Spatial segregation between invasive and native commensal rodents in an urban environment: a case study in Niamey, Niger

Reservoir displacement by an invasive rodent reduces Lassa virus zoonotic spillover risk

The black rat (Rattus rattus) is a globally invasive species that has been widely introduced across Africa. Within its invasive range in West Africa, R. rattus may compete with the native rodent Mastomys natalensis, the primary reservoir host of Lassa virus, a zoonotic pathogen that kills thousands annually. Here, we use rodent trapping data from Sierra Leone and Guinea to show that R. rattus presence reduces M. natalensis density within the human dwellings where Lassa virus exposure is most likely to occur. Further, we integrate infection data from M. natalensis to demonstrate that Lassa virus zoonotic spillover risk is lower at sites with R. rattus. While non-native species can have numerous negative effects on ecosystems, our results suggest that R. rattus invasion has the indirect benefit of decreasing zoonotic spillover of an endemic pathogen, with important implications for invasive species control across West Africa.

Sharing space between native and invasive small mammals: Study of commensal communities in Senegal

Urbanization processes are taking place at a very high rate, especially in Africa. At the same time, a number of small mammal species, be they native or invasive, take advantage of human-induced habitat modifications. They represent commensal communities of organisms that cause a number of inconveniences to humans, including potential reservoirs of zoonotic diseases. We studied via live trapping and habitat characterization such commensal small mammal communities in small villages to large cities of Senegal, to try to understand how the species share this particular space. Seven major species were recorded, with exotic invasive house mice (Mus musculus) and black rats (Rattus rattus) dominating in numbers. The shrew Crocidura olivieri appeared as the main and more widespread native species, while native rodent species (Mastomys natalensis, M. erythroleucus, Arvicanthis niloticus and Praomys daltoni) were less abundant and/or more localized. Habitat preferences, compared between species in terms of room types and characteristics, showed differences among house mice, black rats and M. natalensis especially. Niche (habitat component) breadth and overlap were measured. Among invasive species, the house mouse showed a larger niche breadth than the black rat, and overall, all species displayed high overlap values. Co-occurrence patterns were studied at the global and local scales. The latter show cases of aggregation (between the black rat and native species, for instance) and of segregation (as between the house mouse and the black rat in Tambacounda, or between the black rat and M. natalensis in Kédougou). While updating information on commensal small mammal distribution in Senegal, a country submitted to a dynamic process of invasion by the black rat and the house mouse, we bring original information on how species occupy and share the commensal space, and make predictions on the evolution of these communities in a period of ever-accelerating global changes.

Economic costs of invasive rodents worldwide: the tip of the iceberg

Background

Rodents are among the most notorious invasive alien species worldwide. These invaders have substantially impacted native ecosystems, food production and storage, local infrastructures, human health and well-being. However, the lack of standardized and understandable estimation of their impacts is a serious barrier to raising societal awareness, and hampers effective management interventions at relevant scales.

Methods

Here, we assessed the economic costs of invasive alien rodents globally in order to help overcome these obstacles. For this purpose, we combined and analysed economic cost data from the InvaCost database-the most up-to-date and comprehensive synthesis of reported invasion costs-and specific complementary searches within and beyond the published literature.

Results

Our conservative analysis showed that reported costs of rodent invasions reached a conservative total of US$ 3.6 billion between 1930 and 2022 (annually US$ 87.5 million between 1980 and 2022), and were significantly increasing through time. The highest cost reported was for muskrat Ondatra zibethicus (US$ 377.5 million), then unspecified Rattus spp. (US$ 327.8 million), followed by Rattus norvegicus specifically (US$ 156.6 million) and Castor canadensis (US$ 150.4 million). Of the total costs, 87% were damage-related, principally impacting agriculture and predominantly reported in Asia (60%), Europe (19%) and North America (9%). Our study evidenced obvious cost underreporting with only 99 documents gathered globally, clear taxonomic gaps, reliability issues for cost assessment, and skewed breakdowns of costs among regions, sectors and contexts. As a consequence, these reported costs represent only a very small fraction of the expected true cost of rodent invasions (e.g., using a less conservative analytic approach would have led to a global amount more than 80-times higher than estimated here).

