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

Physiological strategies in wild rodents: immune defenses of commensal rats

The importance of issues associated with urban/commensal rats and mice (property damage, management costs, and health risks) press upon research on these animals. While the demography of commensal rodents is mostly studied, the need for understanding factors influencing their natural morbidity/mortality is also stressed. In this respect, more attention is expected to be paid to immunity, the physiological mechanism of defense against host survival threats (pathogens, parasites, diseases). Commensal rats and mice carry numerous pathogens that evoke diverse immune responses. The state of immunity in commensal house mice is studied in great detail, owing to the use of laboratory strains in biomedical research. Because commensal rats are, compared to mice, carriers of more zoonotic agents, rats' immunity is studied mainly in that context. Some of these zoonotic agents cause chronic, asymptomatic infections, which justified studies of immunological mechanisms of pathogen tolerance versus clearance regulation in rats. Occurrence of some infections in specific tissues/organs pressed upon analysis of local/regional immune responses and/or immunopathology. A survey of immunological activity/responses in commensal rats is given in this review, with mention of existing data in commensal mice. It should throw some light on the factors relevant to their morbidity and lifespan, supplementing the knowledge of commensal rodent ecology.

Prevalence, genetic diversity and eco-epidemiology of pathogenic Leptospira species in small mammal communities in urban parks Lyon city, France

Rodents are recognized as the main reservoirs of Leptospira spp. Rats, in particular, serve as hosts for the widely predominant Leptospira interrogans serovar Icterohaemorrhagiae, found worldwide. Several studies have shown the importance of other reservoirs, such as mice or hedgehogs, which harbor other leptospires' serovars. Nevertheless, our knowledge of circulating Leptospira spp. in reservoirs other than rats remains limited. In this context, we proposed an eco-health approach to assess the health hazard associated with leptospires in urban green spaces, where contacts between human/small mammals and domestic animals are likely. We studied the prevalence, the diversity of circulating strains, and epidemiology of pathogenic Leptospira species in small terrestrial mammal communities (rodents and shrews), between 2020-2022, in two parks in Lyon metropolis, France. Our study showed a significant carriage of Leptospira spp. in small terrestrial mammals in these parks and unveiled a global prevalence rate of 11.4%. Significant variations of prevalence were observed among the small mammal species (from 0 to 26.1%), with Rattus norvegicus exhibiting the highest infection levels (26.1%). We also observed strong spatio-temporal variations in Leptospira spp. circulation in its reservoirs. Prevalence seems to be higher in the peri-urban park and in autumn in 2021 and 2022. This is potentially due to differences in landscape, abiotic conditions and small mammal communities' composition. Our study suggests an important public health relevance of rats and in a lesser extent of other rodents (Apodemus spp., Clethrionomys glareolus and Mus musculus) as reservoirs of L. interrogans, with rodent species carrying specific serogroups/serovars. We also emphasize the potential hazard associated between the shrew Crocidura russula and L. kirschneri. Altogether, these results improve our knowledge about the prevalence of leptospirosis in an urban environment, which is an essential prerequisite for the implementation of prevention of associated risks.

