Global phylogenomic diversity of Brucella abortus: spread of a dominant lineage.

Brucella abortus is a globally important zoonotic pathogen largely found in cattle hosts and is typically transmitted to humans through contaminated dairy products or contact with diseased animals. Despite the long, shared history of cattle and humans, little is known about how trade in cattle has spread this pathogen throughout the world. Whole genome sequencing provides unparalleled resolution to investigate the global evolutionary history of a bacterium such as B. abortus by providing phylogenetic resolution that has been unobtainable using other methods. We report on large-scale genome sequencing and analysis of B. abortus collected globally from cattle and 16 other hosts from 52 countries. We used single nucleotide polymorphisms (SNPs) to identify genetic variation in 1,074 B. abortus genomes and using maximum parsimony generated a phylogeny that identified four major clades. Two of these clades, clade A (median date 972 CE; 95% HPD, 781-1142 CE) and clade B (median date 150 BCE; 95% HPD, 515 BCE-164 CE), were exceptionally diverse for this species and are exclusively of African origin where provenance is known. The third clade, clade C (median date 949 CE; 95% HPD, 766-1102 CE), had most isolates coming from a broad swath of the Middle East, Europe, and Asia, also had relatively high diversity. Finally, the fourth major clade, clade D (median date 1467 CE; 95% HPD, 1367-1553 CE) comprises the large majority of genomes in a dominant but relatively monomorphic group that predominantly infects cattle in Europe and the Americas. These data are consistent with an African origin for B. abortus and a subsequent spread to the Middle East, Europe, and Asia, probably through the movement of infected cattle. We hypothesize that European arrival to the Americas starting in the 15th century introduced B. abortus from Western Europe through the introduction of a few common cattle breeds infected with strains from clade D. These data provide the foundation of a comprehensive global phylogeny of this important zoonotic pathogen that should be an important resource in human and veterinary epidemiology.

Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution.

Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MLST9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.

Case Report: Acute Brucellosis Due to Brucella suis in a Brazilian Gold Miner Diagnosed in French Guiana.

A 29-year-old Brazilian illegal gold miner developed intermittent fever. Blood cultures were positive for Gram-negative coccobacilli and, after an initial misidentification by an automated identification system, the diagnosis of brucellosis caused by Brucella suis was confirmed. We hypothesize an association with domestic or wild swine exposure. The patient responded well to standard antibiotic therapy of brucellosis. We report the first case of human brucellosis on the Guiana Shield. This report underlines the importance of considering brucellosis in the presence of a fever of unknown origin, even in the Amazonian rainforest area, where several zoonotic diseases might be considered in the differential diagnosis of unexplained fever.

Assessing coastline recession for adaptation planning: sea level rise versus storm erosion.

The Sixth Assessment report (AR6) of the Intergovernmental Panel on Climate Change (IPCC) states with high confidence that most sandy coasts around the world will experience an increase in coastal erosion over the twenty-first century. An increase in long term coastal erosion (coastline recession) along sandy coasts can translate into massive socio-economic impacts, unless appropriate adaptation measures are implemented in the next few decades. To adequately inform adaptation measures, it is necessary to have a good understanding of the relative importance of the physical processes driving coastline recession, as well as of linkages between consideration (or not) of certain processes and the level of risk tolerance; understandings that are hitherto lacking. Here, we apply the multi-scale Probabilistic Coastline Recession (PCR) model to two end-member sandy coastal types (swell dominated and storm dominated), to investigate where and when coastline recession projections are dominated by the differential contributions from Sea Level Rise (SLR) and storm erosion. Results show that SLR substantially increases the projected end-century recession at both types of coasts and that projected changes in the wave climate have only a marginal impact. An analysis of the Process Dominance Ratio (PDR), introduced here, shows that the dominance of storm erosion over SLR (and vice versa) on total recession by 2100 depends on both the type of the beach and the risk tolerance levels. For moderately risk-averse decisions (i.e. decisions accounting only for high exceedance probability recessions and hence do not account for very high amounts of potential recession-for example, the placement of temporary summer beach cabins), additional erosion due to SLR can be considered as the dominant driver of end-century recession at both types of beaches. However, for more risk-averse decisions that would typically account for higher potential recession (i.e. lower exceedance probability recessions), such as the placement of coastal infrastructure, multi-storey apartment buildings etc., storm erosion becomes the dominant process. The results of this study provide new insights on which physical processes need to be considered when and where in terms of numerical modelling efforts needed for supporting different management decisions, potentially enabling more streamlined and comprehensive assessments of the efficacy of coastal adaptation measures.

