Materials and Methods
Data used for this study was collected within the KMP on wild meerkats
living at the Kuruman River reserve (26° 580’ S, 21°490’ E), Northern
Cape, South Africa, between the between the 20th of
October 1993 and the 29th of December 2020. During
this time, several meerkat groups well habituated to human observers
were visited multiple times a week and detailed data on individually
recognizable individuals collected by trained volunteers and researchers
following standardized protocols (for details see Clutton-Brock and
Manser, 2016). We included data on all 3,420 individuals encompassed in
the study for individual level analyses. As it is common for newly
founded meerkat groups to quickly fail (Duncan et al., 2021), we limited
the analyses on the group level to 91 groups with a group duration
longer than 6 months.
For each individual, we recorded first date as birthdate or first entry
date into the population and final date as death date or last observed
date as well as available information on clinical signs of TB infection
(see Table 2 for definitions on terminology). Individuals can be
infectious even prior to the onset of clinical signs (Wilkinson et al.,
2000; Donadio et al., 2022), and exposure can vary with social behaviour
(Drewe, 2010; Drewe et al., 2011), so exact time of exposure for each
individual cannot easily determined. However, individuals with overt
signs are likely contributing the most to TB transmission (McDonald et
al., 2019), and most individuals were either born into a TB afflicted
group or came into contact with TB upon immigration into a TB afflicted
group (see below). We consequently chose contact with visibly TB
afflicted conspecifics as a conservative, clearly identifiable and
relatively accurate estimate for TB exposure, despite some remaining
uncertainty regarding individual exposure dates. Individuals were thus
classified as TB exposed from the first day of contact to conspecifics
with externally visible signs of clinical TB, either by clinical TB
emerging in the resident group or by immigrating into a group with
visibly infected individuals. Individuals were considered presenting
clinical signs from the date they were recorded with TB by observers or
displayed clear signs of TB infection (submandibular, inguinal or
cervical lumps). If individuals had records of suspected TB, i.e. lumps
or swelling with no alternative explanation, and progressed to develop
clinical TB, the date of first putative TB symptoms was considered as
onset of clinical TB. Clearance of clinical TB has not been recorded in
meerkats, so we considered TB infections to be purely progressive with
no return to prior states (Patterson et al., 2021). Within KMP,
terminally ill individuals were euthanized to curb the spread of the
disease (Patterson et al., 2021; Duncan et al., 2021), with infections
being confirmed in post-mortem examinations (Patterson et al., 2021). We
classified these individuals as having died of TB and included them in
our dataset of TB progression (see Table 2), as terminally ill
individuals do not recover and are expected to die within a few days or
weeks (Patterson et al., 2021). To be conservative in our
interpretations, individuals displaying clinical signs at time of death
but dying of other or unknown causes (e.g. predation or disappearance)
were not considered as having died of TB. At the group level, groups
were considered as TB exposed upon the first observation of a clinically
ill individual within the group. Groups that did not persist until the
end of the study are considered extinct, irrespective of the reason of
group termination (group abandoned, disintegrated, etc.).
Based on this data, we calculated time from being exposed to developing
clinical signs as proxy of TB-susceptibility, i.e. the risk to become
clinically ill upon exposure, and time between clinical signs and death
as proxy of resistance, i.e. the capacity of a clinically ill individual
to survive despite disease. We also calculated survival (i.e. time from
exposure to death) for all exposed individuals (see Donadio et al. 2022,
see Table 2). To assess TB exposure and prevalence as well as
progression and mortality, we calculated overall and yearly proportion
of exposure, clinical infection and TB related death at the group and
individual level. Plus, the temporal patterns of TB progression, i.e. TB
susceptibility, resistance and survival (definitions see Table 2), were
analyzed. Data was retrieved from the KMP database into R using the
package RMariaDB (Müller et al., 2020) and processed using the packages
tidyverse (Wickham et al., 2019). All analyses were performed in R,
version 3.6.3 (R Core Team, 2019). Research for this study was conducted
with permission of the ethical committee of Pretoria University and the
Northern Cape Conservation Service, South Africa (Permit number:
EC031-13, FAUNA 1020-2016).