Conclusions

These findings strongly suggest that available information represents a substantial underestimation of the global costs incurred. We offer recommendations for improving estimates of costs to fill these knowledge gaps including: systematic distinction between native and invasive rodents' impacts; monetizing indirect impacts on human health; and greater integrative and concerted research effort between scientists and stakeholders. Finally, we discuss why and how this approach will stimulate and provide support for proactive and sustainable management strategies in the context of alien rodent invasions, for which biosecurity measures should be amplified globally.

Fine-scale prevalence and genetic diversity of urban small mammal-borne pathogenic Leptospira in Africa: A spatiotemporal survey within Cotonou, Benin

Leptospirosis is a zoonotic disease that is caused by spirochete bacteria of the genus Leptospira. Around the world, one million people each year are infected, leading to 60,000 deaths. Infection occurs through contact with environmental pathogens excreted by mammals (notably rodents). Data on Leptospira and leptospirosis in Africa are rather scarce, especially in urban habitats though these appear to be favourable environments for the pathogen circulation and human contamination. Using qPCR, DNA sequencing as well as MST/VNTR approaches, we examined Leptospira occurrence and genetic diversity in 779 commensal small mammals that were sampled over 2 years in the city centre of Cotonou, Benin, from three neighbourhoods with contrasting socio-environmental conditions. Overall prevalence reached 9.1%. However, very marked variations in both space and time were observed, with local peaks of high prevalence but no clear seasonal pattern. In most sites that could be regularly sampled, Leptospira-positive rodents were found at least once, thus confirming the widespread circulation of the pathogen within small mammal communities of Cotonou. Interestingly, an unusual diversity of small mammal-borne Leptospira species and genotypes was retrieved, with up to four species and three different genovars within the same neighbourhood, and even instances of two species and two genovars identified simultaneously within the same household. To our knowledge, such a high genetic diversity has never been described at such a fine scale, a fortiori in Africa and, more generally, within an urban environment. Altogether, our results underline that much remains unknown about leptospirosis as well as the associated infectious risk in African cities where the disease may be massively over-looked.

Patterns of diversity, species richness and community structure in West African savannah small mammals (rodents and shrews)

Tropical savannah ecosystems are characterized by extensive grasslands with more or less sparse trees and thickets, and are threatened globally by anthropogenic forces. These grassland habitats house a rich and diversified fauna assemblage, with some of its conspicuous elements (for instance, small mammals) that have not been sufficiently investigated so far. In this paper, we meta-analyze the literature data available on the community structure and diversity patterns of shrews and rodents in West African savannahs. Overall, 10,197 small mammal individuals belonging to 111 species of Rodentia and 55 species of Soricomorpha were found in the various studies carried out in the countries covered by the present study. Studies using a combination of methods (e.g., live trapping, pitfalls, cover boards, visual encounter) detected more species in both Soricomorpha and Rodentia, and there was a positive survey (=trap ⁄ night) effort effect on the species richness in rodents. GLM models showed (i) that there was also no effect of trapping design (transect versus grid) on species richness per site, (ii) in both rodents and soricomorphs, the number of savannah species by country depended on the total species richness of that given country, but there was no effect of the relative surface covered by savannahs in that country. The number of sympatric species per site was 2.73± 1.7 (range = 1-7) in Soricomorpha and 6.33 ± 3.8 (range 1-15) in Rodentia. Dominance index was significantly different among countries, with Nigeria having lower values than all other countries and Ghana, Benin and Sierra Leone had significantly highest values. The conservation implications of the observed patterns are discussed.

The economic costs of biological invasions in Africa: a growing but neglected threat?