Novel Species of Brucella Causing Human Brucellosis, French Guiana.

Human brucellosis is a zoonoses caused by bacteria of the genus Brucella. Infection results in subacute or chronic debilitating disease with nonspecific clinical manifestations and is often associated with consuming unpasteurized dairy products. We report 2 cases of brucellosis in male patients who were hospitalized in distinct towns of French Guiana, an overseas territory of France located on the northeastern shore of South America. Both men were citizens of Brazil working as clandestine goldminers in the deep Amazonian rainforest. Characterization of the 2 bacterial isolates revealed that they represent a potential new species of Brucella. Medical practitioners working in contact with wildlife in this region of the world should be aware of the existence of these pathogens and the potential for human infection.

Analysis of the Brucella suis Twin Arginine Translocation System and Its Substrates Shows That It Is Essential for Viability.

Bacteria use the twin arginine translocator (Tat) system to export folded proteins from the cytosol to the bacterial envelope or to the extracellular environment. As with most Gram-negative bacteria, the Tat system of the zoonotic pathogen Brucella spp. is encoded by a three-gene operon, tatABC. Our attempts, using several different strategies, to create a Brucella suis strain 1330 tat mutant were all unsuccessful. This suggested that, for B. suis, Tat is essential, in contrast to a recent report for Brucella melitensis. This was supported by our findings that two molecules that inhibit the Pseudomonas aeruginosa Tat system also inhibit B. suis, B. melitensis, and Brucella abortus growth in vitro. In a bioinformatic screen of the B. suis 1330 proteome, we identified 28 proteins with putative Tat signal sequences. We used a heterologous reporter assay based on export of the Tat-dependent amidase AmiA by using the Tat signal sequences from the Brucella proteins to confirm that 20 of the 28 candidates can engage the Tat pathway.

First report and whole-genome sequencing of Pseudochrobactrum saccharolyticum in Latin America.

The Brucellaceae family comprises microorganisms similar both phenotypically and genotypically, making it difficult to identify the etiological agent of these infections. This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. Strain 115 was isolated in 2007 from a bovine in Brazil and was initially classified as Brucella spp. by classical microbiological tests and bcsp31 PCR. The antimicrobial susceptibility of strain 115 was tested against drugs used to treat human brucellosis by minimal inhibitory concentration test. Subsequently, the whole genome of the strain was sequenced, assembled, and characterized. Phylogenetic trees built from 16S rRNA and recA gene sequences enabled the classification of strain 115 as Pseudochrobactrum spp. Phylogenomic analysis using Single Nucleotide Polymorphisms and Average Nucleotide Identity allowed the classification of the strain as P. saccharolyticum. Additionally, a Tetra Correlation Search identified one related genome from the same species, which was compared with strain 115 by analyzing genomic islands. This is the first identification and whole-genome sequence of P. saccharolyticum in Latin America and highlights a challenge in the diagnosis of bovine brucellosis, which could be solved by including the sequencing of 16S rRNA and recA genes in routine diagnostics.

CD98hc in host-pathogen interactions: roles of the multifunctional host protein during infections.

The eukaryotic protein CD98hc (also known as 4F2, FRP-1, or SLC3A2) is a membrane glycoprotein and one of the heavy chains of the family of heterodimeric amino acids transporters. It can associate with any of 6 different light chains to form distinct amino acid transporters. CD98hc is also involved in mediation of intracellular integrin signaling. Besides its physiological roles in the development of the placenta and the immune system, CD98hc is important during pathological processes such as tumorigenesis and host-pathogen interaction. Since its first identification as Fusion Regulatory Protein 1 regulating cell fusion in cells infected by the Newcastle disease virus, CD98hc has been reported to be mediating many viral, apicomplexan, and bacterial infectious processes. In this review we describe the role of CD98hc and its associated light chains in bacterial, apicomplexan, and viral pathogenesis. We also discuss the consequences of infection on the expression and localization of these proteins. The identification of the cellular processes in which CD98hc is involved during pathogenesis highlights the key role of this host protein in infectious diseases.

Probabilistic projections of the stability of small tidal inlets at century time scale using a reduced complexity approach.

