Misdiagnosing Melioidosis

Melioidosis is endemic in southern and Southeast Asia and northern Australia. Although relatively few indigenous cases are recognized in the Indian subcontinent, a substantial proportion of cases imported into the United Kingdom originate there, probably reflecting patterns of immigration and travel, and underdiagnosis within the Indian subcontinent

Fish assemblages associated with artificial reefs assessed using multiple gear types in the northwest Gulf of Mexico

Quantitative surveys of fishes associated with artificial reefs in the northwest Gulf of Mexico were conducted over a 4-yr period (2014-2017). Artificial reefs surveyed were comprised of three types: concrete structures, rig jackets, and decommissioned ships. All reefs were surveyed using vertical long line ( VLL), fish traps, and Adaptive Resolution Imaging Sonar (ARIS 1800). Mean fish abundance did not significantly differ using VLL [1.7 ind set(-1) (SD 2.2)] among the three reef types. However, relative abundance among all fishes collected was significantly highest on rig reefs using traps [6.2 ind soak(-1) (SD 3.8)], while results from sonar surveys indicated that the mean relative fish density was highest on concrete reefs [15.3 fish frame(-1) (SD 26.8)]. Red snapper (n = 792), followed by gray triggerfish (n = 130), pigfish (n = 70), tomtate (n = 69), and hardhead catfish (n = 57) were the most numerically abundant species using VLL and traps; red snapper comprised 90.7% of total catch using VLL and 43.9% using traps. Mean Brillouin\u27s diversity (HB) was highest on ships using VLL [0.41 (SD 0.14)] and highest on rigs using traps [0.87 (SD 0.58)] compared to the lowest diversity found on concrete [VLL 0.07 (SD 0.11); traps 0.36 (SD 0.32)]. Findings from this study can be used to inform the planning of future artificial reefs and their effect on the assemblages of reef-associated fishes. Additionally, these results highlight the value of using multiple gear types to survey reef fish assemblages associated with artificial reefs

Observation error statistics for Doppler radar radial wind superobservations assimilated into the DWD COSMO-KENDA system

Currently in operational numerical weather prediction (NWP) the density of high-resolution observations, such as Doppler radar radial winds (DRWs), is severely reduced in part to avoid violating the assumption of uncorrelated observation errors. To improve the quantity of observations used and the impact that they have on the forecast requires an accurate specification of the observation uncertainties. Observation uncertainties can be estimated using a simple diagnostic that utilises the statistical averages of observation-minus-background and observation-minus-analysis residuals. We are the first to use a modified form of the diagnostic to estimate spatial correlations for observations used in an operational ensemble data assimilation system. The uncertainties for DRW superobservations assimilated into the Deutscher Wetterdienst convection-permitting NWP model are estimated and compared to previous uncertainty estimates for DRWs. The new results show that most diagnosed standard deviations are smaller than those used in the assimilation, hence it may be feasible assimilate DRWs using reduced error standard deviations. However, some of the estimated standard deviations are considerably larger than those used in the assimilation; these large errors highlight areas where the observation processing system may be improved. The error correlation length scales are larger than the observation separation distance and influenced by both the superobbing procedure and observation operator. This is supported by comparing these results to our previous study using Met Office data. Our results suggest that DRW error correlations may be reduced by improving the superobbing procedure and observation operator; however, any remaining correlations should be accounted for in the assimilation

Grading antimicrobial susceptibility data quality: room for improvement.