Biological invasions can dramatically impact natural ecosystems and human societies. However, although knowledge of the economic impacts of biological invasions provides crucial insights for efficient management and policy, reliable syntheses are still lacking. This is particularly true for low income countries where economic resources are insufficient to control the effects of invasions. In this study, we relied on the recently developed "InvaCost" database – the most comprehensive repository on the monetised impacts of invasive alien species worldwide – to produce the first synthesis of economic costs of biological invasions on the African continent. We found that the reported costs of invasions ranged between US$ 18.2 billion and US$ 78.9 billion between 1970 and 2020. This represents a massive, yet highly underestimated economic burden for African countries. More alarmingly, these costs are exponentially increasing over time, without any signs of abatement in the near future. The reported costs were mostly driven by damage caused by invaders rather than expenses incurred for management. This trend was highly skewed towards a few regions (i.e. Southern and Eastern Africa) and activity sectors (i.e. agriculture) and incurred by a small number of invasive taxa (i.e. mainly three insect pests: Chilo partellus, Tuta absoluta, Spodoptera frugiperda). We also highlight crucial, large gaps in current knowledge on the economic costs of invasions that still need to be bridged with more widespread research effort and management actions across the continent. Finally, our study provides support for developing and implementing preventive measures as well as integrated post-invasion management actions at both national and regional levels. Considering the complex societal and economic realities in African countries, the currently neglected problem of biological invasions should become a priority for sustainable development.

Mastomys natalensis (Smith, 1834) as a natural host for Schistosoma haematobium (Bilharz, 1852) Weinland, 1858 x Schistosoma bovis Sonsino, 1876 introgressive hybrids

Cercarial emission of schistosomes is a determinant in the transmission to the definitive host and constitutes a good marker to identify which definitive host is responsible for transmission, mainly in introgressive hybridization situations. Our goal was to test the hypothesis that micro-mammals play a role in Schistosoma haematobium, S. bovis, and/or S. haematobium x S. bovis transmission. Small mammal sampling was conducted in seven semi-lacustrine villages of southern Benin. Among the 62 animals trapped, 50 individuals were investigated for Schistosoma adults and eggs: 37 Rattus rattus, 3 Rattus norvegicus, 9 Mastomys natalensis, and 1 Crocidura olivieri. Schistosoma adults were found in four R. rattus and two M. natalensis, with a local prevalence reaching 80% and 50%, respectively. Two cercarial chronotypes were found from Bulinus globosus experimentally infected with miracidia extracted from naturally infected M. natalensis: a late diurnal and nocturnal chronotype, and an early diurnal, late diurnal, and nocturnal chronotype. The cytochrome C oxidase subunit I mtDNA gene of the collected schistosomes (adults, miracidia, and cercariae) belonged to the S. bovis clade. Eleven internal transcribed spacer rDNA profiles were found; four belonged to S. bovis and seven to S. haematobium x S. bovis. These molecular results together with the observed multi-peak chronotypes add M. natalensis as a new host implicated in S. haematobium x S. bovis transmission. We discuss the origin of the new chronotypes which have become more complex with the appearance of several peaks in a 24-h day. We also discuss how the new populations of offspring may optimize intra-host ecological niche, host spectrum, and transmission time period.

First investigation of pathogenic bacteria, protozoa and viruses in rodents and shrews in context of forest-savannah-urban areas interface in the city of Franceville (Gabon)