Increased rat-borne zoonotic disease hazard in greener urban areas

Urban greening has benefits for both human and environmental health. However, urban greening might also have negative effects as the abundance of wild rats, which can host and spread a great diversity of zoonotic pathogens, increases with urban greenness. Studies on the effect of urban greening on rat-borne zoonotic pathogens are currently unavailable. Therefore, we investigated how urban greenness is associated with rat-borne zoonotic pathogen prevalence and diversity, and translated this to human disease hazard. We screened 412 wild rats (Rattus norvegicus and Rattus rattus) from three cities in the Netherlands for 18 different zoonotic pathogens: Bartonella spp., Leptospira spp., Borrelia spp., Rickettsia spp., Anaplasma phagocytophilum, Neoehrlichia mikurensis, Spiroplasma spp., Streptobacillus moniliformis, Coxiella burnetii, Salmonella spp., methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)/AmpC-producing Escherichia coli, rat hepatitis E virus (ratHEV), Seoul orthohantavirus, Cowpox virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Toxoplasma gondii and Babesia spp. We modelled the relationships between pathogen prevalence and diversity and urban greenness. We detected 13 different zoonotic pathogens. Rats from greener urban areas had a significantly higher prevalence of Bartonella spp. and Borrelia spp., and a significantly lower prevalence of ESBL/AmpC-producing E. coli and ratHEV. Rat age was positively correlated with pathogen diversity while greenness was not related to pathogen diversity. Additionally, Bartonella spp. occurrence was positively correlated with that of Leptospira spp., Borrelia spp. and Rickettsia spp., and Borrelia spp. occurrence was also positively correlated with that of Rickettsia spp. Our results show an increased rat-borne zoonotic disease hazard in greener urban areas, which for most pathogens was driven by the increase in rat abundance rather than pathogen prevalence. This highlights the importance of keeping rat densities low and investigating the effects of urban greening on the exposure to zoonotic pathogens in order to make informed decisions and to take appropriate countermeasures preventing zoonotic diseases.

The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages

Nematodes are important parasites of people and animals, and in natural ecosystems they are a major ecological force. Strongyloides ratti is a common parasitic nematode of wild rats and we have investigated its population genetics using single-worm, whole-genome sequencing. We find that S. ratti populations in the UK consist of mixtures of mainly asexual lineages that are widely dispersed across a host population. These parasite lineages are likely very old and may have originated in Asia from where rats originated. Genes that underly the parasitic phase of the parasite's life cycle are hyperdiverse compared with the rest of the genome, and this may allow the parasites to maximise their fitness in a diverse host population. These patterns of parasitic nematode population genetics have not been found before and may also apply to Strongyloides spp. that infect people, which will affect how we should approach their control.

Human Population Density Influences Genetic Diversity of Two Rattus Species Worldwide: A Macrogenetic Approach

On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.

Urban evolutionary ecology brings exaptation back into focus

The contribution of pre-existing phenotypic variation to evolution in novel environments has long been appreciated. Nevertheless, evolutionary ecologists have struggled with communicating these aspects of the adaptive process. In 1982, Gould and Vrba proposed terminology to distinguish character states shaped via natural selection for the roles they currently serve ('adaptations') from those shaped under preceding selective regimes ('exaptations'), with the intention of replacing the inaccurate 'preadaptation'. Forty years later, we revisit Gould and Vrba's ideas which, while often controversial, continue to be widely debated and highly cited. We use the recent emergence of urban evolutionary ecology as a timely opportunity to reintroduce the ideas of Gould and Vrba as an integrated framework to understand contemporary evolution in novel environments.

Large-scale identification of rodenticide resistance in Rattus norvegicus and Mus musculus in the Netherlands based on Vkorc1 codon 139 mutations

BACKGROUND

Resistance to rodenticides has been reported globally and poses a considerable problem for efficacy in pest control. The most-documented resistance to rodenticides in commensal rodents is associated with mutations in the Vkorc1 gene, in particular in codon 139. Resistance to anticoagulant rodenticides has been reported in the Netherlands since 1989. A study from 2013 showed that 25% of 169 Norway rats (Rattus norvegicus) had a mutation at codon 139 of the Vkorc1 gene. To gain insight in the current status of rodenticide resistance amongst R. norvegicus and house mice Mus musculus in the Netherlands, we tested these rodents for mutations in codon 139 of the Vkorc1 gene. In addition, we collected data from pest controllers on their use of rodenticides and experience with rodenticide resistance.

RESULTS

A total of 1801 rodent samples were collected throughout the country consisting of 1404 R. norvegicus and 397 M. musculus. In total, 15% of R. norvegicus [95% confidence interval (CI): 13-17%] and 38% of M. musculus (95% CI: 33-43%) carried a genetic mutation at codon 139 of the Vkorc1 gene.

