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).