Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira . We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira . We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira -positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.

Systematic surveillance tools to reduce rodent pests in disadvantaged urban areas can empower communities and improve public health

Rodents are notorious pests, known for transmitting major public health diseases and causing agricultural and economic losses. The lack of site-specific and national standardised rodent surveillance in several disadvantaged communities has rendered interventions targeted towards rodent control as often ineffective. Here, by using the example from a pilot case-study in the Bahamas, we present a unique experience wherein, through multidisciplinary and community engagement, we simultaneously developed a standardised national surveillance protocol, and performed two parallel but integrated activities: (1) eight days of theoretical and practical training of selected participants; and (2) a three-month post-training pilot rodent surveillance in the urban community of Over-the-Hill, Nassau, The Bahamas. To account for social and environmental conditions influencing rodent proliferation in the Bahamas, we engaged selected influential community members through a semi-structured interview and gathered additional site-specific information using a modified Centers for Diseases Control and Prevention (CDC) exterior and interior rodent evaluation form, along with other validated instruments such as tracking plates and snap trapping, to test and establish a standardised site-specific rodent surveillance protocol tailored for the Bahamas. Our engagement with community members highlighted poor disposal of animal and human food, irregular garbage collection, unapproved refuse storage, lack of accessible dumpsters, poor bulk waste management, ownership problems and structural deficiencies as major factors fuelling rodent proliferation in the study areas. Accordingly, results from our pilot survey using active rodent signs (that is, the presence of rodent runs, burrows, faecal material or gnawed material) as a proxy of rodent infestation in a generalized linear model confirmed that the variables earlier identified during the community engagement program as significantly correlated with rodent activities (and capturing) across the study areas. The successful implementation of the novel site-specific protocol by trained participants, along with the correlation of their findings with those recorded during the community engagement program, underscores its suitability and applicability in disadvantaged urban settings. This experience should serve as a reference for promoting a standardised protocol for monitoring rodent activities in many disadvantaged urban settings of the Global South, while also fostering a holistic understanding of rodent proliferation. Through this pilot case-study, we advocate for the feasibility of developing sustainable rodent control interventions that are acceptable to both local communities and public authorities, particularly through the involvement of a multidisciplinary team of professionals and community members.

Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar

Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat-matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation.

Population dynamics of synanthropic rodents after a chemical and infrastructural intervention in an urban low-income community

Synanthropic rodents are ubiquitous in low-income communities and pose risks for human health, as they are generally resistant to control programs. However, few or no studies have evaluated the long-term effect of chemical and infrastructural interventions on rodent population dynamics, especially in urban low-income communities, or evaluated the potential recovery of their population following interventions. We conducted a longitudinal study in a low-income community in the city of Salvador (BA, Brazil) to characterize the effect of interventions (chemical and infrastructural) on the dynamics of rodent population, and documented the post-intervention recovery of their population. We evaluated the degree of rodent infestation in 117 households/sampling points over three years (2014-2017), using tracking plates, a proxy for rodent abundance/activity. We reported a significant lower rodent activity/abundance after the chemical and infrastructural interventions (Z = -4.691 (p < 0.001)), with track plate positivity decreasing to 28% from 70% after and before interventions respectively. Therefore, the combination of chemical and infrastructural interventions significantly decreased the degree of rodent infestation in the study area. In addition, no rodent population rebound was recorded until almost a year post-intervention, and the post-intervention infestation level did not attain the pre-intervention level all through the study. Moreover, among pre-treatment conditions, access to sewer rather than the availability of food was the variable most closely associated with household rodent infestation. Our study indicates that Integrated Pest Management (IPM)-approaches are more effective in reducing rodent infestation than the use of a single method. Our findings will be useful in providing guidance for long-term rodent control programs, especially in urban low-income communities.

