Fig 1.
Sankey diagram and species distribution of Renibacterium salmoninarum infections in salmonids.
a) Each node in the diagram, rectangles and text, represents one set of the data we collected from the literature (i.e., location, source, species, tissue, and assay). The connections represent the relationship between two nodes and are proportional to number of reports for each of the data nodes. b) Pie chart showing the relative distribution of salmonid species that have had a Renibacterium salmoninarum infection documented in the literature. All citations used to produce the Sankey diagram and pie chart are included in S1 Appendix.
Fig 2.
Geographic distribution of Renibacterium salmoninarum detections in inland United States.
Detections of Renibacterium salmoninarum with PCR in the inland U.S. states. Darker colors represent higher detections of the bacteria among individual fish. Data collected from the U.S. Fish and Wildlife Service, wild fish survey in February 2019.
Table 1.
Detection history and probability of Renibacterium salmoninarum infections across tissues and infection states. Possible detection history for each state of Renibacterium salmoninarum infection consisting of detection (1) or lack thereof (0) from two surveys (S1 and S2) conducted on each tissue (kidney and liver). Probability of infection for each assay (DFAT and qPCR*) is listed for each possible state of infection.
Fig 3.
Conceptual hierarchical occupancy model for Renibacterium salmoninarum detections.
Conceptual diagram of hierarchical occupancy model where is the probability of infection for each state of infection,
is the true occupancy within each state of infection,
is the probability of detecting Renibacterium salmoninarum from either DFAT or qPCR (modeled independently) for the state of infection
during survey
, and
is the detection data (1, 2, 3 or 4) for each state of infection
during survey
.
Fig 4.
Observed versus true infection states for Renibacterium salmoninarum detection.
Conceptual diagram of observed and true infection states and possible combinations of how a true infection state may be observed with DFAT or qPCR (indicated by colored lines; K: Kidney, L: Liver, − : negative detection, + : positive detection). Solid lines indicate the probability the observed fish is in the true state and dashed lines indicate the probability of the observed fish is in a different state.
Fig 5.
Standard curve for quantification of Renibacterium salmoninarum using qPCR.
Standard curve generated from 58, five-log10 serial dilutions of R. salmoninarum with associated confidence intervals. Cq values are plotted as a function of five-log10 of the known number of bacterial cells that were quantified by membrane-filtration fluorescent antibody test from pure culture of R. salmoninarum collected from rainbow trout at the Colorado Parks and Wildlife Bellvue Fish Research Hatchery. The green shaded area around the linear fit represents the standard error.
Fig 6.
Comparison of tissue-specific detection of Renibacterium salmoninarum using DFAT and qPCR.
Number of positive Renibacterium salmoninarum detections from three tissues (spleen, kidney, liver) using qPCR (black bars) and DFAT (white bars). Total number of samples for each tissue are as follows: 781 spleen samples, 778 kidney samples, and 776 liver samples.
Fig 7.
Detection probabilities of true infection states for Renibacterium salmoninarum.
Each panel represents the probability that the observed state of infection was the true state of infection or not (i.e., the detection probability of the true state of infection) when using either DFAT or qPCR. Solid lines represent the probability of observing a fish in the true state of infection. Dashed lines indicate the probability of observing a state of infection different from the true infection state due to false negative results with DFAT and/or qPCR. (a: State 1 , b: State 2
, c: State 3
, d: State 4
).
Fig 8.
Conditional probability of detecting Renibacterium salmoninarum in different tissues.
Conditional probability of detecting Renibacterium salmoninarum (DSe) in liver (blue circles), kidney (grey squares), or both tissues combined (black triangles) is shown as the function of the number of surveys conducted using either DFAT or qPCR. DSe values are indicated next to the dotted lines for cases where only one survey was conducted with kidney or liver tissue for each assay, as well as when DSe exceeds 90% (after three surveys with DFAT or two surveys with qPCR).