Rodents are reservoirs of numerous zoonotic diseases caused by bacteria, protozoans, or viruses. In Gabon, the circulation and maintenance of rodent-borne zoonotic infectious agents are poorly studied and are often limited to one type of pathogen. Among the three existing studies on this topic, two are focused on a zoonotic virus, and the third is focused on rodent Plasmodium. In this study, we searched for a wide range of bacteria, protozoa and viruses in different organs of rodents from the town of Franceville in Gabon. Samples from one hundred and ninety-eight (198) small mammals captured, including two invasive rodent species, five native rodent species and 19 shrews belonging to the Soricidae family, were screened. The investigated pathogens were bacteria from the Rickettsiaceae and Anaplasmataceae families, Mycoplasma spp., Bartonella spp., Borrelia spp., Orientia spp., Occidentia spp., Leptospira spp., Streptobacillus moniliformis, Coxiella burnetii, and Yersinia pestis; parasites from class Kinetoplastida spp. (Leishmania spp., Trypanosoma spp.), Piroplasmidae spp., and Toxoplasma gondii; and viruses from Paramyxoviridae, Hantaviridae, Flaviviridae and Mammarenavirus spp. We identified the following pathogenic bacteria: Anaplasma spp. (8.1%; 16/198), Bartonella spp. (6.6%; 13/198), Coxiella spp. (5.1%; 10/198) and Leptospira spp. (3.5%; 7/198); and protozoans: Piroplasma sp. (1%; 2/198), Toxoplasma gondii (0.5%; 1/198), and Trypanosoma sp. (7%; 14/198). None of the targeted viral genes were detected. These pathogens were found in Gabonese rodents, mainly Lophuromys sp., Lemniscomys striatus and Praomys sp. We also identified new genotypes: Candidatus Bartonella gabonensis and Uncultured Anaplasma spp. This study shows that rodents in Gabon harbor some human pathogenic bacteria and protozoans. It is necessary to determine whether the identified microorganisms are capable of undergoing zoonotic transmission from rodents to humans and if they may be responsible for human cases of febrile disease of unknown etiology in Gabon.

Need for preventive and control measures for Lassa fever through the One Health strategic approach

Lassa virus (LASV) has increasingly been recognised as a significant public-health pathogen transmitted by rodents. LASV infection leads to life-threatening Lassa fever, which has high potential for severe morbidity and mortality. There have been several scientific efforts to understand the genomics and ecological epidemiology of Lassa. However, very limited studies have focused on the short- and long-term impacts of environmental factors, human behaviours and rodent activities on LASV transmission dynamics and control. Recently, a very plausible and ideal way to address the Lassa epidemic has been considered through the One Health approach. The One Health system of intervention is capable of providing better and comprehensive information necessary to address the complex interplay between human, ecological, and environmental determinants of LASV transmission, persistence and re-emergence. Thus, the aim of this article was to review critically the impacts of various environmental factors on rodent infestations, LASV transmission and how human activities contribute to the persistence of Lassa with regard to exploring how they could be harnessed for better understanding of Lassa prevention and control through a concerted One Health approach.

Native and Invasive Small Mammals in Urban Habitats along the Commercial Axis Connecting Benin and Niger, West Africa

Based on compiled small mammal trapping data collected over 12 years from Benin and Niger (3701 individual records from 66 sampling sites), located in mainland Africa, we here describe the small mammal community assemblage in urban habitats along the commercial axis connecting the two countries, from the seaport of Cotonou to the Sahelian hinterland, with a particular focus on invasive species. In doing so, we document extant species distributions, which highlight the risks of continuing the range expansion of three synanthropic invasive rodent species, namely black rats (Rattus rattus), brown rats (R. norvegicus), and house mice (Mus musculus). Using various diversity estimates and community ecology approaches, we detect a latitudinal gradient of species richness that significantly decreased Northward. We show that shrews (Crocidura) represent a very important component of micro-mammal fauna in West African towns and villages, especially at lower latitudes. We also demonstrate that invasive and native synanthropic rodents do not distribute randomly in West Africa, which suggests that invasive species dynamics and history differ markedly, and that they involve gradual, as well as human-mediated, long distance dispersal. Patterns of segregation are also observed between native Mastomys natalensis and invasive rats R. rattus and R. norvegicus, suggesting potential native-to-invasive species turn over. Consequences of such processes, especially in terms of public health, are discussed.