CONCLUSION

This study demonstrates genetic mutations at codon 139 of the Vkorc1 gene in M. musculus in the Netherlands. Resistance to anticoagulant rodenticides is present in R. norvegicus and M. musculus in multiple regions in the Netherlands. The results of this comprehensive study provide a baseline and facilitate trend analyses of Vkorc1 codon 139 mutations and evaluation of integrated pest management (IPM) strategies as these are enrolled in the Netherlands. © 2022 The Dutch Pest and Wildlife. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Impact of fertility versus mortality control on the demographics of Mastomys natalensis in maize fields

The multimammate mouse, Mastomys natalensis, is the most common rodent pest species in sub-Saharan Africa. Currently, rodenticides are the preferred method used to reduce the population of rodent pests, but this method poses direct and indirect risks to humans and other non-target species. Fertility control is a promising alternative that has been argued to be a more sustainable and humane method for controlling rodent pests. In this study, we compared the effectiveness of fertility control bait EP-1 (quinestrol (E) and levonorgestrel (P), 10 ppm) and an anticoagulant rodenticide bait (bromadiolone, 50 ppm) on the population dynamics of M. natalensis in maize fields in Zambia during 2 cropping seasons. M. natalensis was the most abundant species in maize fields (77% of total captures). Fertility control reduced the number of juveniles and suppressed population growth of M. natalensis at the end of the 2019-2020 cropping season. The population density initially decreased after rodenticide treatment, but the population rapidly recovered through immigration. None of the treatments influenced maize damage by rodents at germination (F_2,67 = 1.626, P = 0.204). Applying the treatments during the maize seeding time was effective at suppressing population growth at the end of the cropping season than application the month before maize seeding. This research indicates that a single-dose delivery of EP-1 and rodenticide have comparable effects on the population dynamics of M. natalensis. These findings are important in developing fertility control protocols for rodent pest populations to reduce maize crop damage and improve yields.

Biodiversity in Urban Green Space: A Bibliometric Review on the Current Research Field and Its Prospects

Understanding the development process of urban green space and biodiversity conservation strategies in urban green space is vital for sustainable urban development. However, a systematic review of the urban green space biodiversity research is still lacking. We have retrieved 3806 articles in WOS core journals and carried out the bibliometrics analysis through the three related search terms: urban, green space, and biodiversity. We found that: (1) the year 2009 was a changing point, and the number of articles have increased exponentially since 2009. The United States, China, Europe, and Australia are closely linked, and four research centers have formed; (2) all studies can be classified into three research themes: "Pattern of Urban Green Biodiversity", "Ecological Function of Urban Green Biodiversity", and "Sustainability of Urban Green Biodiversity"; (3) based on the evolution of keywords, this field is divided into the budding stage (1998-2012) and the development stage (2012-2021). The keywords in the budding stage focus on the diversity of different species, and the keywords in the development stage focus on the ecosystem services, biodiversity protection, and residents' satisfaction; (4) the future research focus may be in three aspects: studies on green space in the less urbanized area and urban-rural ecotone, the regulation mechanism and cultural services of urban green space, and the rational layout and management of urban green space. This study hopes to provide a reference for future research on urban green space biodiversity and promote the sustainable development of urban green space.

Monitoring of Leptospira species diversity in freshwater bathing area and in rats in Paris, France

