Estimating species richness using environmental DNA

The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion‐based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.     

Effects of Including Misidentified Sharks in Life History Analyses: A Case Study on the Grey Reef Shark Carcharhinus amblyrhynchos from Papua New Guinea

Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species’ life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L¯∞ = 159 cm TL and L¯0 = 72 cm TL. Females mature at a greater length (l₅₀ = 136 cm TL) and older age (A₅₀ = 9.1 years) than males (l₅₀ = 123 cm TL; A₅₀ = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.     

Potential Impacts of Future Warming and Land Use Changes on Intra-Urban Heat Exposure in Houston,Texas

Extreme heat events in the United States are projected to become more frequent and intense as a result of climate change. We investigated the individual and combined effects of land use and warming on the spatial and temporal distribution of daily minimum temperature (T_min) and daily maximum heat index (HI_max) during summer in Houston, Texas. Present-day (2010) and near-future (2040) parcel-level land use scenarios were embedded within 1-km resolution land surface model (LSM) simulations. For each land use scenario, LSM simulations were conducted for climatic scenarios representative of both the present-day and near-future periods. LSM simulations assuming present-day climate but 2040 land use patterns led to spatially heterogeneous temperature changes characterized by warmer conditions over most areas, with summer average increases of up to 1.5°C (T_min) and 7.3°C (HI_max) in some newly developed suburban areas compared to simulations using 2010 land use patterns. LSM simulations assuming present-day land use but a 1°C temperature increase above the urban canopy (consistent with warming projections for 2040) yielded more spatially homogeneous metropolitan-wide average increases of about 1°C (T_min) and 2.5°C (HI_max), respectively. LSM simulations assuming both land use and warming for 2040 led to summer average increases of up to 2.5°C (T_min) and 8.3°C (HI_max), with the largest increases in areas projected to be converted to residential, industrial and mixed-use types. Our results suggest that urbanization and climate change may significantly increase the average number of summer days that exceed current threshold temperatures for initiating a heat advisory for metropolitan Houston, potentially increasing population exposure to extreme heat.     

Development and Evaluation of a Blood Culture PCR Assay for Rapid Detection of Salmonella Paratyphi A in Clinical Samples

Background

Enteric fever remains an important cause of morbidity in many low-income countries and Salmonella Paratyphi A has emerged as the aetiological agent in an increasing proportion of cases. Lack of adequate diagnostics hinders early diagnosis and prompt treatment of both typhoid and paratyphoid but development of assays to identify paratyphoid has been particularly neglected. Here we describe the development of a rapid and sensitive blood culture PCR method for detection of Salmonella Paratyphi A from blood, potentially allowing for appropriate diagnosis and antimicrobial treatment to be initiated on the same day.

Methods

Venous blood samples from volunteers experimentally challenged orally with Salmonella Paratyphi A, who subsequently developed paratyphoid, were taken on the day of diagnosis; 10 ml for quantitative blood culture and automated blood culture, and 5 ml for blood culture PCR. In the latter assay, bacteria were grown in tryptone soy broth containing 2.4% ox bile and micrococcal nuclease for 5 hours (37°C) before bacterial DNA was isolated for PCR detection targeting the fliC-a gene of Salmonella Paratyphi A.

Results

An optimized broth containing 2.4% ox bile and micrococcal nuclease, as well as a PCR test was developed for a blood culture PCR assay of Salmonella Paratyphi A. The volunteers diagnosed with paratyphoid had a median bacterial burden of 1 (range 0.1–6.9) CFU/ml blood. All the blood culture PCR positive cases where a positive bacterial growth was shown by quantitative blood culture had a bacterial burden of ≥ 0.3 CFU/ ml blood. The blood culture PCR assay identified an equal number of positive cases as automated blood culture at higher bacterial loads (≥0.3 CFU/ml blood), but utilized only half the volume of specimens.

Conclusions

The blood culture PCR method for detection of Salmonella Paratyphi A can be completed within 9 hours and offers the potential for same-day diagnosis of enteric fever. Using 5 ml blood, it exhibited a lower limit of detection equal to 0.3 CFU/ml blood, and it performed at least as well as automated blood culture at higher bacterial loads (≥0.3 CFU/ml blood) of clinical specimens despite using half the volume of blood. The findings warrant its further study in endemic populations with a potential use as a novel diagnostic which fills the present gap of paratyphoid diagnostics.     

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus.     

Solving the Border Control Problem: Evidence of Enhanced Face Matching in Individuals with Extraordinary Face Recognition Skills

Photographic identity documents (IDs) are commonly used despite clear evidence that unfamiliar face matching is a difficult and error-prone task. The current study set out to examine the performance of seven individuals with extraordinary face recognition memory, so called “super recognisers” (SRs), on two face matching tasks resembling border control identity checks. In Experiment 1, the SRs as a group outperformed control participants on the “Glasgow Face Matching Test”, and some case-by-case comparisons also reached significance. In Experiment 2, a perceptually difficult face matching task was used: the “Models Face Matching Test”. Once again, SRs outperformed controls both on group and mostly in case-by-case analyses. These findings suggest that SRs are considerably better at face matching than typical perceivers, and would make proficient personnel for border control agencies.     

Design Characteristics Influence Performance of Clinical Prediction Rules in Validation: A Meta-Epidemiological Study

Background

Many new clinical prediction rules are derived and validated. But the design and reporting quality of clinical prediction research has been less than optimal. We aimed to assess whether design characteristics of validation studies were associated with the overestimation of clinical prediction rules’ performance. We also aimed to evaluate whether validation studies clearly reported important methodological characteristics.

Methods

Electronic databases were searched for systematic reviews of clinical prediction rule studies published between 2006 and 2010. Data were extracted from the eligible validation studies included in the systematic reviews. A meta-analytic meta-epidemiological approach was used to assess the influence of design characteristics on predictive performance. From each validation study, it was assessed whether 7 design and 7 reporting characteristics were properly described.

Results

A total of 287 validation studies of clinical prediction rule were collected from 15 systematic reviews (31 meta-analyses). Validation studies using case-control design produced a summary diagnostic odds ratio (DOR) 2.2 times (95% CI: 1.2–4.3) larger than validation studies using cohort design and unclear design. When differential verification was used, the summary DOR was overestimated by twofold (95% CI: 1.2 -3.1) compared to complete, partial and unclear verification. The summary RDOR of validation studies with inadequate sample size was 1.9 (95% CI: 1.2 -3.1) compared to studies with adequate sample size. Study site, reliability, and clinical prediction rule was adequately described in 10.1%, 9.4%, and 7.0% of validation studies respectively.

Conclusion

Validation studies with design shortcomings may overestimate the performance of clinical prediction rules. The quality of reporting among studies validating clinical prediction rules needs to be improved.