonica, respectively. The inhibitory activity of these marine derived sulfated glycans on the interactions between RBD of S-protein and heparin was evaluated using Surface Plasmon Resonance (SPR). The RBDs of S-proteins from both Omicrion XBB.1.5 and wild-type (WT) were found to bind to heparin, which is a highly sulfated form of HS. All the tested marine-sourced sulfated glycans exhibited strong inhibition of WT and XBB.1.5 S-protein binding to heparin. We believe the study on the molecular interactions between S-proteins and host cell glycosaminoglycans provides valuable insight for the development of marine-sourced, glycan-based inhibitors as potential anti-SARS-CoV-2 agents.

Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

Frontal sinus stenting in endoscopic sinus surgery: the 10-year Oxford experience

BACKGROUND

Frontal sinus stents have been introduced to reduce frontal sinus re-stenosis after surgery and to improve outcomes.

METHOD

This study was a retrospective analysis of 19 patients who had endoscopic sinus surgery with approach to the frontal sinus and insertion of a soft sinus stent.

RESULTS

The frontal recess was patent in 78.9 per cent and stenosed in 21.1 per cent of patients; no completely closed recesses were observed. Mean follow up was 20.7 months, and time period of stenting was 9.8 months on average; complications were observed in 47.4 per cent of the patients, with post-operative sinonasal infection being the most common.

CONCLUSION

In the authors' experience, indications for frontal sinus stenting include recalcitrant chronic rhinosinusitis after multiple functional endoscopic sinus surgeries (especially in chronic rhinosinusitis with nasal polyps), patients with history of important craniofacial surgery or trauma, and recurrent mucoceles. The stent was overall well tolerated as only minor complications were observed. Close clinical follow up is mandatory.

Specimen collection is essential for modern science

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Hearing Outcomes in Cisplatin or Cetuximab Combined with Radiation for Patients with HPV-Associated Oropharyngeal Cancer in NRG/RTOG 1016

PURPOSE/OBJECTIVE(S)

NRG/RTOG 1016 was a noninferiority phase 3 trial comparing the efficacy of radiation with either cisplatin (RT+Cisp) or cetuximab (RT+Cetux) for patients with HPV+ oropharyngeal cancer (OPC). Perceived hearing handicap was included as a patient-reported outcome (PRO) secondary endpoint. The primary hypothesis was that perceived hearing handicap would be greater for patients receiving RT+Cisp compared to RT+Cetux.

MATERIALS/METHODS

Perceived hearing handicap was measured at baseline, end of treatment, 3, 6, and 12-months post-treatment using the Hearing Handicap Inventory for Adults Screening Version (HHIA-S), a 10-item self-assessment questionnaire designed to measure patients' reactions to their hearing loss. Total HHIA-S scores range from 0 to 40; higher total score indicates more severe perceived hearing handicap. Hearing handicap categories (none, mild/moderate, and severe) were also analyzed. Mixed ordinal logistic models were used to analyze the raw HHIA-S scores and handicap categories (2-sided alpha 0.05).

RESULTS

Participation in the PRO assessments was optional, with 368 patients participating in the hearing PRO. No significant differences in patient/tumor characteristics were found between PRO participants/non-participants. Pre-treatment (mean [SD]) HHIA-S scores were not different for RT+Cisp (3.23 [6.28]) and RT+Cetux (4.77 [8.14]) groups. Post-treatment HHIA-S scores increased for RT+Cisp, and remained stable at the later follow-up time points. RT+Cetux scores remained stable from baseline. Change score from pre- to post-treatment was higher for RT+Cisp (4.32, 95% CI = [2.57, 6.07]) than RT+Cetux (0.08, 95% CI = [-1.15, 1.31]; p < 0.001). For hearing handicap category, post-treatment RT+Cisp had a significantly higher percentage of mild/moderate and severe cases (32%) compared to RT+Cetux (20%). From pre- to post-treatment, worsening of hearing handicap category from normal to mild/moderate or severe was greater for RT+Cisp (24%) than for RT+Cetux (9%). The conditional odds of being in a higher self-perceived hearing handicap category in the RT+Cisp arm were 3.57 (95% CI [2.04, 6.25]) times that in the RT+Cetux arm. Averaging over patients, the marginal odds ratio was 2.46 (95% CI [1.65, 3.66]).

