Amphibians are one of the most vulnerable groups of vertebrates with 41% of all species currently threatened with extinction (Stuart et al., 2004; Wake & Vredenburg, 2008; The IUCN Red List of Threatened Species, 2021). An emerging infectious disease, chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has been a major driver of amphibian declines (Skerratt et al., 2007; Wake and Vredenburg, 2008; Fisher et al., 2009). Invasion and spread of the Bd pathogen are linked with declines and extinctions of hundreds of amphibian species worldwide and Bd has been documented on every continent where amphibians occur (Skerratt et al., 2007; Fisher et al., 2009; Olson et al., 2013; Scheele et al., 2019; Fisher and Garner, 2020). However, the pathogen’s specific historical distribution and geographic spread remain unclear, hampering efforts to predict which amphibian species are at greatest risk of disease outbreak (Berger et al., 2016).

While effects of Bd on vertebrates are greater than those of any other observed pathogen (Scheele et al., 2019; Fisher and Garner, 2020), there is still much that is not understood. For example, while Bd-caused epizootics resulting in amphibian species decline or extirpation have been documented in detail in various parts of the world (Lips et al., 2006; Fisher et al., 2009; Vredenburg et al., 2010; Walker et al., 2010), it is still not known why epizootics are found in some areas but not others (Berger et al., 2016). Delineating the geographic origin and spread of the pathogen, as well as its evolutionary history and population genetic structure, are necessary to describe the dynamics of this pathogen-host system. Recent studies reveal a complicated geographic and phylogenetic history for Bd, including multiple lineages that vary in pathogenicity and may have spread across and between continents over a period of hundreds or even thousands of years. The genetic structure of Bd populations suggests that competition and hybridization among and between Bd lineages has occurred (Farrer et al., 2011; Schloegel et al., 2012; Bataille et al., 2013; Rosenblum et al., 2013; O’Hanlon et al., 2018). The global panzootic lineage (Bd-GPL; Farrer et al., 2011) is regarded as the most virulent lineage, has the widest geographic distribution, and is associated with epizootic events (Schloegel et al., 2012; O’Hanlon et al., 2018). Although Bd is believed to have originated in Asia, it is unclear when, where, or how Bd-GPL diverged from older lineages (O’Hanlon et al., 2018). Other lineages thought to be less virulent are associated with areas that generally lack epizootics (Berger et al., 2016; O’Hanlon et al., 2018), including several identified in Asia (Bd-ASIA-1, believed to have originated in Korea, which includes Bd-CH, originally thought to have originated in Switzerland), South America (Bd-ASIA-2/Bd-BRAZIL) and southern Africa (Bd-CAPE, first described from Cape Province, South Africa) (Farrer et al., 2011; Bataille et al., 2013; Rodriguez et al., 2014; O’Hanlon et al., 2018).

Africa harbors nearly 16% of known living species of amphibians (AmphibiaWeb, 2021) and multiple lineages of Bd have been found to infect these hosts in the wild (including Bd-CAPE and Bd-GPL). There are few relevant Bd host studies in Africa and no described Bd-epizootics in the region (Berger et al., 2016; O’Hanlon et al., 2018; Doherty-Bone et al., 2020; Zimkus et al., 2020). However, this is likely due to a lower Bd sampling effort in Africa relative to other continents rather than a true absence of such events. Several studies have reported a small number of Bd-infected amphibians collected in the early 20^th century in Africa (Weldon et al., 2004; Soto-Azat et al., 2010). More recent African amphibian studies have revealed much higher Bd infection prevalence that may be associated with host declines (Goldberg et al., 2007; Kielgast et al., 2010; Bell et al., 2011; Gower et al., 2012; Tarrant et al., 2013; Seimon et al., 2015; Hirschfeld et al., 2016; Jongsma et al., 2016). Although these Bd-host infection data vary in spatial and temporal resolution, they suggest a pattern of Bd emergence that may represent a threat to African amphibian species, warranting a comprehensive analysis encompassing the broadest possible temporal and geographic scales.