Climate change is widely expected to affect the thousands of small tidal inlets (STIs) dotting the global coastline. To properly inform effective adaptation strategies for the coastal areas in the vicinity of these inlets, it is necessary to know the temporal evolution of inlet stability over climate change time scales (50-100 years). As available numerical models are unable to perform continuous morphodynamic simulations at such time scales, here we develop and pilot a fast, probabilistic, reduced complexity model (RAPSTA - RAPid assessment tool of inlet STAbility) that can also quantify forcing uncertainties. RAPSTA accounts for the key physical processes governing STI stability and for climate change driven variations in system forcing. The model is very fast, providing a 100 year projection in less than 3 seconds. RAPSTA is demonstrated here at 3 STIs, representing the 3 main Types of STIs; Permanently open, locationally stable inlet (Type 1); Permanently open, alongshore migrating inlet (Type 2); Seasonally/Intermittently open, locationally stable inlet (Type 3). Model applications under a high greenhouse gas emissions scenario (RCP 8.5), accounting for forcing uncertainties, show that while the Type 1 STI will not change type over the twenty-first century, the Type 2 inlet may change into a more unstable Type 3 system around mid-century, and the Type 3 STI may change into a less unstable Type 2 system in about 20 years from now, further changing into a stable Type 1 STI around mid-century. These projections underscore the need for future adaptation strategies to remain flexible.

Barriers and facilitators to implementing community-based physical activity interventions: a qualitative systematic review.

BACKGROUND: Over the past decade several physical activity (PA) interventions have been shown to be efficacious in a controlled research setting, however there is a continued lack of evidence for how to successfully implement these PA interventions in real-world settings such as the community. This review aims to explore the barriers and facilitators that affect the implementation of community-based PA interventions and make recommendations to improve implementation from the included studies. METHODS: A systematic literature search of EBSCOhost, Scopus, PUBMED and Web of Science was conducted to identify articles that reported qualitative data on the implementation factors of community-based interventions where PA was a primary outcome. Data were extracted using the Consolidated Framework for Implementation Research (CFIR) as a guide. Implementation factors and recommendations were then mapped onto the 5 domains of the CFIR and synthesised thematically. RESULTS: From 495 articles, a total of 13 eligible studies were identified, with 6 studies using a mixed methods approach, and 7 reporting qualitative methods only. There were 82 implementation factors identified, including 37 barriers and 45 facilitators, and a further 26 recommendations from the papers across all 5 domains of the CFIR. More barriers than facilitators were identified within the CFIR domain inner setting, in contrast to all other domains where facilitator numbers outweighed barriers. CONCLUSIONS: This review identified many facilitators and barriers of implementing physical activity interventions in the community. A key finding of this review was the impact of implementation strategies on successful implementation of community PA interventions. From the evidence, it was clear that many barriers to implementation could have been negated or reduced by an implementation plan in which several strategies are embedded. The findings of this review also suggest more attention to individual' skills and involvement is needed to improve self-efficacy and knowledge. The role of individuals across all organisational levels, from providers to leaders, can impact on the implementation of an intervention and its success. TRIAL REGISTRATION: PROSPERO - CRD42020153821 .

Health Promoting Sports Club in Practice: A Controlled Evaluation of the GAA Healthy Club Project.

Sport is a developing setting and a relevant system in health promotion but there are few examples of settings-based initiatives and systems thinking in sport. The Gaelic Athletic Association (GAA) Healthy Club Project (HCP) adopts a settings approach delivered through and by grassroots clubs who respond to local needs while working within a national support system. The aim of this evaluation was to assess and describe the health promotion impact and experience of the HCP. Healthy Clubs (n = 23) and Control Clubs (n = 10) completed a Healthy Club Questionnaire at the start and end of the 20-month HCP and Healthy Clubs took part in focus group discussions. Healthy Clubs, using the structures of the HCP, a commitment to health and community engagement, demonstrated a significant improvement in their overall orientation to health promotion, which was not apparent in Control Clubs. The health promotion message is pervading into many aspects of the GAA club apart from that which relates to the day to day business of coaching and providing physical activity for all. The HCP represents health promotion activity embedded within and across systems, with further development and evaluation recommended to measure delivery and impact at the individual level, organisational, and wider societal levels.

Joint development recovery on resumption of embryonic movement following paralysis.