CONCLUSION

Patients receiving concurrent RT+Cisp for HPV-associated OPC have significantly higher odds of worsening self-perceived hearing handicap after treatment than with RT+Cetux. This was consistent across time through one-year post-treatment. These findings inform hearing-related outcomes for patients with HPV-associated OPC.

Unsupervised representation learning improves genomic discovery and risk prediction for respiratory and circulatory functions and diseases

High-dimensional clinical data are becoming more accessible in biobank-scale datasets. However, effectively utilizing high-dimensional clinical data for genetic discovery remains challenging. Here we introduce a general deep learning-based framework, REpresentation learning for Genetic discovery on Low-dimensional Embeddings (REGLE), for discovering associations between genetic variants and high-dimensional clinical data. REGLE uses convolutional variational autoencoders to compute a non-linear, low-dimensional, disentangled embedding of the data with highly heritable individual components. REGLE can incorporate expert-defined or clinical features and provides a framework to create accurate disease-specific polygenic risk scores (PRS) in datasets which have minimal expert phenotyping. We apply REGLE to both respiratory and circulatory systems: spirograms which measure lung function and photoplethysmograms (PPG) which measure blood volume changes. Genome-wide association studies on REGLE embeddings identify more genome-wide significant loci than existing methods and replicate known loci for both spirograms and PPG, demonstrating the generality of the framework. Furthermore, these embeddings are associated with overall survival. Finally, we construct a set of PRSs that improve predictive performance of asthma, chronic obstructive pulmonary disease, hypertension, and systolic blood pressure in multiple biobanks. Thus, REGLE embeddings can quantify clinically relevant features that are not currently captured in a standardized or automated way.

The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves)

We present the complete genome sequences of 19 species of snipes from 7 genera. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

Evaluation of a training programme for critical incident debrief facilitators

BACKGROUND

Critical incident debriefs are a commonly used occupational health tool for supporting staff after traumatic work incidents. However, there is a dearth of literature evaluating training programmes for debrief facilitators.

AIMS

To evaluate a 5-day training programme to equip healthcare, social care and voluntary, community and social enterprise sector staff to act as post-incident peer supporters and debrief facilitators.

METHODS

A mixed-methods, single-arm, before-and-after study. Data were collected at baseline and post-training. The quantitative outcome measure was 'Confidence'; the sum of two items measuring confidence in (i) supporting peers after critical incidents and (ii) facilitating post-incident structured team discussions. At post-training, quantitative and qualitative feedback regarding experiences and perceptions of the training was also gathered.

RESULTS

We recruited 45 participants between October 2021 and January 2022. Confidence in supporting peers following incidents and facilitating post-incident structured team discussions increased significantly following the training, t(35) = -6.77, P < 0.001. A majority of participants reported they would do things differently because of the training and that they found the training relevant, useful and engaging. Summative content analysis of qualitative feedback indicated that participants (i) believed the role plays were an important learning tool and (ii) thought it was important that the trainer was engaging. Some participants would have preferred in-person delivery.

CONCLUSIONS

Participants valued training in post-incident peer support and debriefing skills. Organizations implementing post-incident support pathways could usefully include this training and ensure optimal uptake and engagement by (i) providing in-person and online delivery options and (ii) including role play as a learning technique.

Genomic architecture of autism from comprehensive whole-genome sequence annotation

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves)

We present the complete genome sequences of 94 species of parrots from 40 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.