We set out to address an important prediction regarding continent-wide infection dynamics of Bd: that the emergence of Bd in Africa is not limited to isolated outbreaks but instead represents a broad pattern of synchronized emergence across the entire continent. We address this prediction by comparing the historical frequency of Bd occurrence (spanning over a century) to the recent frequency of Bd occurrence (roughly the last 20 years). These comparisons of the frequency of Bd occurrence (revealing epizootic dynamics) are made both within African countries and within broader geographic regions. In addition, we include comparisons of changes in overall Bd infection intensity (zoospore counts) for specific countries in central Africa (Cameroon) and eastern Africa (Kenya) that are known to harbor widespread Bd in recent years (Hirschfeld et al., 2016; Kielgast et al., 2010). For our analyses, we have gathered 16,920 original and previously published museum- and field-collected records between 1852 and 2017 from a total of 36 countries. Importantly, our survey of Africa is unique in that it includes both positive and negative Bd samples as opposed to a more restricted reporting of only the number of Bd positives over time (Zimkus et al., 2020).

Additionally, if there is a continent-wide synchronous emergence of Bd, there could be regional differences in the magnitude of Bd prevalence. Such differences are likely associated with the distributions of the two described Bd lineages detected on the African continent (Bd-CAPE and Bd-GPL), depending on the presence of one or a combination of both in certain areas. Bd-CAPE has been detected in Cameroon and was found to be widely present in South Africa, while the Bd-GPL lineage has invaded almost every region of the continent (Rosenblum et al., 2013; O’Hanlon et al., 2018; Byrne et al., 2019). While it is speculated that the hypervirulent Bd-GPL is the more virulent of these two lineages based on ex situ experiments, less is known about the impacts of Bd-CAPE in nature, and there is evidence that Bd-CAPE does exhibit high virulence under certain conditions (Doddington et al., 2013; O’Hanlon et al., 2018; Fisher et al., 2021). Competition among invasive Bd strains, and the potential for hybridization has been documented on other continents (Jenkinson et al., 2016) and genotyping has revealed lineages in Africa that are intermediary to the more derived Bd-GPL complex and the more early diverging Bd-CAPE clade (Rosenblum et al., 2013; O’Hanlon et al., 2018; Byrne et al., 2019). These intermediaries are likely to be hybrids of the two described lineages and could be impacting disease dynamics (Farrer et al., 2011; Greenspan et al., 2018).

To understand how the dynamics of Bd lineage competition and/or hybridization may lead to future epizootics in some areas and not in others, we utilize our large database to document changes in Bd prevalence in regions that have experienced invasion by different lineages. To predict the risk to future populations of amphibians across the continent, we develop a spatially explicit model of Bd risk across regions of Africa, based on our current understanding of the habitat suitability of these Bd lineages and amphibian species richness. Combined, this work provides novel predictions for the regions in Africa that are at high risk of Bd invasion and is complementary to a recent spatially explicit suitability model for the African continent (Zimkus et al., 2020).

The 165 years of amphibian sample collections show a distinct signal of Bd emergence and geographic spread across the African continent that began in the first decade of the 21st century. In general, in the 20^th century (1852-1999), we found few, geographically scattered Bd-positives, showing no signal of epizootic spread ( Figures 1A, B ; earliest Bd infected host was 1933 in Cameroon; Soto-Azat et al., 2010). However, beginning in the 2000–2009 sample period ( Figures 1A, B ) we saw a large increase in prevalence and evidence of widespread infection across the continent, which are signals consistent with epizootics. Similarly, in Central America and western North America, studies found few and scattered Bd-infected specimens historically in areas that decades later experienced rapid Bd expansion, epizootics and host population collapse (Vredenburg et al., 2010; Cheng et al., 2011; Sette et al., 2015; Yap et al., 2016; Adams et al., 2017; De León et al., 2017; Yap et al., 2018; Vredenburg et al., 2019; Sette et al., 2020). In Africa, we saw only one major exception to this general pattern of emergence: in South Africa, infections were widespread even in our oldest samples ( Table 1 ). Thus, generally we found strong evidence indicating a recent surge (beginning in 2000) in the frequency of Bd occurrence in amphibian specimens collected across a large portion of the continent ( Figures 1A, B ; Tables 1 , S1 ). Disturbingly, we found this broad pattern of Bd emergence in areas of Africa where many amphibian species are either suspected or known to have collapsed (Channing et al., 2006; Gower et al., 2012; Gower et al., 2013; Hirschfeld et al., 2016; Weldon et al., 2020). Considering that Bd invasion was followed by Bd-epizootics resulting in extinctions of amphibian populations in western North America (Briggs et al., 2010; Vredenburg et al., 2010), Central America (Berger et al., 1998; Lips et al., 2006), South America (Catenazzi et al., 2011; Carvalho et al., 2017), Europe (Walker et al., 2010; Bates et al., 2018), and Australia (Laurance et al., 1996; Berger et al., 1998), amphibian declines in Africa that coincide with widespread expansions of Bd may also be linked.