Leptospirosis is a neglected zoonotic disease with a worldwide distribution caused by bacterial pathogenic Leptospira. Rodents are considered as the main reservoir of Leptospira and transmission usually occurs through exposure to urine-contaminated environment. However, interactions between environment, rodent reservoir and human leptospirosis remain poorly studied. Here, we evaluated the concentration of Leptospira in surface water and captured rats in the city of Paris (France) from 2018 to 2020 using an integrity qPCR (Quantitative Polymerase Chain Reaction). All environmental samples (n = 1031) were positive for saprophytic Leptospira but pathogenic Leptospira P1 group were only found in 40% (n = 363; 2018) to 0% (n = 264; 2020) of samples. In the same time, analysis of 200 brown rat corpses trapped in the city, showed about 15% of positivity for Leptospira but the different method used for rats conservation (based on presence or absence of conservative agent) showed important variations in the Leptospira prevalence. Metagenomic analysis, based on rrs gene sequencing, was also carried out to evaluate the distribution of Leptospira in samples. Results could indicate that some species of Leptospira are found in surface waters as well as rats, but further study is needed to accurately describe the nature of the link between these two reservoirs. Quantification of Leptospira and pathogenic species description circulating inside animal reservoir living in the vicinity of freshwater in urban areas, will be helpful to understand the eco-epidemiology of leptospirosis and to establish prevention and intervention strategies, especially in the context of organization of recreative activity events in these urban areas.

Demographic drivers of Norway rat populations from urban slums in Brazil

The Norway rat is a globally distributed pest, known for its resilience to eradication and control programs. Efficient population control, especially in urban settings, is dependent on knowledge of rat demography and population ecology. We analyzed the relationship between four demographic outcomes, estimated by live-trapping data, and fine-scale environmental features measured at the capture site. Wounds, a proxy for agonistic interactions, were associated with mature individuals. Areas with environmental features favorable to rats, such as open sewers and unpaved earth, were associated with more mature individuals with a better body condition index. The control measures (environmental stressors) are likely to be disrupting the social structure of rat colonies, increasing the frequency and distribution of agonistic interactions, which were common in both sexes and maturity states. The relationship between the favorable environmental conditions and the demographic markers analyzed indicate possible targets for infestation control through environmental manipulation, and could be incorporated into current pest management programs to achieve long-term success. Our study indicate that urban interventions focused on removal of potential resources for rats could be potential long-term solutions by reducing the carrying capacity of the environment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11252-020-01075-2.

Detection and distribution of zoonotic pathogens in wild Norway rats (Rattus norvegicus) from Tehran, Iran

This is the first study on the prevalence of vector-borne zoonotic pathogens found in Rattus norvegicus (R. norvegicus) in urban areas of Tehran, Iran. Serological tests were used to detect IgG antibodies against Coxiella burnetii (C. burnetii) and Rickettsia spp. using a commercial qualitative rat ELISA kit. The frequency of Streptobacillus moniliformis (S. moniliformis) and Bartonella spp. was determined using a conventional PCR method. Molecular detection and characterization of Leptospira spp. were conducted using TaqMan real-time PCR based on lipL32 gene and SecY typing methods. A total of 100 R. norvegicus rats were collected from five regions in Tehran, Iran, and investigated to determine their zoonotic pathogens. S. moniliformis and Bartonella spp. were detected in 23 of 100 (23%) and 17 of 100 (17%) R. norvegicus populations, respectively. The highest prevalence of S. moniliformis and Bartonella spp. with similar frequency rates (n = 6/20; 30%) was seen among the R. norvegicus rats captured from the northern and southern parts of Tehran, respectively. Seroreactivity against C. burnetii and Rickettsia spp. was detected in 4% and 1% of R. norvegicus, respectively. C. burnetii. was identified only in one rat captured from the eastern part of Tehran. Results showed that Leptospira spp. was detected only in two rats, collected from the southern part (n = 2/20; 10%) of Tehran. The secY typing method identified two different Leptospira species including L. interrogans and L. kirschneri. The results showed that urban rats might play an important role in transmission of zoonotic pathogens to humans.