The Complete Genome Sequence of Cyanopsitta spixii, the Spix's Macaw

The Spix's Macaw (Cyanopsitta spixii) is a critically endangered parrot that was once endemic to Brazil. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR15037507) and Assembly (GCA_024336845).

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.

Outcomes of Patients with a pH<7.0 Presenting to the Emergency Department (OPpHED Study)

Objectives The aim of this study was to assess the mortality and predictive factors in patients presenting with a pH<7.0 to the emergency department (ED). Methods A retrospective study of patients presenting to the ED of University Hospital Galway with a pH<7.0 from January 2014 to December 2017 was performed. A pH<7.0 on arrival to the ED from either an arterial or venous sample as measured by the blood gas analyser machine were assessed for inclusion. Results A total of 130 patients presented to ED over a 4-year period, with a mean age of 58 ±20 years. Eighty-one (63%) patients of the total cohort were male. In terms of aetiology of presentation, 66 (51%) cases were from cardiac arrest (CA), while the remaining 64 (49%) cases were non-cardiac arrest (NCA) related. Twenty-eight-day mortality was 69.5% overall, with significant mortality in the CA group (89%) compared to the NCA group (48%) (p<0.00). A modified early warning score (MEWS) (odds ratio [OR] 1.37, 95% CI: 1.18-1.59) and PCO2 ([OR] 1.35, 95% CI: 1.08-1.68.) were predictive of mortality. Conclusion In patients presenting to the ED with a pH of <7.0 the overall mortality was 69.5%, with survival more likely in NCA aetiologies. Mortality was associated with higher pCO2 and MEWS.

Ruptured Urinary Bladder Diagnosed by Point-of-care Ultrasound

Case Presentation

We describe a case of abdominal pain in a male patient who performed daily self-catheterization and developed a ruptured urinary bladder, which was diagnosed at bedside in the emergency department with point-of-care ultrasound (POCUS).

Discussion

Ruptured urinary bladder is commonly associated with blunt abdominal trauma. It is a rare complication of Foley catheter insertion. These images demonstrate that POCUS can be used as a screening tool to evaluate for bladder rupture when clinically suspected.

What are the predictors of hand hygiene compliance in the intensive care unit? A cross-sectional observational study

Background:

Although appropriate hand hygiene (HH) practices are recognised as the most effective preventative strategy for infection, adherence is suboptimal. Previous studies in intensive care units (ICUs) have found differences in HH compliance between those moments that protect the patient, and those that protect the healthcare provider. However, such studies did not control for other variables known to impact HH compliance.

Aim:

To examine HH among healthcare workers (HCWs) in ICU settings, and identify whether there is a statistical difference in HH compliance between patient-protective and self-protective moments, while controlling for other variables known to influence HH compliance (i.e. professional role, unit and shift time).

Methods:

A cross-sectional observational study was conducted in four ICUs across three Irish hospitals. Compliance was assessed according to the WHO’s ‘five moments for hand hygiene’. HCW professional role, total number of ‘opportunities’ for HH and whether compliance was achieved were recorded.

Results:

A total of 712 HH opportunities were recorded, with an overall compliance rate of 56.9%. Logistic regression analysis revealed that physicians, allied healthcare professionals and auxiliary staff were less likely than nurses to engage in HH. HCWs were more likely to comply during night shifts compared to morning shifts, and with self-protective as compared to patient-protective HH moments.

Conclusion:

The information provided in this study provides a data-driven approach that ICUs can use to tailor HH interventions to where, when and for whom they are most required.