Recent Bd emergence was most pronounced in eastern and central Africa where many species are threatened amid reports of declines and die-offs. In fact, most reports place the declines and extinctions occurring near or after the year 2000 (e.g. in Tanzania, Ethiopia, and Cameroon; Channing et al., 2006; Gower et al., 2012; Gower et al., 2013; Hirschfeld et al., 2016; Weldon et al., 2020), which coincides with our Bd emergence data. The historical and recent Bd occurrence data from Cameroon and Kenya are the most complete. In these countries, we saw a large and significant increase in the number and proportion of Bd infected hosts after 2000 ( Figures 1C, D ; Tables S2 , S3 ). Studies have shown that high levels of infection (i.e. Bd infection intensity or Bd load) are associated with severe chytridiomycosis, death, and population collapse (e.g., mortality threshold, Vredenburg’s “10,000 zoospore rule”; Vredenburg et al., 2010; Kinney et al., 2011); and, low Bd infection intensity is associated with host survival and coexistence with Bd suggestive of enzootic dynamics (Briggs et al., 2010; Knapp et al., 2016; Catenazzi et al., 2017). In both Cameroon and Kenya, we detected a recent increase in the average Bd-infection intensity of hosts. We note, however, that Bd infection intensities from historical Bd occurrences may be unreliable (see Methods). Regardless, the maximum values for infection intensity that we documented from live animals in the most recent decade for Cameroon and Kenya surpass the mortality threshold ( Figures 1C, D ; Tables S2 , S3 ). Thus, we conclude that our evidence of recent and rapid emergence of Bd and presence of highly infected animals signal that Bd epizootics may be occurring in these regions. By contrast, in South Africa, we found no evidence of a recent Bd emergence ( Table 1 ). There have been a few cases of observed mortality and population bottlenecks associated with Bd in some regions of South Africa, however no widespread declines or extinctions have been linked to Bd despite comprehensive population survey data (Hopkins & Channing, 2003; Tarrant et al., 2013; Griffiths et al., 2018; Doherty-Bone et al., 2020). This suggests that either Bd may be endemic to South Africa, that there may be Bd genetic lineages with lower virulence there, or that sampling remains incomplete.

Global studies on Bd genomics suggest that Bd has a complex history with many lineages that appear to have varied effects on amphibian populations (Rosenblum et al., 2013; Fisher and Garner, 2020). Generally, lineages identified as endemic to a single part of the world are thought to have a long evolutionary history of co-occurrence with hosts, and thus have evolved lower virulence than invasive (or novel) lineages that cause epizootics and host die-offs. In some places, endemic and invasive lineages are hypothesized to be co-occurring and hybridizing to form new lineage variants (O’Hanlon et al., 2018), and the effects of these hybrid lineages on hosts is unknown. Bd-epizootics can also be triggered by enigmatic abiotic or biotic factors that have not been deeply explored (Fisher and Garner, 2020; Fisher et al., 2021). Previous work has reported multiple genetic lineages of Bd in Africa (O’Hanlon et al., 2018; Byrne et al., 2019), suggesting the potential for complex hybridization and epizootic dynamics.

