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

Estimating Space Use of Mobile Fishes in a Large Marine Protected Area With Methodological Considerations in Acoustic Array Design

Marine protected areas (MPAs) have become an increasingly important tool to protect and conserve marine resources. However, there remains much debate about how effective MPAs are, especially in terms of their ability to protect mobile marine species such as teleost and chondrichthyan fishes. We used satellite and acoustic tags to assess the ability of a large oceanic MPA, the British Indian Ocean Territory MPA (BIOT MPA), to protect seven species of pelagic and reef-associated teleost and chondrichthyan fishes. We satellite-tagged 26 animals from six species (Blue Marlin, Reef Mantas, Sailfish, Silky Sharks, Silvertip Sharks, and Yellowfin Tuna), producing 2,735 days of movement data. We also acoustically tagged 121 sharks from two species (Grey Reef and Silvertip Sharks), which were monitored for up to 40 months across a large acoustic receiver array spanning the MPA. We found that the activity spaces of all satellite-tagged animals, including pelagic species, were much smaller than the area of the BIOT MPA, even taking into account errors associated with position estimates. Estimates of space use of acoustically tagged sharks, based on dynamic Brownian Bridge Movement Models (dBBMM), were also much smaller than the size of the MPA. However, we found important limitations when using dBBMM and demonstrate its sensitivity to both study duration and array design. We found that Grey Reef Sharks should be monitored for at least 1 year and Silvertip Sharks for 2 years before their activity space can be effectively estimated. We also demonstrate the potentially important role that intraspecific variability in spatial ecology may play in influencing the ability of MPAs to effectively protect populations of mobile species. Overall, our results suggest that, with effective enforcement, MPAs on the scale of the BIOT MPA potentially offer protection to a variety of pelagic and reef species with a range of spatial ecologies. We suggest that animals need to be tagged across seasons, years, and ontogenetic stages, in order to fully characterize their spatial ecology, which is fundamental to developing and implementing effective MPAs to conserve the full life history of target species

Range expansion and the origin of USA300 north american epidemic methicillin-resistant Staphylococcus aureus

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread

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