Multi-character taxonomic review, systematics, and biogeography of the Black-capped/Tawny-bellied Screech Owl (emMegascops/em ematricapilla/em-emM. watsonii/em) complex (Aves: Strigidae)

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. watsonii might include more than one species, and that the Atlantic Forest endemic M. atricapilla is closely related to the M. watsonii complex, but these relationships are as yet poorly understood. A recently published phylogeny of Megascops demonstrated that M. watsonii is paraphyletic with respect to M. atricapilla and that genetic divergences among some populations of M. watsonii are equal to or surpass the degree of differentiation between some M. watsonii and M. atricapilla. To shed light on the taxonomic status of these species and populations within them, we conducted a multi-character study based on molecular, morphological, and vocal characters. We sequenced three mitochondrial (cytb, CO1 and ND2) and three nuclear genes (BF5, CHD and MUSK) for 49 specimens, covering most of the geographic ranges of M. watsonii and M. atricapilla, and used these sequences to estimate phylogenies under alternative Bayesian, Maximum Likelihood, and multilocus coalescent species tree approaches. We studied 252 specimens and vocal parameters from 83 recordings belonging to 65 individuals, distributed throughout the ranges of M. watsonii and M. atricapilla. We used Discriminant Function Analysis (DFA) to analyze both morphometric and vocal data, and a pairwise diagnostic test to evaluate the significance of vocal differences between distinct genetic lineages. Phylogenetic analyses consistently recovered six statistically well-supported clades whose relationships are not entirely in agreement with currently recognized species limits in M. watsonii and M. atricapilla. Morphometric analyses did not detect significant differences among clades. High plumage variation among individuals within clades was usually associated with the presence of two or more color morphs. By contrast, vocal analyses detected significant differentiation among some clades but considerable overlap among others, with some lineages (particularly the most widespread one) exhibiting significant regional variation. The combined results allow for a redefinition of species limits in both M. watsonii and M. atricapilla, with the recognition of four additional species, two of which we describe here as new. We estimated most cladogenesis in the Megascops atricapilla-M. watsonii complex as having taken place during the Plio-Pleistocene, with the development of the modern Amazonian and São Francisco drainages and the expansion and retraction of forest biomes during interglacial and glacial periods as likely events accounting for this relatively recent burst of diversification.

Breast Implant-associated Anaplastic Large Cell Lymphoma Affecting a Neosubpectoral Pocket

The complications associated with breast implants are under perpetual scrutiny to maximize patient safety. In this era of plastic surgery, a new concern being addressed is breast implant-associated anaplastic large cell lymphoma (BIA-ALCL). Patients with BIA-ALCL most commonly present several years after implant placement with a periprosthetic fluid collection. The body of literature and reports of BIA-ALCL continues to grow with additional nuances in proposed causes as well as management. Most recently, this has led to a recall of breast implants manufactured utilizing a specific texturing. We describe here the time course, diagnosis, and management of BIA-ALCL in a 52-year-old patient who underwent submuscular implant-based reconstruction and subsequent revision of that reconstruction with the creation of a neosubpectoral pocket. The patient was managed in accordance with current guidelines under the supervision of a multidisciplinary team. In our review of the literature, several case reports, case series, and guideline publications were identified. Current guidelines for management are based on the staging of BIA-ALCL at diagnosis and span from only surgical with implant removal, excision of the lymphoma, and excision of the surrounding fibrous capsule to addition of chemotherapeutic regimens or radiation for distant and locally advanced disease. 

Life history predicts flight muscle phenotype and function in birds

Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals' ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. We asked how age- and sex-dependent demands on flight muscle function are reconciled in birds. The flight muscle is an essential multifunctional organ, mediating a large range of functions associated with powered flight and thermoregulation. These functions must be balanced over an individual's lifetime. We leveraged within- and between-species comparisons in a clade of small passerines (Tarsiger bush-robins) from the eastern edge of the Qinghai-Tibet Plateau. We integrated measurements of flight muscle physiology, morphology, behaviour, phenology and environmental data, analysing trait data within a context of three widespread, adaptive life-history strategies-sexual dichromatism, age and sex-structured migration, and delayed plumage maturation. This approach provides a framework of the selective forces that shape functional variation within and between species. We found more variation in flight muscle traits within species than has been previously described between species of birds under 20 g. This variation was associated with the discovery of mixed muscle fibre types (i.e. both fast glycolytic and fast oxidative fibres), which differ markedly in their physiological and functional attributes. This result is surprising given that the flight muscles of small birds are generally thought to contain only fast oxidative fibres, suggesting a novel ecological context for glycolytic muscle fibres in small birds. Within each species, flight muscle phenotypes varied by age and sex, reflecting the functional demands at different life-history stages and the pressures that individuals face as a result of their multi-class identity (i.e. species, age and sex). Our findings reveal new links between avian physiology, ecology, behaviour and life history, while demonstrating the importance of demographic-dependent selection in shaping functional phenotypic variation.