Socio-ecological drivers of multiple zoonotic hazards in highly urbanized cities

The ongoing COVID-19 pandemic is a stark reminder of the devastating consequences of pathogen spillover from wildlife to human hosts, particularly in densely populated urban centers. Prevention of future zoonotic disease is contingent on informed surveillance for known and novel threats across diverse human-wildlife interfaces. Cities are a key venue for potential spillover events because of the presence of zoonotic pathogens transmitted by hosts and vectors living in close proximity to dense human settlements. Effectively identifying and managing zoonotic hazards requires understanding the socio-ecological processes driving hazard distribution and pathogen prevalence in dynamic and heterogeneous urban landscapes. Despite increasing awareness of the human health impacts of zoonotic hazards, the integration of an eco-epidemiological perspective into public health management plans remains limited. Here we discuss how landscape patterns, abiotic conditions, and biotic interactions influence zoonotic hazards across highly urbanized cities (HUCs) in temperate climates to promote their efficient and effective management by a multi-sectoral coalition of public health stakeholders. We describe how to interpret both direct and indirect ecological processes, incorporate spatial scale, and evaluate networks of connectivity specific to different zoonotic hazards to promote biologically-informed and targeted decision-making. Using New York City, USA as a case study, we identify major zoonotic threats, apply knowledge of relevant ecological factors, and highlight opportunities and challenges for research and intervention. We aim to broaden the toolbox of urban public health stakeholders by providing ecologically-informed, practical guidance for the evaluation and management of zoonotic hazards.

Rats and the COVID-19 pandemic: considering the influence of social distancing on a global commensal pest

Rats contaminate foods and spread pathogens. Thus, changes in rat populations have consequences for society, especially in densely-populated cities. Following widespread social distancing and lockdown measures to curtail SARS-CoV-2, worldwide media outlets reported increased sightings of rats. To document possible changes in rat populations, we: (i) examined public service requests in the 6 years before, and during, ‘lockdown’ in New York City; (ii) used spatial analyses to identify calls in proximity to food service establishments (FSE); and (iii) surveyed pest-management companies. Over 6 years prior to the pandemic, we found a consistent moderate spatial association (r = 0.35) between FSE and rat-related calls. During the early stages of the pandemic, the association between rat reports and food services did not decrease as would be expected by restaurant closures, but instead modestly increased (r = 0.45). There was a 29.5% decrease in rat reports, overall. However, hotspot analysis showed that new reports were highly localized, yet absent in several industrial areas they were previously observed in, potentially masking a higher proportion of calls in neighborhoods near closed restaurants. Additionally, 37% of pest management companies surveyed reported that, unlike previous years, 50–100% of requests were from new clients and addresses. The finding that hotspots remained nearby dense clusters of restaurants does not support the common narrative that rats moved long distances. Rather, our results are consistent with rats finding nearby alternative food resources. Tracking these dynamics as the COVID-19 pandemic abates will be an important step to identifying how rats respond to society returning to normal activity patterns.

Socio-eco-evolutionary dynamics in cities

Cities are uniquely complex systems regulated by interactions and feedbacks between nature and human society. Characteristics of human society-including culture, economics, technology and politics-underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing research on urban ecology and evolutionary biology has coincided with growing interest in eco-evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco-evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological-and even social-significance. Still, little work fully integrates urban evolutionary biology and eco-evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban "socio-eco-evolutionary dynamics." Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.

Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient

As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.

Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens

Urban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada, and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models, we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens Leptospira interrogans, Bartonella tribocorum, and Clostridium difficile, and found that an individual's pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.

The ecological and evolutionary consequences of systemic racism in urban environments

Urban areas are dynamic ecological systems defined by interdependent biological, physical, and social components. The emergent structure and heterogeneity of urban landscapes drives biotic outcomes in these areas, and such spatial patterns are often attributed to the unequal stratification of wealth and power in human societies. Despite these patterns, few studies have effectively considered structural inequalities as drivers of ecological and evolutionary outcomes and have instead focused on indicator variables such as neighborhood wealth. In this analysis, we explicitly integrate ecology, evolution, and social processes to emphasize the relationships that bind social inequities—specifically racism—and biological change in urbanized landscapes. We draw on existing research to link racist practices, including residential segregation, to the heterogeneous patterns of flora and fauna observed by urban ecologists. In the future, urban ecology and evolution researchers must consider how systems of racial oppression affect the environmental factors that drive biological change in cities. Conceptual integration of the social and ecological sciences has amassed considerable scholarship in urban ecology over the past few decades, providing a solid foundation for incorporating environmental justice scholarship into urban ecological and evolutionary research. Such an undertaking is necessary to deconstruct urbanization’s biophysical patterns and processes, inform equitable and anti-racist initiatives promoting justice in urban conservation, and strengthen community resilience to global environmental change.