In Cameroon, we found evidence of Bd-CAPE, a lineage generally considered to be endemic to Africa and less virulent than Bd-GPL; however, our emergence data and results of histology (see Supplementary Material ) suggest this lineage may in fact be virulent in Africa. All genotyped samples from Cameroon clustered genetically with Bd-CAPE ( Figure 2B ), which supports previous work (O’Hanlon et al., 2018). Histological examination of animals from Cameroon show evidence of chytridiomycosis (see Supplementary Material ; Table S5 ; Figure S2 ), and we found Bd prevalence in the area has increased and spread geographically. The reported amphibian declines from Cameroon (Hirschfeld et al., 2016) coincide with the recent increase in frequency of Bd occurrence that we report here. We concur with previous work that states that pathogen lineage alone cannot fully predict disease outcomes since lineages that appear less pathogenic in native hosts may cause negative impacts on new or naïve host populations, especially when abiotic factors promote infection and disease (O’Hanlon et al., 2018; Fisher et al., 2021). We suggest this may be the case with Bd-CAPE in parts of Africa. It is possible that Bd-CAPE was present in Cameroon historically and has only recently increased in frequency due to shifts in some environmental, human, or other unknown factor, but it is also possible that the recent increase in prevalence represents a new invasion and spread of Bd-CAPE in Cameroon, perhaps from elsewhere on the continent. Bd-CAPE has been widely detected in South Africa (O’Hanlon et al., 2018; Byrne et al., 2019) and may be endemic there. In South Africa, we found a relatively constant proportional occurrence of Bd in hosts through a long time-period, and while there have been cases of Bd-associated mortality there, these could be associated with different Bd lineages (Bd-GPL is also present) or result from cofactors that are not yet known. Previous work has proposed that Bd-CAPE spread from South Africa to Europe, where it has thus far been associated with host declines (Doddington et al., 2013; O’Hanlon et al., 2018). Thus, we propose that Bd-CAPE may have recently spread within continental Africa and may also be associated with Bd-epizootics in some locations where conditions are suitable. Studies have reported recent evidence of mass amphibian die-offs in Cameroon (Blackburn et al., 2010; Hirschfeld et al., 2016) and Lesotho (Minter et al., 2004), areas where more detailed studies are needed to discern whether Bd-CAPE is associated with Bd-epizootics.

Our genomic data also identified Bd-GPL (Global Panzootic Lineage) in samples from Burundi. The Bd-GPL lineage is considered the most virulent Bd lineage (Farrer et al., 2011; Rosenblum et al., 2013; O’Hanlon et al., 2018; Byrne et al., 2019). Consistent with this, histological examination of specimens from Burundi showed signs of chytridiomycosis (see Supplementary Material ; Table S5 ). In fact, our samples from Burundi had the highest proportion of Bd infected hosts in our recent time frame (73.7%; 66.3–80.2% CI), and this could suggest Bd-epizootics are occurring there. Furthermore, we found no historical Bd positive data in Burundi ( Table 1 ) or in adjacent Tanzania (samples collected 1926–2003). In 2003, the Tanzanian Kihansi spray toad (Nectophrynoides asperginis) went extinct in the wild purportedly due to a Bd epizootic (Weldon et al., 2020). While there was no statistical support that frequency of Bd occurrence increased in the recent timeframe in Burundi and Tanzania (due to low availability of historical samples), we did find that frequency of occurrence was significantly higher statistically after 2000 in eastern Africa overall ( Table 1 ). Therefore, the recent presence of Bd-GPL detected after a dramatic increase in Bd occurrence in eastern Africa along with histological evidence of chytridiomycosis, may indicate that Bd-GPL driven epizootics are occurring there.