Commercial platforms for Security Sensitive Biological Agents testing

The rapid testing for Security Sensitive Biological Agents is carried out by Public Health laboratories. The commercial platforms for performing such tasks in Australia are described.

Source Attribution of Salmonella in Macadamia Nuts to Animal and Environmental Reservoirs in Queensland, Australia

Salmonella enterica is a common contaminant of macadamia nut kernels in the subtropical state of Queensland (QLD), Australia. We hypothesized that nonhuman sources in the plantation environment contaminate macadamia nuts. We applied a modified Hald source attribution model to attribute Salmonella serovars and phage types detected on macadamia nuts from 1998 to 2017 to specific animal and environmental sources. Potential sources were represented by Salmonella types isolated from avian, companion animal, biosolids-soil-compost, equine, porcine, poultry, reptile, ruminant, and wildlife samples by the QLD Health reference laboratory. Two attribution models were applied: model 1 merged data across 1998-2017, whereas model 2 pooled data into 5-year time intervals. Model 1 attributed 47% (credible interval, CrI: 33.6-60.8) of all Salmonella detections on macadamia nuts to biosolids-soil-compost. Wildlife and companion animals were found to be the second and third most important contamination sources, respectively. Results from model 2 showed that the importance of the different sources varied between the different time periods; for example, Salmonella contamination from biosolids-soil-compost varied from 4.4% (CrI: 0.2-11.7) in 1998-2002 to 19.3% (CrI: 4.6-39.4) in 2003-2007, and the proportion attributed to poultry varied from 4.8% (CrI: 1-11) in 2008-2012 to 24% (CrI: 11.3-40.7) in 2013-2017. Findings suggest that macadamia nuts were contaminated by direct transmission from animals with access to the plantations (e.g., wildlife and companion animals) or from indirect transmission from animal reservoirs through biosolids-soil-compost. The findings from this study can be used to guide environmental and wildlife sampling and analysis to further investigate routes of Salmonella contamination of macadamia nuts and propose control options to reduce potential risk of human salmonellosis.

Variation in water disappearance, daily dose, and synovial fluid concentrations of tylvalosin and 3-O-acetyltylosin in commerical pigs during five day water medication with tylvalosin under field conditions

Tylvalosin (TVN) is a water soluble macrolide used in swine production to treat enteric, respiratory, and arthritic pathogens. There is limited data on its distribution to synovial fluid beyond gavage studies, which do not represent field conditions. This study measured water disappearance, TVN concentration in the medicated water, daily dose, and concentrations of TVN and 3-O-acetyltylosin (3AT) in the synovial fluid and plasma of treated pigs over the administration period. The study emphasized understanding variation in tissue TVN concentrations within the context of a field setting. Sixty finisher pigs were housed individually with individual waterers. Six pigs were randomly allocated to the following time points for sample collection: 0, 48, 60, 72, 84, 96, 102, 108, 114, and 120 hr on medication. TVN was administered daily in the water for 5 days. Water disappearance and medicated water concentration were measured daily. At each time point, six pigs were euthanized and plasma and synovial fluid were collected for analysis. Median TVN synovial fluid concentrations ranged between <1 ng/ml (hour 0) to 3.6 ng/ml (hour 84). There was substantial variation between individual pigs for water disappearance (mean 4.36L and range 0-7.84). Median TVN water concentration was 59 ppm (range 38-75 ppm).

Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing

Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated between November 2015 and March 2016. We identified a common egg grading facility in five of the outbreaks. While no Salmonella Typhimurium was detected at the grading facility and eggs could not be traced back to a particular farm, whole genome sequencing (WGS) of isolates from cases from all seven outbreaks indicated a common source. WGS was able to provide higher discriminatory power than MLVA and will likely link more Salmonella Typhimurium cases between states and territories in the future. National harmonization of Salmonella surveillance is important for effective implementation of WGS for Salmonella outbreak investigations.

Pulling together and pulling apart: influences of convergence and divergence on distributed healthcare teams

Effective healthcare requires both competent individuals and competent teams. With this recognition, health professions education is grappling with how to factor team competence into training and assessment strategies. These efforts are impeded, however, by the absence of a sophisticated understanding of the the relationship between competent individuals and competent teams . Using data from a constructivist grounded theory study of team-based healthcare for patients with advanced heart failure, this paper explores the relationship between individual team members' perceived goals, understandings, values and routines and the collective competence of the team. Individual interviews with index patients and their healthcare team members formed Team Sampling Units (TSUs). Thirty-seven TSUs consisting of 183 interviews were iteratively analysed for patterns of convergence and divergence in an inductive process informed by complex adaptive systems theory. Convergence and divergence were identifiable on all teams, regularly co-occurred on the same team, and involved recurring themes. Convergence and divergence had nonlinear relationships to the team's collective functioning. Convergence could foster either shared action or collective paralysis; divergence could foster problematic incoherence or productive disruption. These findings advance our understanding of the complex relationship between the individual and the collective on a healthcare team, and they challenge conventional narratives of healthcare teamwork which derive largely from acute care settings and emphasize the importance of common goals and shared mental models. Complex adaptive systems theory helps us to understand the implications of these insights for healthcare teams' delivery of care for the complex, chronically ill.

The effects of culture independent diagnostic testing on the diagnosis and reporting of enteric bacterial pathogens in Queensland, 2010 to 2014

Changes in diagnostic laboratory testing procedures can impact on the number of cases notified and the public health surveillance of enteric pathogens. Culture independent diagnostic testing using a multiplex polymerase chain reaction (PCR) test was introduced for the rapid detection of bacterial enteric pathogens in pathology laboratories in Queensland, Australia, from late 2013 onwards. We conducted a retrospective descriptive study using laboratory data to assess the impact of the introduction of PCR testing on four common enteric pathogens, Salmonella, Campylobacter, Shigella and Yersinia, in Queensland between 2010 and 2014. The number of stool specimens tested and the proportion positive for each of the four pathogens increased in 2014 after the introduction of culture independent diagnostic testing. Among the specimens tested by both PCR and culture, 12% of Salmonella positive stools, 36% of Campylobacter positive stools, 74% of Shigella / enteroinvasive Escherichia coli positive stools and 65% of Yersinia positive stools were PCR positive only. Including those where culture was not performed, 19% of Salmonella positive stools, 44% of Campylobacter positive stools, 83% of Shigella positive stools and 79% of Yersinia positive stools had no cultured isolate available for further characterisation. The detection and tracking of foodborne and non-foodborne gastrointestinal outbreaks will become more difficult as culture independent diagnostic testing becomes more widespread. Until new techniques for characterisation of pathogens directly from clinical specimens have been developed, we recommend laboratories continue to culture specimens concurrently or reflexively with culture independent diagnostic tests.