Gridlock and beltways: the genetic context of urban invasions

The rapid expansion of urban land across the globe presents new and numerous opportunities for invasive species to spread and flourish. Ecologists historically rejected urban ecosystems as important environments for ecology and evolution research but are beginning to recognize the importance of these systems in shaping the biology of invasion. Urbanization can aid the introduction, establishment, and spread of invaders, and these processes have substantial consequences on native species and ecosystems. Therefore, it is valuable to understand how urban areas influence populations at all stages in the invasion process. Population genetic tools are essential to explore the driving forces of invasive species dispersal, connectivity, and adaptation within cities. In this review, we synthesize current research about the influence of urban landscapes on invasion genetics dynamics. We conclude that urban areas are not only points of entry for many invasive species, they also facilitate population establishment, are pools for genetic diversity, and provide corridors for further spread both within and out of cities. We recommend the continued use of genetic studies to inform invasive species management and to understand the underlying ecological and evolutionary processes governing successful invasion.

A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape

The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds and the timescale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 single nucleotide polymorphism (SNP) data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an ~1,000-km² region of eastern Kentucky, USA. Nonspatial population-based assignment and clustering methods supported little to no population structure. However, using individual-based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from c. 1920 to 1970 before losing most traffic to a newly constructed alternative route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, although a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine-scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.

Partitioning drivers of spatial genetic variation for a continuously distributed population of boreal caribou: Implications for management unit delineation

Isolation by distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using nonspatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1,221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies, and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation, and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.

A model for leptospire dynamics and control in the Norway rat (Rattus norvegicus) the reservoir host in urban slum environments

Leptospirosis is a zoonosis that humans can contract via contact with animal reservoirs directly or with water contaminated with their urine. The primary reservoir of pathogenic leptospires within urban slum environments is the Norway rat (Rattus norvegicus). Motivated by the annual outbreaks of human leptospirosis in slum urban settings, the within population infection dynamics of the Norway rat were investigated in Pau da Lima, an community in Salvador, Brazil. A mechanistic model of the dynamics of leptospire infection was informed by extensive field and laboratory data was developed and explored analytically. To identify the intraspecific transmission route of most importance, a global sensitivity analysis of the basic reproduction number to its components was performed. In addition, different methods of rodent control were investigated by calculating target reproduction numbers. Our results suggest environmental transmission plays an important role in the maintenance of infection in the rodent population. To control numbers of wild Norway rats, combinations of controls are recommended but environmental control should also be investigated to reduce prevalence of infection in rats.

Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal

The rock pigeon, Columba livia, is a cosmopolitan human commensal, domesticated thousands of years ago. However, the human-mediated factors governing its distribution and dispersal are not well understood. In this study, we performed (a) hierarchical distance sampling on ~400 island-wide point transects, (b) a population genomic inquiry based on ~7,000 SNPs from almost 150 individuals, and (c) landscape genomic analyses on the basis of extensive ecological and socio-economic databases to characterize the distribution and dispersal patterns of rock pigeons across Singapore. Our distance sampling results indicated that the volume of intentional "mercy feeding" and availability of high-rise buildings are the most reliable predictors of high pigeon densities in Singapore. Genomic analyses demonstrated that rock pigeons in Singapore form a single population possibly derived from rapid expansion from a genetically homogenous group of founder individuals. In specific, rock pigeons in Singapore lack sex-biased dispersal and are clustered with a genetic patch size of ~3 km. Landscape genomic analyses of great precision pointed to the presence of dense trees as agents of resistance to dispersal, whereas a high road density reduces this resistance. By pinpointing a range of ecological and socio-economic variables determining the distribution and dispersal of pigeons, our study provides urban planners with the tools for optimal management of this human commensal, such as a curtailment of the practice of mercy feeding and modifications to the urban landscape to reduce pigeon density and to lower the likelihood of repopulation by dispersal.

Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; and New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15 000 genome-wide single nucleotide polymorphisms. Levels of genome-wide diversity were similar across cities, but varied across neighbourhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (less than 500 m) owing to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.

Evolution of life in urban environments

Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.

Spatial variation in the parasite communities and genomic structure of urban rats in New York City

Brown rats (Rattus norvegicus) are a globally distributed pest. Urban habitats can support large infestations of rats, posing a potential risk to public health from the parasites and pathogens they carry. Despite the potential influence of rodent-borne zoonotic diseases on human health, it is unclear how urban habitats affect the structure and transmission dynamics of ectoparasite and microbial communities (all referred to as "parasites" hereafter) among rat colonies. In this study, we use ecological data on parasites and genomic sequencing of their rat hosts to examine associations between spatial proximity, genetic relatedness and the parasite communities associated with 133 rats at five sites in sections of New York City with persistent rat infestations. We build on previous work showing that rats in New York carry a wide variety of parasites and report that these communities differ significantly among sites, even across small geographical distances. Ectoparasite community similarity was positively associated with geographical proximity; however, there was no general association between distance and microbial communities of rats. Sites with greater overall parasite diversity also had rats with greater infection levels and parasite species richness. Parasite community similarity among sites was not linked to genetic relatedness of rats, suggesting that these communities are not associated with genetic similarity among host individuals or host dispersal among sites. Discriminant analysis identified site-specific associations of several parasite species, suggesting that the presence of some species within parasite communities may allow researchers to determine the sites of origin for newly sampled rats. The results of our study help clarify the roles that colony structure and geographical proximity play in determining the ecology of R. norvegicus as a significant urban reservoir of zoonotic diseases. Our study also highlights the spatial variation present in urban rat parasite communities, indicating that rats across New York City are not reservoirs for a homogenous set of parasites and pathogens. As a result, the epidemiological risks may be similarly heterogeneous for people in urban habitats.

Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population

Brown rats are one of the most widespread urban species worldwide. Despite the nuisances they induce and their potential role as a zoonotic reservoir, knowledge on urban rat populations remains scarce. The main purpose of this study was to characterize an urban brown rat population from Chanteraines park (Hauts-de-Seine, France), with regards to haematology, population genetics, immunogenic diversity, resistance to anticoagulant rodenticides, and community of parasites. Haematological parameters were measured. Population genetics was investigated using 13 unlinked microsatellite loci. Immunogenic diversity was assessed for Mhc-Drb. Frequency of the Y139F mutation (conferring resistance to rodenticides) and two linked microsatellites were studied, concurrently with the presence of anticoagulant residues in the liver. Combination of microscopy and molecular methods were used to investigate the occurrence of 25 parasites. Statistical approaches were used to explore multiple parasite relationships and model parasite occurrence. Eighty-six rats were caught. The first haematological data for a wild urban R. norvegicus population was reported. Genetic results suggested high genetic diversity and connectivity between Chanteraines rats and surrounding population(s). We found a high prevalence (55.8%) of the mutation Y139F and presence of rodenticide residues in 47.7% of the sampled individuals. The parasite species richness was high (16). Seven potential zoonotic pathogens were identified, together with a surprisingly high diversity of Leptospira species (4). Chanteraines rat population is not closed, allowing gene flow and making eradication programs challenging, particularly because rodenticide resistance is highly prevalent. Parasitological results showed that co-infection is more a rule than an exception. Furthermore, the presence of several potential zoonotic pathogens, of which four Leptospira species, in this urban rat population raised its role in the maintenance and spread of these pathogens. Our findings should stimulate future discussions about the development of a long-term rat-control management program in Chanteraines urban park.

Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units - the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post-intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city-wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m-well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high-traffic roads as strong impediments to rat movement. Migration data suggest that most (71-90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual-based analyses at different spatial scales in urban landscapes.