Hybridization between distinct Bd lineages has been proposed as a way that virulent lineages have emerged, and these hybrid lineages may be more virulent than either parent lineage (Farrer et al., 2011; Greenspan et al., 2018). Three of our genotyped samples from Burundi did not clearly cluster with previously characterized Bd lineages on the phylogenetic tree, but rather were positioned between Bd-GPL and Bd-CAPE ( Figure 2B ). We see three possibilities for the identity of Bd lineages from these samples: (i) Bd-GPL and Bd-CAPE are able to hybridize, and while our ambiguous samples did not cluster with known hybrids, they could be novel hybrids of these two lineages ( Figure 2B ; O’Hanlon et al., 2018); (ii) these samples could each contain multiple lineages of Bd, as evidenced by a higher average number of alleles found in one of these samples than any other ( Figure S1 ), and this supports the possibility that more than one lineage was present in that sample; or (iii) Bd detected in these samples could represent novel genetic variation that has not previously been characterized. Further work on ambiguous lineages in Burundi could resolve this issue and help in our general understanding of this complex pathogen. Further studies may identify lethal and sub-lethal infections (potentially from different Bd lineages) that could help us understand factors that could affect pathogen success (and how it may vary across lineages) such as differences in pathogen dispersal ability, reproductive ability, and vulnerability to predators. Additionally, we emphasize that future studies should prioritize genotyping Bd throughout Africa. The genotyping work presented here is limited, and further Bd genotyping is needed to better characterize the distribution of lineages across the continent.

Habitat suitability models combined with potential host availability provide an opportunity to understand the potential distribution of Bd risk over large geographic areas (Murray et al., 2011; Liu et al., 2013; Yap et al., 2018). The results of our HSM generally align with previous potential distribution models (Penner et al., 2013; Zimkus et al., 2020); however, two key distinctions in our model are that (1) we incorporated potential host availability to determine risk of disease spread (Yap et al., 2015; Yap et al., 2016), and (2) we included the global human footprint (Venter et al., 2016). Although host abundance data at the community and continental scale would be ideal to identify host availability, such data are not available. Therefore, as a proxy, we used species richness, which has been shown to be an important factor in Bd spread (Rödder et al., 2009; Liu et al., 2013; Boria et al., 2014; Yap et al., 2016; Hydeman et al., 2017; Yap et al., 2018). We included the global human footprint (Venter et al., 2016) in our model because the presence of humans or human activities can play a role in disease spread (Liu et al., 2013; James et al., 2015). We also took additional steps to reduce sampling bias and minimize the chances of overfitting due to multicollinearity of the abiotic variables. Thus, our model is complementary to previous potential distribution models (Penner et al., 2013; Zimkus et al., 2020). Our model identifies geographic areas with moderate to high risk of Bd spread as well as further highlighting African regions with high Bd suitability and supporting the assertion that countries in these regions are potential hotspots for the negative impacts of Bd ( Figure 3 ).

In central Africa, the HSM predicted high Bd risk in Angola, Cameroon, Democratic Republic of Congo, Equatorial Guinea, Gabon, and Republic of Congo. The observed Bd dynamics in Cameroon and Democratic Republic of Congo, coupled with population declines in Cameroon (Hirschfeld et al., 2016) suggest a recent emergence, yet more information and monitoring is also needed in Angola, Equatorial Guinea, Gabon, and Republic of Congo to determine their Bd status ( Table 1 ). We found a high proportion of Bd positives from Bioko Island (Equatorial Guinea) from 1998, and Bd-GPL has also been detected there (O’Hanlon et al., 2018; Byrne et al., 2019; Zimkus et al., 2020), but the lack of population survey data across a longer timescale prevents a proper understanding of Bd-host dynamics there.

In eastern Africa, the HSM model predicted high Bd risk in Kenya, Malawi, Mozambique, Tanzania, Zambia, and Zimbabwe. Mozambique and Zimbabwe border South Africa, where Bd-CAPE may be endemic and there is evidence suggesting spread to Lesotho could be associated with amphibian declines (Minter et al., 2004). Tanzania experienced a documented Bd-driven species extinction in the wild in 2003 (Weldon et al., 2020). Additionally, Tanzania borders Kenya, where we found evidence of Bd emergence and high Bd risk, and Burundi, where we report high Bd prevalence and ambiguous Bd lineages (Seimon et al., 2015). Because eastern Africa is identified as having widespread high Bd risk and multiple locations have high recent Bd prevalence, Bd-host dynamics in these countries should be closely monitored and studied.