Fetal activity in utero is a normal part of pregnancy and reduced or absent movement can lead to long-term skeletal defects, such as Fetal Akinesia Deformation Sequence, joint dysplasia and arthrogryposis. A variety of animal models with decreased or absent embryonic movements show a consistent set of developmental defects, providing insight into the aetiology of congenital skeletal abnormalities. At developing joints, defects include reduced joint interzones with frequent fusion of cartilaginous skeletal rudiments across the joint. At the spine, defects include shortening and a spectrum of curvature deformations. An important question, with relevance to possible therapeutic interventions for human conditions, is the capacity for recovery with resumption of movement following short-term immobilisation. Here, we use the well-established chick model to compare the effects of sustained immobilisation from embryonic day (E)4-10 to two different recovery scenarios: (1) natural recovery from E6 until E10 and (2) the addition of hyperactive movement stimulation during the recovery period. We demonstrate partial recovery of movement and partial recovery of joint development under both recovery conditions, but no improvement in spine defects. The joints examined (elbow, hip and knee) showed better recovery in hindlimb than forelimb, with hyperactive mobility leading to greater recovery in the knee and hip. The hip joint showed the best recovery with improved rudiment separation, tissue organisation and commencement of cavitation. This work demonstrates that movement post paralysis can partially recover specific aspects of joint development, which could inform therapeutic approaches to ameliorate the effects of human fetal immobility. This article has an associated First Person interview with the first author of the paper.

First Case of Brucellosis Caused by an Amphibian-type Brucella.

We report the first case of brucellosis caused by an isolate whose genome is identical that of a frog isolate from Texas, demonstrating the zoonotic potential of amphibian-type Brucella. Importantly, with such atypical Brucella, correct diagnosis cannot be performed using routine serological tests or identification methods.

Synthesising wave attenuation for seagrass: Drag coefficient as a unifying indicator.

An estimated 100 million people inhabit coastal areas at risk from flooding and erosion due to climate change. Seagrass meadows, like other coastal ecosystems, attenuate waves. Due to inconsistencies in how wave attenuation is measured results cannot be directly compared. We synthesised data from laboratory and field experiments of seagrass-wave attenuation by converting measurements to drag coefficients (CD). Drag coefficients varied from 0.02-5.12 with CD¯ = 0.74 for studies conducted in turbulent flow in non-storm conditions. A statistical model suggested that seagrass species affects CD although the exact mechanism remains unclear. A wave model using the estimated CD¯ as an input parameter demonstrated that wave attenuation increased with meadow length, shoot density, shoot width and canopy height. Findings can be used to estimate wave attenuation by seagrass, in any given set of conditions.

Seagrass losses since mid-20th century fuelled CO2 emissions from soil carbon stocks.

Seagrass meadows store globally significant organic carbon (Corg ) stocks which, if disturbed, can lead to CO2 emissions, contributing to climate change. Eutrophication and thermal stress continue to be a major cause of seagrass decline worldwide, but the associated CO2 emissions remain poorly understood. This study presents comprehensive estimates of seagrass soil Corg erosion following eutrophication-driven seagrass loss in Cockburn Sound (23 km2 between 1960s and 1990s) and identifies the main drivers. We estimate that shallow seagrass meadows (<5 m depth) had significantly higher Corg stocks in 50 cm thick soils (4.5 ± 0.7 kg Corg /m2 ) than previously vegetated counterparts (0.5 ± 0.1 kg Corg /m2 ). In deeper areas (>5 m), however, soil Corg stocks in seagrass and bare but previously vegetated areas were not significantly different (2.6 ± 0.3 and 3.0 ± 0.6 kg Corg /m2 , respectively). The soil Corg sequestration capacity prevailed in shallow and deep vegetated areas (55 ± 11 and 21 ± 7 g Corg  m-2  year-1 , respectively), but was lost in bare areas. We identified that seagrass canopy loss alone does not necessarily drive changes in soil Corg but, when combined with high hydrodynamic energy, significant erosion occurred. Our estimates point at ~0.20 m/s as the critical shear velocity threshold causing soil Corg erosion. We estimate, from field studies and satellite imagery, that soil Corg erosion (within the top 50 cm) following seagrass loss likely resulted in cumulative emissions of 0.06-0.14 Tg CO2-eq over the last 40 years in Cockburn Sound. We estimated that indirect impacts (i.e. eutrophication, thermal stress and light stress) causing the loss of ~161,150 ha of seagrasses in Australia, likely resulted in the release of 11-21 Tg CO2 -eq since the 1950s, increasing cumulative CO2 emissions from land-use change in Australia by 1.1%-2.3% per annum. The patterns described serve as a baseline to estimate potential CO2 emissions following disturbance of seagrass meadows.

Brucellosis in China: history, progress and challenge.

Brucellosis is a neglected zoonosis. It causes acute febrile illness and a potentially debilitating chronic infection in humans, and livestock infection has substantial socioeconomic impact. Over the past two decades, improvements have been made to better understand the various aspects of human and animal brucellosis. Meanwhile, especially in the developing world, immense challenges that remain in controlling and eradicating brucellosis are novel diagnostics tools and efficacious vaccines. Here, we will focus on the remarkable issues on epidemiological survey, as well as the priority and challenge of brucellosis in China. Brucellosis will be controlled with meaningful collaboration between local and public partnerships effectively applying a One Health framework.