Spatio-temporal survey of small mammal-borne Trypanosoma lewisi in Cotonou, Benin, and the potential risk of human infection

Human trypanosomoses are the sleeping sickness in Africa and Chagas disease in Latin America. However, atypical human infections by animal trypanosomes have been described, but poorly investigated. Among them, the supposed rat-specific T. lewisi was shown to be responsible for a few severe cases. In Africa, the scarcity of data and the null awareness about the atypical human trypanosomoses suggest that the number of cases may be higher that currently thought. Furthermore, T. lewisi is resistant to normal human serum and therefore a potential human pathogen. In order to document T. lewisi distribution and ecology, a qPCR- and 16DNA sequencing-based survey was conducted in 369 rodents from three urban districts of Cotonou city, Benin, during three different periods of the same year. Our study demonstrated very high prevalence (57.2%) even when considering only individuals identified as positive through DNA sequencing (39.2%). Black rats represented the most dominant as well as the most T. lewisi-parasitized species. No difference was retrieved neither between seasons nor districts, suggesting a large infestation of rodents by trypanosomes throughout the year and the city. Our results suggest that conditions are gathered for rat to human transmission of T. lewisi in these socio-environmentally degraded urban areas, thus pointing towards the rapidly urbanizing Abidjan-Lagos corridor as a region at particular risk.

Rodents of Senegal and their role as intermediate hosts of Hydatigera spp. (Cestoda: Taeniidae)

Hydatigera (Cestoda: Taeniidae) is a recently resurrected genus including species seldom investigated in sub-Saharan Africa. We surveyed wild small mammal populations in the areas of Richard Toll and Lake Guiers, Senegal, with the objective to evaluate their potential role as intermediate hosts of larval taeniid stages (i.e. metacestodes). Based on genetic sequences of a segment of the mitochondrial DNA gene cytochrome c oxidase subunit 1 (COI), we identified Hydatigera parva metacestodes in 19 out of 172 (11.0%) Hubert's multimammate mice (Mastomys huberti) and one out of six (16.7%) gerbils (Taterillus sp.) and Hydatigera taeniaeformis sensu stricto metacestodes in one out of 215 (0.5%) Nile rats (Arvicanthis niloticus). This study reports epidemiological and molecular information on H. parva and H. taeniaeformis in West African rodents, further supporting the phylogeographic hypothesis on the African origin of H. parva. Our findings may indicate significant trophic interactions contributing to the local transmission of Hydatigera spp. and other parasites with similar life-cycle mechanisms. We therefore propose that further field investigations of rodent population dynamics and rodent-borne infectious organisms are necessary to improve our understanding of host-parasite associations driving the transmission risks of rodent parasites in West Africa.

Landscape epidemiology in urban environments: The example of rodent-borne Trypanosoma in Niamey, Niger

Trypanosomes are protozoan parasites found worldwide, infecting humans and animals. In the past decade, the number of reports on atypical human cases due to Trypanosoma lewisi or T. lewisi-like has increased urging to investigate the multiple factors driving the disease dynamics, particularly in cities where rodents and humans co-exist at high densities. In the present survey, we used a species distribution model, Maxent, to assess the spatial pattern of Trypanosoma-positive rodents in the city of Niamey. The explanatory variables were landscape metrics describing urban landscape composition and physiognomy computed from 8 land-cover classes. We computed the metrics around each data location using a set of circular buffers of increasing radii (20m, 40m, 60m, 80m and 100m). For each spatial resolution, we determined the optimal combination of feature class and regularization multipliers by fitting Maxent with the full dataset. Since our dataset was small (114 occurrences) we expected an important uncertainty associated to data partitioning into calibration and evaluation datasets. We thus performed 350 independent model runs with a training dataset representing a random subset of 80% of the occurrences and the optimal Maxent parameters. Each model yielded a map of habitat suitability over Niamey, which was transformed into a binary map implementing a threshold maximizing the sensitivity and the specificity. The resulting binary maps were combined to display the proportion of models that indicated a good environmental suitability for Trypanosoma-positive rodents. Maxent performed better with landscape metrics derived from buffers of 80m. Habitat suitability for Trypanosoma-positive rodents exhibited large patches linked to urban features such as patch richness and the proportion of landscape covered by concrete or tarred areas. Such inferences could be helpful in assessing areas at risk, setting of monitoring programs, public and medical staff awareness or even vaccination campaigns.