'Multi-cropping', Intercropping and Adaptation to Variable Environments in Indus South Asia

Past human populations are known to have managed crops in a range of ways. Various methods can be used, singly or in conjunction, to reconstruct these strategies, a process which lends itself to the exploration of socio-economic and political themes. This paper endeavours to unpack the concept of 'multi-cropping' by considering diversity and variation in the cropping practices of the populations of South Asia's Indus Civilisation. It argues that nuanced interpretations of the evidence provided by the combinations of crop seeds and weeds present in specific contexts and phases of occupation can reveal much about Indus cropping strategies, which in turn enables consideration of issues related to adaptation, intensification and resilience in the face of changing social, political, economic and environmental climates.

The Edinburgh Malawi Cancer Partnership: helping to establish multidisciplinary cancer care in Blantyre, Malawi

In response to the growing incidence of cancer in Malawi, a new oncology unit was established at the Queen Elizabeth Central Hospital, Blantyre. The unit opened in 2010, the first in the country, and is led by a single consultant oncologist. In 2012, a healthcare partnership was formed between the oncology and palliative care unit at Queen Elizabeth Central Hospital and the Edinburgh Cancer Centre, UK. The principal objective of the partnership is to help develop high quality multidisciplinary cancer care in Malawi. Methods A needs assessment identified three priority areas for further improvement of cancer services: nurse-led treatment delivery; management of clinical data; and multidisciplinary working. The partnership received grant funding from the Scottish Government Malawi Development Programme in 2013 and a three year project plan was implemented. This has been conducted through a series of reciprocal training visits. Results Key achievements have been completion of a programme of oncology nursing education attended by 32 oncology nurses and other healthcare professionals, which has resulted in increased experience in cancer practice and standardisation of chemotherapy delivery procedures; development of a clinical database that enables prospective collection of data of all new patients with cancer and which links to the Malawi Cancer Registry; development of weekly multidisciplinary meetings involving oncology, gynaecology and surgery that has enabled a cross-specialty approach to patient care. Conclusion The Edinburgh Malawi Cancer Partnership is supporting nursing education, data use and cross-specialty collaboration that we are confident will improve cancer care in Malawi. Future work will focus on the further development of multidisciplinary breast cancer care and the development of a radiotherapy service for patients in Malawi.

Approaching rice domestication in South Asia: New evidence from Indus settlements in northern India

The nature and timing of rice domestication and the development of rice cultivation in South Asia is much debated. In northern South Asia there is presently a significant gap (c.4200 years) between earliest evidence for the exploitation of wild rice (Lahuradewa c.6000 BCE) and earliest dated evidence for the utilisation of fully domesticated rice (Mahagara c.1800 BCE). The Indus Civilisation (c.3000-1500 BCE) developed and declined during the intervening period, and there has been debate about whether rice was adopted and exploited by Indus populations during this 'gap'. This paper presents new analysis of spikelet bases and weeds collected from three Indus Civilisation settlements in north-west India, which provide insight into the way that rice was exploited. This analysis suggests that starting in the period before the Indus urban phase (Early Harappan) and continuing through the urban (Mature Harappan/Harappan), post-urban (Late Harappan) and on into the post-Indus Painted Grey Ware (PGW) period, there was a progressive increase in the proportion of domesticated-type spikelet bases and a decrease in wild-types. This pattern fits with a model of the slow development of rice exploitation from wild foraging to agriculture involving full cultivation. Importantly, the accompanying weeds show no increased proportions of wetland species during this period. Instead a mix of wetland and dryland species was identified, and although these data are preliminary, they suggest that the development of an independent rice tradition may have been intertwined with the practices of the eastern most Indus peoples. These data also suggest that when fully domesticated Oryza sativa ssp. japonica was introduced around 2000 BCE, it arrived in an area that was already familiar with domesticated rice cultivation and a range of cultivation techniques.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Concentrations of tylvalosin and 3-O-acetyltylosin attained in the synovial fluid of swine after administration by oral gavage at 50 and 5 mg/kg

