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

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.]

Potential detection of illegal fishing by passive acoustic telemetry

Abstract Acoustic tagging is typically used to gather data on the spatial ecology of diverse marine taxa, informing questions about spatio-temporal attributes such as residency and home range, but detection data may also reveal unanticipated insights. Many species demonstrate predictable site fidelity, and so a sudden cessation of detections for multiple individuals may be evidence of an atypical event. During 2013 and 2014, we acoustically tagged 47 grey reef sharks (Carcharhinus amblyrhynchos) and 48 silvertip sharks (Carcharhinus albimarginatus) near reefs in the British Indian Ocean Territory (BIOT) Marine Protected Area (MPA). From March 2013 to November 2014 inclusive, tags were ‘lost’, i.e. permanently ceased to be detected within the monitoring area, at an average rate of 2.6 ± 1.0 tags per month. Between 1 and 10 December 2014, detection data suggest the near-simultaneous loss of 15 of the remaining 43 active tagged sharks, a monthly loss rate over five times higher than during the previous 21 months. Between 4 and 14 December of 2014, the BIOT patrol vessel encountered 17 vessels engaged in suspected illegal fishing in the northern BIOT MPA; such sightings averaged one per month during the previous 8 months. Two of these vessels were arrested with a total of 359 sharks on board, of which grey reef and silvertip sharks constituted 47% by number. The unusual and coincident peaks in tag loss and vessel sightings, and the catch composition of the arrested vessels, suggest illegal fishing as a plausible explanation for the unusual pattern in our detection data. A Cox proportional hazards model found that the presence of fishing vessels increased the risk of tag loss by a factor of 6.0 (95% CI 2.6–14.0, p < 0.001). Based on the number of vessels sighted and the average number of sharks on vessels arrested in BIOT during 2014, we conservatively estimate that over 2000 sharks may have been removed during the suspected fishing event. Based on average catch compositions, over 1000 would have been grey reef and silvertip sharks. Assuming a closed population mark-recapture model, over one-third of the locally resident reef sharks may have been removed from the monitoring area. The data suggest that even sporadic fishing events may have a marked impact on local reef shark populations, but also demonstrate the potential of electronic tagging a tool for detecting illegal or otherwise unreported fishing activity

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