Methylnaltrexone for the treatment of opioid-induced constipation and gastrointestinal stasis in intensive care patients. Results from the MOTION trial.

PURPOSE: Constipation can be a significant problem in critically unwell patients, associated with detrimental outcomes. Opioids are thought to contribute to the mechanism of bowel dysfunction. We tested if methylnaltrexone, a pure peripheral mu-opioid receptor antagonist, could reverse opioid-induced constipation. METHODS: The MOTION trial is a multi-centre, double blind, randomised placebo-controlled trial to investigate whether methylnaltrexone alleviates opioid-induced constipation (OIC) in critical care patients. Eligibility criteria included adult ICU patients who were mechanically ventilated, receiving opioids and were constipated (had not opened bowels for a minimum 48 h) despite prior administration of regular laxatives as per local bowel management protocol. The primary outcome was time to significant rescue-free laxation. Secondary outcomes included gastric residual volume, tolerance of enteral feeds, requirement for rescue laxatives, requirement for prokinetics, average number of bowel movements per day, escalation of opioid dose due to antagonism/reversal of analgesia, incidence of ventilator-associated pneumonia, incidence of diarrhoea and Clostridium difficile infection and finally 28 day, ICU and hospital mortality. RESULTS: A total of 84 patients were enrolled and randomized (41 to methylnaltrexone and 43 to placebo). The baseline demographic characteristics of the two groups were generally well balanced. There was no significant difference in time to rescue-free laxation between the groups (Hazard ratio 1.42, 95% CI 0.82-2.46, p = 0.22). There were no significant differences in the majority of secondary outcomes, particularly days 1-3. However, during days 4-28, there were fewer median number of bowel movements per day in the methylnaltrexone group, (p = 0.01) and a greater incidence of diarrhoea in the placebo group (p = 0.02). There was a marked difference in mortality between the groups, with ten deaths in the methylnaltrexone group and two in the placebo group during days 4-28 (p = 0.007). CONCLUSION: We found no evidence to support the addition of methylnaltrexone to regular laxatives for the treatment of opioid-induced constipation in critically ill patients; however, the confidence interval was wide and a clinically important difference cannot be excluded.

Age-Friendly Environments, Active Lives? Associations Between the Local Physical and Social Environment and Physical Activity Among Adults Aged 55 and Older in Ireland.

Despite the benefits, one in three older adults in Ireland has low activity levels. This study examined associations between the local social and built environment and physical activity of older adults to identify age-friendly factors that support physical activity among the aging population. Data were from the population-representative Healthy and Positive Ageing Initiative Age-Friendly City and Counties Survey (N = 10,540). Physical activity was measured using a short-form of the International Physical Activity Questionnaire. Mixed-effects negative binomial regression models were adjusted for known health and sociodemographic correlates of physical activity. Results are reported as unstandardized beta coefficients (ß) with standard errors. Loneliness, community participation, and difficulty in accessing green spaces partially explained the differences in the number of minutes that respondents were physically active. Combined with individual-level behavior change interventions, improvements to the local environment and promoting social connectedness may also be useful in promoting physical activity among older adults.

Infection by Brucella melitensis or Brucella papionis modifies essential physiological functions of human trophoblasts.

Brucellosis is a zoonosis caused by bacteria of the Brucella genus. In ruminants, brucellosis causes abortion, followed by chronic infection and secretion of bacteria in milk. In humans, it usually presents as flu-like symptoms, with serious complications if untreated. Epidemiological studies have only recently established that brucellosis can also cause pregnancy complications in women, but the pathogenic mechanisms are unknown. Pioneering studies in ruminants showed that Brucella infect trophoblasts and then colonise the placenta where they grow to high density. A recent study showed that the main zoonotic Brucella species can infect human cytotrophoblasts (CTB) and extravillous trophoblasts (EVT). In this work, we show that Brucella papionis (associated with stillbirth in primates) also infects human trophoblasts. However, it replicates actively in CTB, whereas its replication is very restricted within EVT. We also observed alteration of several trophoblastic functions upon infection by B. papionis or Brucella melitensis (the most prevalent species in human brucellosis). Infection altered the production of hormones, the ability of CTB to form syncytiotrophoblasts, and the invasion capacity of EVT. We also found that infection can spread between different types of trophoblasts. These findings constitute a new step in understanding how Brucella infection causes adverse pregnancy outcomes.