The pests of a pest: A systematic review of ectoparasitic fauna among synanthropic rodents in the 21st century with meta-analysis

Synanthropic rodents are important urban pests that frequently carry hematophagous ectoparasites. These blood-sucking pests are capable of transmitting epizootic and zoonotic pathogens by landing on one host after feeding on an infected animal. This study aimed to estimate the prevalence of ectoparasites carried by synanthropic rodents and discuss the pathogens that are associated with these external parasites. We searched relevant literatures using predefined criteria in the following databases: EMBASE, PUBMED, Web of Science and Scopus from January 2000 to June 2020. Quality of studies was evaluated using Newcastle-Ottawa scale (NOS). Of 35 included studies from 15 countries in Africa, America, Asia, Europe and Oceania, black rats (R. rattus), brown rats (R. norvegicus), pacific rats (R. exulans) and house mice (Mus musculus) were common synanthropic rodents. Mites (Mesostigmata, Sarcoptiformes and Trombidiformes) were the most prevalent (42.6%, 95% CI 26-59.2), followed by ticks (Ixodida) (21.5%, 95% CI 10.5-32.6), lice (Phthiraptera) (17.8%, 95% CI 7.7-27.9) and fleas (Siphonaptera) (14.1%, 95% CI 10.1-18.1). Heterogeneity (I2>96%) across studies was statistically significant. The ectoparasitic fauna was shared considerably by different urban rodent species and appeared to be more diverse in R. rattus and R. norvegicus. Nonetheless, pathogens carried by these ectoparasites were rarely investigated. In conclusion, ectoparasites are ubiquitous in urban-dwelling rodents but our understanding of the epidemiology and the associated pathogens of these parasites remains limited. Further studies are warranted to unravel the pathogen landscape found in rodent-associated ectoparasites.

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.

The evolutionary consequences of human-wildlife conflict in cities

Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.

Severe pneumonia in a street rat (Rattus norvegicus) caused by Rodentibacter rarus strain RMC2

Background

Rodents are one of the most dangerous reservoirs and carriers of infectious diseases. Gradually, rats have become predominant in cities, sometimes staying in close vicinity to humans, pets, and other animals. Consequently, they tend to increase the transmission risk of pathogens.

Case Description

Here, we report an original case of bacterial pneumonia in a street rat (Rattus norvegicus). The rat was found dead on a street in the chief town of Marseille (France) after being run over by a car. The necropsy of the corpse revealed generalized granulomatous pneumonia in almost all the pulmonary lobes. Lung lesions and predominantly multiple fibro-inflammatory areas are presumably the witness of an infectious etiology. Bacterial isolation was carried out from lung tissues. Colonies were identified by MALDI-TOF MS and confirmed by 16S rRNA sequencing. The following bacteria were identified: Staphylococcus cohnii, Bordetella bronchiseptica, Bordetella parapertussi, Corynebacterium glucuronolyticum, Pelistega suis and Rodentibacter rarus. Based on the histopathological diagnosis and the avoidance approach, the most likely etiological agent of pneumonia is therefore R. rarus, a little-known Pasteurellales bacterium that is closely related to Rodentibacter pneumotropicus.

Conclusion

These data emphasize the severity of R. rarus infection in rodents. Thus, pointing out a potential risk for other animals (dogs, cats, and birds), as well as humans. The health monitoring program for rodents and rabbits pasteurellosis should now include R. rarus. Therefore, the pathological effect of the Rodentibacterspecies and/or strains needs to be better explored.

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.

Helminths of urban rats in developed countries: a systematic review to identify research gaps

Although black (Rattus rattus) and brown (Rattus norvegicus) rats are among the most widespread synanthropic wild rodents, there is a surprising scarcity of knowledge about their ecology in the urban ecosystem. In particular, relatively few studies have investigated their helminth species diversity in such habitat. We followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guideline to synthesize the existing published literature regarding the helminth fauna of urban rats in developed countries (North America, Europe, Australia, New Zealand and Japan). We aimed at describing the species diversity and richness of urban rat helminths, the species prevalence and associations, the methods of investigation, the pathological changes observed in the hosts, the risk factors of infection and the public health significance of rat-borne helminthiases. Twenty-three scientific papers published between 1946 and 2019 were reviewed, half of them were conducted in Europe. Twenty-five helminth species and eight genera were described from the liver, digestive tract, lungs and muscles of urban rats. The most commonly reported parasite was Calodium hepaticum. Prevalence and risk factors of helminth infection in urban rats varied greatly between studies. Observed pathological findings in the rat host were generally minor, except for C. hepaticum. Several rat helminths can parasitize humans and are therefore of public health significance. The lack of references to identification keys and the rare use of molecular tools for species confirmation represent the main limitation of these studies. Knowledge gap on this topic and the needs for future research are discussed.