In their Review of antimicrobial resistance in children in sub-Saharan Africa,1 Phoebe Williams and colleagues remark upon the poor quality of the studies included. We would like to highlight specific concerns regarding the reliability of some of the antimicrobial susceptibility data. By our assessment, only nine of the 18 studies included had no detectable errors or non-compliances to the reporting standards stated to have been used. Examples include reporting antimicrobial susceptibilities for which no breakpoints exist (eg, gentamicin susceptibility for Streptococcus pneumoniae and Salmonella species) or unexpected susceptibility patterns given the known intrinsic resistance of the pathogen (eg, amoxicillin and Klebsiella species; appendix). Identification of genuine meticillin-resistant Staphylococcus aureus was problematic with discordant cloxacillin and cefuroxime susceptibility patterns in two studies, suggesting non-adherence to standard methods

Importance of low-relief nursery habitat for reef fishes

Coastal restoration projects to mitigate environmental impacts have increased global demand for sand resources. Unfortunately, these resources are often extracted from sand/shell banks on the inner continental shelf, resulting in significant alteration or loss of low-relief reefs in coastal oceans. Experimental reefs (oyster shell, limestone rubble, composite) were deployed in the western Gulf of Mexico to assess their potential value as nurseries for newly settled reef fishes. Occurrence, abundance, and species richness of juvenile fishes were significantly higher on all three types of low-relief reefs compared with unconsolidated sediment. Moreover, reefs served as nursery habitat for a range of reef fish taxa (angelfishes, grunts, sea basses, snappers, and triggerfishes). Red snapper (Lutjanus campechanus) was the dominant species present on all experimental reefs (100% occurrence), and mean density of this species was markedly higher on each of the three low-relief reefs (\u3e40.0 individuals/reef) relative to comparable areas over unconsolidated sediment (0.2 individuals). Our results suggest creation or restoration of structurally complex habitat on the inner shelf has the potential to markedly increase early life survival and expedite the recovery of exploited reef fish populations, and therefore may represent a critical conservation tool for increasing recruitment and maintaining reef fish diversity

Global burden of melioidosis in 2015: a systematic review and data synthesis.

BACKGROUND: Melioidosis is an infectious disease caused by the environmental bacterium Burkholderia pseudomallei. It is often fatal, with a high prevalence in tropical areas. Clinical presentation can vary from abscess formation to pneumonia and sepsis. We assessed the global burden of melioidosis, expressed in disability-adjusted life-years (DALYs), for 2015. METHODS: We did a systematic review of the peer-reviewed literature for human melioidosis cases between Jan 1, 1990, and Dec 31, 2015. Quantitative data for cases of melioidosis were extracted, including mortality, age, sex, infectious and post-infectious sequelae, antibiotic treatment, and symptom duration. These data were combined with established disability weights and expert panel discussions to construct an incidence-based disease model. The disease model was integrated with established global incidence and mortality estimates to calculate global melioidosis DALYs. The study is registered with PROSPERO, number CRD42018106372. FINDINGS: 2888 articles were screened, of which 475 eligible studies containing quantitative data were retained. Pneumonia, intra-abdominal abscess, and sepsis were the most common outcomes, with pneumonia occurring in 3633 (35·7%, 95% uncertainty interval [UI] 34·8-36·6) of 10 175 patients, intra-abdominal abscess in 1619 (18·3%, 17·5-19·1) of 8830 patients, and sepsis in 1526 (18·0%, 17·2-18·8) of 8469 patients. We estimate that in 2015, the global burden of melioidosis was 4·6 million DALYs (UI 3·2-6·6) or 84·3 per 100 000 people (57·5-120·0). Years of life lost accounted for 98·9% (UI 97·7-99·5) of the total DALYs, and years lived with disability accounted for 1·1% (0·5-2·3). INTERPRETATION: Melioidosis causes a larger disease burden than many other tropical diseases that are recognised as neglected, and so it should be reconsidered as a major neglected tropical disease. FUNDING: European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Research Grant 2018, AMC PhD Scholarship, The Netherlands Organisation for Scientific Research (NWO), H2020 Marie Skłodowska-Curie Innovative Training Network European Sepsis Academy

An inventory of supranational antimicrobial resistance surveillance networks involving low- and middle-income countries since 2000.