Understanding the cryptic nature of Lassa fever in West Africa

Lassa fever (LF) is increasingly recognized by global health institutions as an important rodent-borne disease with severe impacts on some of West Africa's poorest communities. However, our knowledge of LF ecology, epidemiology and distribution is limited, which presents barriers to both short-term disease forecasting and prediction of long-term impacts of environmental change on Lassa virus (LASV) zoonotic transmission dynamics. Here, we synthesize current knowledge to show that extrapolations from past research have produced an incomplete picture of the incidence and distribution of LF, with negative consequences for policy planning, medical treatment and management interventions. Although the recent increase in LF case reports is likely due to improved surveillance, recent studies suggest that future socio-ecological changes in West Africa may drive increases in LF burden. Future research should focus on the geographical distribution and disease burden of LF, in order to improve its integration into public policy and disease control strategies.

Rodent-borne Trypanosoma from cities and villages of Niger and Nigeria: A special role for the invasive genus Rattus?

Although they are known to sometimes infect humans, atypical trypanosomes are very poorly documented, especially in Africa where one lethal case has yet been described. Here we conducted a survey of rodent-borne Trypanosoma in 19 towns and villages of Niger and Nigeria, with a special emphasis on Niamey, the capital city of Niger. The 1298 rodents that were captured yielded 189 qPCR-positive animals from 14 localities, thus corresponding to a 14.6% overall prevalence. Rats, especially black rats, displayed particularly elevated prevalence (27.4%), with some well sampled sites showing 40-50% and up to 68.8% of Trypanosoma-carrying individuals. Rattus were also characterized by significantly lower Ct values than in the other non-Rattus species. DNA sequences could be obtained for 43 rodent-borne Trypanosoma and corresponded to 41 T. lewisi (all from Rattus) and 2 T. microti (from Cricetomys gambianus). These results, together with data compiled from the available literature, suggest that Rattus may play a particular role for the maintaining and circulation of Trypanosoma, especially T. lewisi, in Africa. Taken into account its strong abilities to invade coastal and inland regions of the continent, we believe that this genus deserves a particular attention in regards to potentially under-looked but emerging atypical trypanosome-related diseases.

Serological Prevalence Against Japanese Encephalitis Virus-Serocomplex Flaviviruses in Commensal and Field Rodents in South China

BACKGROUND

Japanese encephalitis caused by Japanese encephalitis virus (JEV) is an endemic zoonotic disease of high public health importance in the Asian Pacific region. The aim of this study was to investigate the presence of JEV infection in commensal and field rodents in South China.

MATERIALS AND METHODS

RNA copies of JEV were detected in brain samples of rodents using real-time RT-PCR. Detection of serum against JEV-reactive antibodies was performed using indirect enzyme-linked immunosorbent assay and microneutralization test.

RESULTS

In total, 198 rodents were collected from Guangzhou City and Xiamen City between November 2013 and May 2014. JEV RNA was not detected in 188 brain samples. Forty-four in 96 serum samples (45.8%) were positive for JEV-reactive IgG antibodies. The prevalence of neutralizing antibodies to against JEV-reactive in these serum samples was 61.5% (24/39), with titers ranging from 1:10 to 1:56.

