DOI: 10.5061/dryad.djh9w0w4k
title: Data from: Bartonella infections are prevalent in rodents despite efficient immune responses

description: Pathogens face strong selection from host immune responses, yet many host
 populations support pervasive pathogen populations. We investigated this
 puzzle in a model system of Bartonella and rodents from Israel’s
 northwestern Negev Desert. We chose to study this system because in this
 region, 75–100% of the rodents are infected with Bartonella at any given
 time, despite an efficient immunological response. In this region,
 Bartonella species circulate in three rodent species, and we tested the
 hypothesis that at least some of these hosts exhibit a waning immune
 response to Bartonella, which allows reinfections. To that end, we
 inoculated captive rodents from all three species with the same Bartonella
 strain, and we quantified the bacterial dynamics and Bartonella-specific
 IgG antibody kinetics through 139 days after the primary inoculation and
 then for 60 days following re-inoculation with the same strain. Contrary
 to our hypothesis, we found a strong, long-lasting IgG antibody response,
 with a protective immunological memory in all three rodent species. That
 response prevented re-infection upon exposure to the same Bartonella
 strain. This study constitutes an initial step toward a better
 understanding of the interplay between Bartonella pathogens and rodent
 traits, and how the interplay of those traits influences epidemiological
 dynamics in nature.
description: # Data from: Bartonella infections are prevalent in rodents despite
 efficient immune responses This file contains: Descriptions of the data
 sets associated with the analyses presented in the paper. code.R – R file
 containing all code necessary to analyze the data. A list of the required
 packages and is included. The analyses used R v4.1.3, but newer versions
 are also usable. NOTE: for all files below "NA" values represent
 data that was not available for a specific animal on a specific day
 because that animal either died or was removed from the experiment.
 bacterial_loads.csv – this is the data file containing information on
 bacterial dynamics. For the "Negt.Ctr." samples, these are
 negative controls from each bacterial extraction session. As such, there
 is no animal code, NA for species and dpi, as well as empty cells for the
 "Infected" column for these samples, as these data do not come
 from an experimental animal. The following are explanations of the
 variables: * animal.code - unique id for each rodent * Species - species
 of the rodent * Infected - code for treatment (1) and control (0) rodents
 * dpi - days post inoculation * Purpose - denotes if data came from the
 experiment (Dynamics) or represents a negative control *
 Bacteria.load.per.ml.of.blood - bacterial concentration growth_rates.csv –
 this is the data file containing information on rate of immune increase
 during the primary infection. The following are explanations of the
 variables: * animal.code - unique id for each rodent * Species - species
 of the rodent * points - number of points used to measure rate * rate -
 the rate of increase * days - which two times points were used
 growth_rates_reinf.csv – this is the data file containing information on
 rate of immune increase during the secondary infection. The following are
 explanations of the variables: * animal.code - unique id for each rodent *
 Species - species of the rodent * points - number of points used to
 measure rate * slope - the rate of increase * days - which two times
 points were used immune_inoculated.csv – this is the data file containing
 information on antibody dynamics for treatment animals. The following are
 explanations of the variables: * animal.code - unique id for each rodent *
 Species - species of the rodent * dpi - days post infection *
 Concentration.ng/ml.corrected.for.original.sample - antibody concentration
 immune_cont_only.csv – this is the data file containing information on
 antibody dynamics for control animals. The following are explanations of
 the variables: * animal.code - unique id for each rodent * Species -
 species of the rodent * dpi - days post infection *
 Concentration.ng/ml.corrected.for.original.sample - antibody concentration
 immune_inoculated_with_no_missing_cells.csv – this is the data file
 containing information on antibody dynamics for treatment animals,
 replacing missing cells with the species average for that day. The
 following are explanations of the variables: * animal.code - unique id for
 each rodent * Species - species of the rodent * dpi - days post infection
 * Concentration.ng/ml.corrected.for.original.sample - antibody
 concentration Excel_master_file_for_dryad.xlsx - this is the Excel file
 with all of the relevant data in Excel format. The first page contains an
 index