Low- and middle-income countries (LMICs) shoulder the bulk of the global burden of infectious diseases and drug resistance. We searched for supranational networks performing antimicrobial resistance (AMR) surveillance in LMICs and assessed their organization, methodology, impacts and challenges. Since 2000, 72 supranational networks for AMR surveillance in bacteria, fungi, HIV, TB and malaria have been created that have involved LMICs, of which 34 are ongoing. The median (range) duration of the networks was 6 years (1-70) and the number of LMICs included was 8 (1-67). Networks were categorized as WHO/governmental (n = 26), academic (n = 24) or pharma initiated (n = 22). Funding sources varied, with 30 networks receiving public or WHO funding, 25 corporate, 13 trust or foundation, and 4 funded from more than one source. The leading global programmes for drug resistance surveillance in TB, malaria and HIV gather data in LMICs through periodic active surveillance efforts or combined active and passive approaches. The biggest challenges faced by these networks has been achieving high coverage across LMICs and complying with the recommended frequency of reporting. Obtaining high quality, representative surveillance data in LMICs is challenging. Antibiotic resistance surveillance requires a level of laboratory infrastructure and training that is not widely available in LMICs. The nascent Global Antimicrobial Resistance Surveillance System (GLASS) aims to build up passive surveillance in all member states. Past experience suggests complementary active approaches may be needed in many LMICs if representative, clinically relevant, meaningful data are to be obtained. Maintaining an up-to-date registry of networks would promote a more coordinated approach to surveillance

A pragmatic strategy for implementing spatially correlated observation errors in an operational system: an application to Doppler radial winds

Recent research has shown that high resolution observations, such as Doppler radar radial winds, exhibit spatial correlations. High resolution observations are routinely assimilated into convection permitting numerical weather prediction models assuming their errors are uncorrelated. To avoid violating this assumption observation density is severely reduced. To improve the quantity of observations used and the impact that they have on the forecast requires the introduction of full, correlated, error statistics. Some operational centres have introduced satellite inter-channel observation error correlations and obtained improved analysis’ accuracy and forecast skill scores. Here we present a strategy for implementing spatially correlated observation errors in an operational system. We then provide the first demonstration of the practical feasibility of incorporating spatially correlated Doppler radial wind error statistics in the Met Office numerical weather prediction system. Inclusion of correlated Doppler radial winds error statistics has little impact on the computation cost of the data assimilation system, even with a four-fold increase in the number of Doppler radial winds observations assimilated. Using the correlated observation error statistics with denser observations produces increments with shorter length scales than the control. Initial forecast trials show a neutral to positive impact on forecast skill overall, notably for quantitative precipitation forecasts. There is potential to improve forecast skill by optimising the use of Doppler radial winds and applying the technique to other observation types

Movement, Behavior, and Habitat Use of a Marine Apex Predator, the Scalloped Hammerhead

Conservation and management efforts of marine apex predators are more reliable when information on movement and habitat use patterns are known. The scalloped hammerhead (Sphyrna lewini) was the first shark species to be protected under the U.S. Endangered Species Act and has life history characteristics that make this species particularly at risk for local depletion. Consequently, the goal of this study was to better understand the movement dynamics of this species in the Gulf of Mexico (GOM) where discards through the longline fishery can be substantial. A total of 33 scalloped hammerheads were tagged with fin mounted satellite tags and tracked for an average of 146 days (ranging from 5 to 479 days) to examine horizontal movements and quantify space use. Scalloped hammerheads showed a wide range of movements throughout the GOM continental shelf with limited long-distance dispersal and females displayed a shelf-edge association relative to more mid-shelf use by males. A generalized additive model was developed to identify habitat suitability for scalloped hammerheads in the GOM, while state-space modeling was used to examine movement behaviors. Model results highlighted the use of continental shelf waters with high occurrence at close proximities to both artificial and hard-bottom habitat combined with low chlorophyll a concentrations (∼0–4 mg m-3) and moderate salinities (33–35.5). Habitat suitability for scalloped hammerheads was predicted to be high on the mid to outer continental shelf inside the 200 m isobath and state-space model results suggest area-restricted behavior was most common relative to transient behavior. Findings from this study provide important information on movement of this species in the GOM and highlight their restricted use of continental shelf habitat and resident behavior that will need to be incorporated in future stock assessments and extinction risk analyses