CONCLUSION

Rodents are not known to play a role in transmission of JEV in Asia, nor is there an evidence to support a role for rodents in transmission of other related flaviviruses in China. However, in the current study, we detected evidence of JEV-reactive antibodies in large numbers of Rattus norvegicus and Rattus losea Swinhoe. Further studies of rodents as potential hosts of JEV or other related flaviviruses are warranted.

From Human Geography to Biological Invasions: The Black Rat Distribution in the Changing Southeastern of Senegal

In the contemporary context of zoonosis emergence and spread, invasive species are a major issue since they represent potential pathogen hosts. Even though many progresses have been done to understand and predict spatial patterns of invasive species, the challenge to identify the underlying determinants of their distribution remains a central question in invasion biology. This is particularly exacerbated in the case of commensal species that strictly depend on humankind for dispersal and perennial establishment of new populations. The distribution of these species is predicted to be influenced by dispersal opportunities and conditions acting on establishment and proliferation, such as environmental characteristics, including spatio-temporal components of the human societies. We propose to contribute to the understanding of the recent spread of a major invasive rodent species, the black rat (Rattus rattus), in the changing southeastern of Senegal. We address the factors that promote the dispersal and distribution of this invasive rodent from the perspective of human geography. We first describe characteristics of human settlements in terms of social and spatial organization of human societies (i.e. economic activities, commercial and agricultural networks, roads connectivity). We then explore the relationship between these characteristics and the distribution of this invasive rodent. Finally we propose that historical and contemporary dynamics of human societies have contributed to the risk of invasion of the black rat. We argue that the diffusion processes of invasive species cannot be considered as a result of the spatial structure only (i.e. connectivity and distance), but as a part of the human territory that includes the social and spatial organization. Results suggest that the distribution of invasive rodents partly results from the contemporary and inherited human socio-spatial systems, beyond the existence of suitable ecological conditions that are classically investigated by biologists.

Cryptic diversity in Black rats Rattus rattus of the Galápagos Islands, Ecuador

Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15 islands in the archipelago. The genetic data suggest that there are at least three genetic lineages of R. rattus present on the Galápagos Islands. The spatial distributions of these lineages correspond to the main centers of human settlement in the archipelago. There was limited admixture among these three lineages, and these finding coupled with low rates of gene flow among island populations suggests that interisland movement of R. rattus is rare. The low migration among islands recorded for the species will have a positive impact on future eradication efforts.

Urban Market Gardening and Rodent-Borne Pathogenic Leptospira in Arid Zones: A Case Study in Niamey, Niger

Leptospirosis essentially affects human following contact with rodent urine-contaminated water. As such, it was mainly found associated with rice culture, recreational activities and flooding. This is also the reason why it has mainly been investigated in temperate as well as warm and humid regions, while arid zones have been only very occasionally monitored for this disease. In particular, data for West African countries are extremely scarce. Here, we took advantage of an extensive survey of urban rodents in Niamey, Niger, in order to look for rodent-borne pathogenic Leptospira species presence and distribution across the city. To do so, we used high throughput bacterial 16S-based metabarcoding, lipL32 gene-targeting RT-PCR, rrs gene sequencing and VNTR typing as well as GIS-based multivariate spatial analysis. Our results show that leptospires seem absent from the core city where usual Leptospira reservoir rodent species (namely R. rattus and M. natalensis) are yet abundant. On the contrary, L. kirschneri was detected in Arvicanthis niloticus and Cricetomys gambianus, two rodent species that are restricted to irrigated cultures within the city. Moreover, the VNTR profiles showed that rodent-borne leptospires in Niamey belong to previously undescribed serovars. Altogether, our study points towards the importance of market gardening in maintain and circulation of leptospirosis within Sahelian cities. In Africa, irrigated urban agriculture constitutes a pivotal source of food supply, especially in the context of the ongoing extensive urbanization of the continent. With this in mind, we speculate that leptospirosis may represent a zoonotic disease of concern also in arid regions that would deserve to be more rigorously surveyed, especially in urban agricultural settings.