The objectives of this study were to determine the concentration of tylvalosin (TVN) and its metabolite, 3-O-acetyltylosin (3AT) in the synovial fluid of growing pigs when administered as a single bolus by oral gavage at target doses of 50 mg/kg (Trial 1) and 5 mg/kg (Trial 2). TVN is a water soluble macrolide antimicrobial used in swine production. The stability of the drug in synovial fluid samples stored at -70 °C up to 28 days was also evaluated in Trial 2. In Trial 1, eight pigs were randomly assigned to one of eight time points for euthanasia and synovial fluid collection: 0, 1, 2, 3, 4, 6, 9, 12 h postgavage. For Trial 2, 24 pigs were randomly allocated to one terminal collection time point at 0, 2, 4, 6, 8 or 10 h postgavage. Synovial fluid was analyzed to determine TVN and 3AT concentrations. TVN and 3AT were detected in Trial 1 at all time points, except 0 h. At 2 h postgavage for trial 2, the mean concentrations peaked at 31.17 ng/mL (95% CI: 18.62-52.16) for TVN and at 58.82 ng/mL (95% CI: 35.14-98.46) for 3AT. Storage duration did not impact TVN or 3AT concentrations (P-value 0.9732).

Markers to differentiate between Kaposi's sarcoma and tuberculous pleural effusions in HIV-positive patients

BACKGROUND

Kaposi's sarcoma (KS) and tuberculosis (TB) commonly cause pleural effusions in high human immunodeficiency virus (HIV) burden resource-limited countries. Differentiating between them is challenging, as pleural biopsy and TB culture are rarely available.

OBJECTIVES

To identify markers to differentiate between TB effusions and KS effusions in HIV-positive patients, and to compare liquid culture and Xpert MTB/RIF in pleural fluid.

METHODS

Fifty HIV-positive patients with pleural effusions recruited in Malawi underwent pleural ultrasound and aspiration. Fluid visual inspection, cell count, bacterial culture, glucose/protein, solid and liquid TB culture and Xpert were performed.

RESULTS

The mean age of the patients was 32 years; 30/50 (60%) were male and 29 (58%) had cutaneous/oral KS. Thirteen (26%) pleural fluid samples were liquid culture-positive for TB, while 9/13 (69%) were Xpert-positive. Three (10.3%) KS patients had culture-positive TB effusions; 17 (58.6%) had KS effusions. The relative risk of TB in KS patients increased with limited KS, loculated fluid and low glucose. Eleven (52.3%) non-KS patients had culture-positive TB effusions associated with male sex, straw-coloured fluid and fibrin stranding on ultrasound.

CONCLUSIONS

KS patients were most likely to have KS effusion, but TB should be considered. Most non-KS patients had TB, supporting the use of World Health Organization guidelines. Xpert identified two thirds of liquid culture-positive results.

Estimating the prevalence of mixed-type gonococcal infections in Queensland, Australia

Background Mixed gonococcal infections within the one anatomical site have been recognised but questions remain over how often they occur. In this study, the aim was to estimate the prevalence of mixed gonococcal infections using novel real-time polymerase chain reaction (PCR) methods that were developed and validated, targeting the gonococcal porB gene.

METHODS

Neisseria gonorrhoeae strains were categorised into three different porB groups, based on sequence data derived from N. gonorrhoeae multi-antigen sequence typing (NG-MAST) analyses of local isolates. Specific PCR methods for each group were then developed and these PCR methods were used to test clinical samples (n=350) that were positive for gonorrhoea as determined by nucleic acid amplification test (NAAT) diagnostic screening.

RESULTS

Initial validation using isolates showed the group PCR methods proved 100% sensitive and 100% specific for their respective porB groups. When applied to the clinical specimens, 298/350 (85%) provided positive results by the group PCR methods. Of these, four specimens showed evidence of mixed infections, supported by subsequent DNA sequencing of the PCR products.

CONCLUSIONS

The data provide further evidence of mixed gonococcal infections at the same anatomical site, but show that such infections may be relatively infrequent (1.3%; 95% confidence interval 0.01-2.6%) in a general screening population.