DOI: 10.5061/dryad.x69p8czsq
title: Data from: Density matters: How population dynamics of house mice (Mus musculus) inform the epidemiology of Leptospira

description: Rodents are maintenance hosts of numerous pathogens, and both their
 density and the pathogen prevalence determine the risk they pose to other
 animals or humans. However, density is often overlooked. We investigated a
 capture-mark-recapture-sampling strategy to study introduced mice (Mus
 musculus) and Leptospira as a model and demonstrate the advantages of a
 combined approach. We estimated population density and Leptospira
 prevalence in mice in a replicated longitudinal survey conducted between
 2016 and 2018. Capture-mark-recapture sessions were undertaken at two
 sites in Spring and Autumn and blood and kidney samples were collected at
 the end of each session. Mouse density and areas of activity were
 estimated using spatially explicit capture-recapture (SECR) models and
 both were compared between Leptospira positive and negative mice.
 Leptospira exposure and shedding status were estimated using Microscopic
 Agglutination Test, and a combination of culture and lipL32 PCR on
 kidneys. Leptospira prevalence was higher in spring (83% to 86%)
 than in autumn (31% to 37%) and mouse densities simultaneously varied from
 3.6 to 55.9/ha. However, despite these variations in prevalence and
 density, the density of infected animals remained relatively constant over
 time (3 to 8/ha). Shedding or being seropositive was also associated with
 the activity of mice. Shedding or seropositive mice had a larger activity
 area, and seropositive mice were trapped on average one day earlier than
 seronegative mice.  Synthesis and applications. Our results show
 how understanding the population dynamics of pathogen-carrying rodents is
 critical in epidemiology. The wider movement patterns and easier
 encounters of positive mice highlight the possibility of biases in
 classical prevalence surveys and have implications for disease
 transmission within and between species. Importantly, and quite
 counter-intuitively, Leptospira prevalence was negatively associated with
 mouse density, resulting in a constant density of shedders that
 contradicts the conventional view of higher exposure risk at high rodent
 density. More broadly, such hybrid sampling designs can improve animal and
 disease control policies and better inform modelling studies by providing
 more parameter estimates than classical prevalence surveys.
description: This data was obtained using capture-mark recapture and
 bacteriology methods. Between Spring 2016 and Autumn 2018, four
 live-trapping sessions were conducted using two grids of 36 Longworth
 small mammal live-traps, and each session contained two phases. During the
 Capture-Mark Recapture (CMR) phase (first five nights), mice
 (<em>Mus musculus</em>) were captured, ear-tagged, sexed,
 weighed, and released. In the subsequent Removal phase, mice were also
 blood-sampled, euthanized, and their kidneys tested for
 <em>Leptospira</em> infection. Antibodies
 against <em>Leptospira </em>spp. and in particular
 <em>L. borgpetersenii</em> serovar Ballum were tested using
 the Microscopic Agglutination Test (MAT), and the presence
 of <em>Leptospira</em> spp. in the kidneys was determined via
 culture and real-time PCR.
description: # Density matters: How population dynamics of house mice (*Mus musculus*)
 inform the epidemiology of *Leptospira*
 [https://doi.org/10.5061/dryad.x69p8czsq](https://doi.org/10.5061/dryad.x69p8czsq) ## Description of the data and file structure This dataset provides the raw data necessary to recreate the SECR models in the associated manuscript. It comprises the capture history of mice, their associated test results, trap coordinates (anonymized) and an R script to perform partially explicit capture recapture modelling. ### **CONTACTS** Dr. Marie Moinet, [marie.moinet+SECR@gmail.com](mailto:marie.moinet+SECR@gmail.com) Prof. Jackie Benschop [J.Benschop@massey.ac.nz](mailto:J.Benschop@massey.ac.nz) Prof. James C. Russell, [j.russell@auckland.ac.nz](mailto:j.russell@auckland.ac.nz) ### **DATE AND LOCATION OF DATA COLLECTION**: 10/2016 - 04/2018, Massey University, New Zealand ### **FILES ASSOCIATED WITH THIS DATASET**: **SECR_script.R -** annotated R code to rebuild the SECR models **CA1.txt** - Capture history of mice secrSession: encompasses the capture session (1L, 3L, 4L, 5L) and the grid (s1, s2) FKAnimalID: animal unique ID (MM0001 to MM0380) Occasion: day captured within the session (e.g. MM0004 captured on days 2, 3, and 7, with -7 indicating the animal was euthanized and not released) FKTrapID: Trap unique ID (Foreign key, see Traps .txt files for primary key data) Age: Adult (Ad), Subadult (Sub) or Juvenile (J) Sex: Male (M), Female (F) MAT_Positives: MAT test positive, yes (1) or no (0) BallumPositive: MAT test positive for serovar Ballum, yes (1) or no (0) CulturePos: Culture positive for Leptospira, yes (1) or no (0) PCRpositive: PCR positive for Leptospira, yes (1) or no (0) Weight: weight of the animal in grams Occaz: Occasion in absolute values FirstCapt: At which occasion did the first capture happen LastCapt: At which occasion did the last capture happen newage: Age simplified in two categories according to weight, &gt;11g for Ad,