In western Africa, our HSM predicted high Bd risk in Ghana, Côte d’Ivoire, Liberia, Guinea, and Sierra Leone. However, there are no records of Bd positives there, and it has been hypothesized that the Dahomey Gap (a non-forested area between western Nigeria and eastern Ghana) may act as a natural barrier creating a safe haven from chytridiomycosis for amphibians (Penner et al., 2013). However, it is worrisome that in nearby Nigeria (a country where we identified moderate Bd risk) the frequency of Bd occurrence is very high (44.5%; 40.1–48.2% CI), and our model predicted highly suitable habitat just west of the Dahomey Gap, similar to previous studies (Penner et al., 2013; Zimkus et al., 2020). Also, other studies have shown that once Bd invades an area, it spreads over large distances and into remote areas rapidly (Lips et al., 2006; Berger et al., 2016; Yap et al., 2016; Vredenburg et al., 2019; Fisher and Garner, 2020). We suggest that future research should focus on Bd-host relationships in western Africa, including monitoring disease presence and spread to determine whether species are threatened by future Bd invasion and surveillance of amphibians in Nigeria to determine whether population declines have occurred.

In northern Africa, our HSM predicted moderate risk in Morocco and in northern Algeria, Tunisia, and Egypt. However, this risk may be underestimated as our analysis did not include recent studies showing an expansion of Bd positives in Morocco (El Cadi et al., 2019; Thumsová et al., 2022). Despite these newer records for Morocco, data for northern Africa are limited; in fact, we are not aware of any published records for other countries in the region. Thus, northern Africa represents another understudied region where monitoring of amphibian populations and Bd are crucial.

New studies of Bd-host dynamics and interactions between Bd lineages in African amphibians could greatly advance our knowledge of chytridiomycosis. By bringing together new and published data spanning 165 years, our study demonstrates recent increases in the frequency of Bd occurrence in much of Africa; yet, we also find areas where frequency of Bd occurrence has not changed over time. In some areas, increases in frequency of Bd occurrence are coincident with amphibian declines (e.g., Cameroon Tanzania, and Ethiopia;Hirschfeld et al., 2016; Channing et al., 2006; Weldon et al., 2020; Gower et al., 2012; Gower et al., 2013), whereas in regions where Bd has not changed in frequency over long periods of time, evidence of widespread declines has not been detected (e.g., South Africa; Hopkins and Channing, 2003; Tarrant et al., 2013). Combined, these results indicate that Africa may harbor regions of Bd endemism (where host species may not be susceptible to epizootics) as well as regions where Bd is invading (posing large risks to host species). We find that multiple genetic lineages of Bd occur in Africa and suggest that (1) lineages generally considered to be low in virulence may actually be responsible for epizootic dynamics in some areas (e.g. Bd-CAPE), and that (2) co-occurring lineages may be hybridizing. Our results provide an opportunity to further investigate virulence of Bd lineages in nature and to determine how Bd hybridization may affect virulence, pathogenicity, and health outcomes in hosts. Finally, our initial data and model predictions help expand our study to enable risk prediction in areas where no Bd data are presently available. Our study highlights the importance of determining the temporal context of host-pathogen dynamics and emphasizes the need to bridge historical and contemporary datasets to better describe host-pathogen dynamics over larger temporal scales and predict future scenarios.

The datasets presented in this study are deposited in the following repositories: Zenodo, doi: https://zenodo.org/record/5514129#.Y_Th5XbP02w; Amphibian Disease Project hosted on the Genomic Observatories MetaDatabase, doi: https://n2t.net/ark:/21547/Dvp2; National Center for Biotechnology Information Sequence Read Archive, bioproject PRJNA555719.

The animal study was reviewed and approved by San Francisco State University Institutional Animal Care and Use Committee (#A20-05-SFSU).

VV and DB conceived and designed the study. DB, EG, MTK, and DP collected field samples. DB and SG collected museum samples. SG and AB performed laboratory work. DM performed histology. SG, TY, HS, AC-A, SC, KL, AM, EP, MSK, and HR compiled and organized data from the literature. SG, TY, AB, ER, VV, and HS contributed to the analysis of the data. SG, VV, TY, AB, HS, DM, and AZ wrote the manuscript. All authors contributed to the article and approved the submitted version.