Evaluation of the Xpert Carba-R Nxg Assay for Detection of Carbapenemase Genes in a Global Challenge Set of \u3cem\u3ePseudomonas aeruginosa \u3c/em\u3e Isolates

The growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global collection of P. aeruginosa. The challenge set included 123 P. aeruginosa clinical isolates from 12 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP)-harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and the Carba-R tests per the manufacturer’s instructions. Carba-R NxG testing was completed by Cepheid (Sunnyvale, CA), blinded to genotype. Both assays gave negative results for all non-CP isolates and positive results for all VIM, NDM, and KPC isolates. An improvement in IMP detection among isolates was observed (100% detection by Carba-R NxG versus 58% by Carba-R). All SPM and GES isolates, targets not present in commercially available Carba-R, were positive by Carba-R NxG. Two isolates harbored both VIM and GES, while a third isolate contained VIM and NDM. The Carba-R NxG identified both targets in all 3 isolates, while the Carba-R was negative for both GES-containing isolates. Overall, the Carba-R NxG successfully categorized 100% of isolates tested compared with 68% for its predecessor. The Carba-R NxG will expand the detection spectrum of the current Carba-R assay to include SPM, GES, and expanded IMP variants, increasing the global utility of the test

Pop-up archival tags reveal environmental influences on the vertical movements of silvertip sharks (Carcharhinus albimarginatus)

Vertical space use informs the ecology and management of marine species, but studies of reef-associated sharks often focus on horizontal movements. We analysed the vertical movements of silvertip sharks (Carcharhinus albimarginatus) using pop-up archival tags deployed on seven individuals in the Chagos Archipelago, central Indian Ocean. The sharks changed depth predictably with water column thermal structure, moving deeper with seasonal increases in mixed layer depth while occupying a narrow ambient water temperature range around ~27°C. At shorter timescales, higher resolution data from five tags showed that silvertip shark depth varied cyclically with surface light levels, increasing during daylight and on nights around full moon. This matches the diel vertical migrations of many fish species, suggesting the sharks’ light-driven depth changes might relate to foraging. While most vertical movements (>98%) were within the mixed layer, deeper dives to 200-800 m occurred approximately every three days. High-resolution data from one recovered tag showed the shark ascending deep (>200 m) dives in two sharply defined phases, initially fast then slow. Analysis of dive profiles against dissolved oxygen (DO) data suggested that the shark may have ascended rapidly to escape low DO levels at depth, then reduced its ascent rate 50-80% once DO levels increased. While a small sample, the electronic tags deployed in this study revealed the silvertip sharks’ predictable use of mixed layer waters, narrow thermal range and apparent intolerance of hypoxic conditions. These characteristics may exacerbate the species’ vulnerability as oceanic warming and shoaling oxygen minimum zones modify vertical habitat availability

Coral bleaching impacts from back-to-back 2015–2016 thermal anomalies in the remote central Indian Ocean

Studying scleractinian coral bleaching and recovery dynamics in remote, isolated reef systems offers an opportunity to examine impacts of global reef stressors in the absence of local human threats. Reefs in the Chagos Archipelago, central Indian Ocean, suffered severe bleaching and mortality in 2015 following a 7.5 maximum degree heating weeks (DHWs) thermal anomaly, causing a 60% coral cover decrease from 30% cover in 2012 to 12% in April 2016. Mortality was taxon specific, with Porites becoming the dominant coral genus post-bleaching because of an 86% decline in Acropora from 14 to 2% cover. Spatial heterogeneity in Acropora mortality across the Archipelago was significantly negatively correlated with variation in DHWs and with chlorophyll-a concentrations. In 2016, a 17.6 maximum DHWs thermal anomaly caused further damage, with 68% of remaining corals bleaching in May 2016, and coral cover further declining by 29% at Peros Banhos Atoll (northern Chagos Archipelago) from 14% in March 2016 to 10% in April 2017. We therefore document back-to-back coral bleaching and mortality events for two successive years in the remote central Indian Ocean. Our results indicate lower coral mortality in 2016 than 2015 despite a more severe thermal anomaly event in 2016. This could be caused by increased thermal resistance and resilience within corals surviving the 2015 thermal anomaly; however, high bleaching prevalence in 2016 suggests there remained a high sensitivity to bleaching. Similar coral mortality and community change were seen in the Chagos Archipelago following the 1998 global bleaching event, from which recovery took 10 yr. This relatively rapid recovery suggests high reef resiliency and indicates that the Archipelago’s lack of local disturbances will increase the probability that the reefs will again recover over time. However, as the return time between thermal anomaly events becomes shorter, this ability to recover will become increasingly compromised

Phenotypic/Genotypic Profile of Oxa-10-like-Harboring, Carbapenem-Resistant \u3cem\u3ePseudomonas aeruginosa: \u3c/em\u3eUsing Validated Pharmacokinetic/Pharmacodynamic \u3cem\u3ein Vivo \u3c/em\u3eModels to Further Evaluate Enzyme Functionality and Clinical Implications

In vitro MICs and in vivo pharmacodynamics of ceftazidime and cefepime human-simulated regimens (HSR) against modified carbapenem inactivation method (mCIM)-positive Pseudomonas aeruginosa isolates harboring different OXA-10-like subtypes were described. The murine thigh model assessed ceftazidime (2 g every 8 h [q8h] HSR) and cefepime (2 g and 1 g q8h HSR). Phenotypes were similar despite possessing OXA-10-like subtypes with differing spectra. Ceftazidime produced ≥1-log10 killing in all isolates. Cefepime activity was dose dependent and MIC driven. This approach may be useful in assessing the implications of β-lactamase variants

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Correction: Drivers of abundance and spatial distribution of reef-associated sharks in an isolated atoll reef system.

[This corrects the article DOI: 10.1371/journal.pone.0177374.]

Linear regression model parameters for shark a) species richness b) abundance and c) biomass based on n = 33 sites.

<p>β = standardised model parameters.</p

The Chagos Archipelago

The Chagos Archipelago, located in the central Indian Ocean and officially known as the British Indian Ocean Territory, contains some of the most remote reefs in the Indian Ocean. The Chagos Archipelago is comprised of a series of atolls, including the largest atoll in the world, the Great Chagos Bank. Records from surveys of mesophotic coral ecosystems (MCEs; reefs 30-150 m depth) in Chagos stretch back to 1905, with more extensive work conducted in the 1970s and post-2010. Coral and fish communities vary considerably with depth and among habitat types. Coral cover generally declines with increased depth across the shallow reef to MCE depth gradient, though in several locations close to 100% scleractinian coral cover has been observed on MCEs. Consistent with earlier studies, we identify five coral species as indicative of Chagos MCEs. Recently collected fish community data are analyzed to illustrate, for the first time, patterns in reef fish species richness, abundance, biomass, and trophic groups across a shallow to upper-MCE depth gradient (0-60 m). Fish species richness, abundance, and biomass declined with increased depth, while richness, abundance, and trophic group patterns were also influenced by habitat type (seaward versus lagoonal reef). To date, the vast majority of MCE research in Chagos has focused on upper mesophotic depths. We recommend future work consider the full MCE depth range within the Chagos Archipelago