Rats as potential reservoirs for neglected zoonotic Bartonella species in Flanders, Belgium

BACKGROUND

Bartonella spp. are vector-borne pathogens transmitted to humans via blood-sucking arthropods. Rodents such as the black rat (Rattus rattus) and Norway rat (R. norvegicus) are thought to be the main reservoirs. An infection with rodent-associated Bartonella spp. may cause severe symptoms in humans such as endocarditis and neuroretinitis. The current knowledge of Bartonella prevalence in rats from western Europe is scarce.

METHODS

Rats and a few other rodent by-catches were trapped in the context of a rodenticide resistance study at different sites in Flanders, Belgium. During dissection, biometric data were collected, and spleen tissues were taken. DNA was extracted from spleen samples and tested for Bartonella spp. by conventional generic polymerase chain reaction (PCR). To determine the Bartonella species, a selected number of amplicons were sequenced and compared with GenBank entries.

RESULTS

In total, 1123 rodents were trapped. The predominate species was R. norvegicus (99.64%). Other rodents trapped included: two water voles (Arvicola amphibius, 0.18%); one colour rat (R. norvegicus forma domestica, 0.09%); and one muskrat (Ondatra zibethicus, 0.09%). PCR analysis of 1097 rodents resulted in 410 (37.37%, 95% CI: 34.50-40.31%) Bartonella spp. DNA-positive samples. Bartonella tribocorum (94.68%, 95% CI: 88.02-98.25%) was the most frequently detected Bartonella species, followed by B. grahamii (3.19%, 95% CI: 0.66-9.04%) and B. doshiae (1.06%, 95% CI: 0.03-5.79%). An uncultured Bartonella species occurred in one water vole (1.06%, 95% CI: 0.03-5.79%). There was a significantly higher Bartonella prevalence in older rats compared to juveniles and a significant difference in Bartonella prevalence concerning the localisation of trapping sites. In contrast, there was no statistically significant difference in Bartonella prevalence regarding sex, degree of urbanisation and season.

CONCLUSIONS

Based on the high prevalence found, we conclude that the Norway rat seems to be a key reservoir host for zoonotic B. tribocorum in Belgium.

Resistance to anticoagulant rodenticides in Martinique could lead to inefficient rodent control in a context of endemic leptospirosis

Leptospirosis is a re-emergent worldwide zoonosis. It is endemic in Martinique where transmission conditions are favourable. Humans are usually infected through contact with water contaminated with urine of rodents. Recent human leptospirosis outbreaks in Martinique require today effective rodent management to prevent leptospirosis transmission. Nowadays, use of anticoagulant rodenticides (AR) is the main method implemented to control rodent populations. Nevertheless, intensive use of these AR has selected worldwide many VKORC1-based resistant rodent strains to AR. Our aim was to characterize the sensitivity of Martinique commensal rodents to AR to better prevent leptospirosis transmission. Resistance of house mice to first-generation and in rare cases even to second-generation ARs were clearly demonstrated in Martinique with the detection of the Y139C mutation with a very high allelic frequency of 40% and the A26T/Y139C double-mutation with an allelic frequency of 0.9%. In black rat, the most prevalent rodent in Martinique, 3 new Vkorc1 coding mutations were detected, the H68N, A115T and S149N mutations associated with moderate resistance to first generation AR. Therefore, rodent management in Martinique must be carried carefully to avoid resistance diffusion and maintain long-term effective rodent management, to be able to efficiently prevent leptospirosis transmission.

The potential of VKORC1 polymorphisms in Mustelidae for evolving anticoagulant resistance through selection along the food chain

In response to strong selection, new mutations can arise quickly and sweep through populations, particularly, if survival and reproduction depend on certain allele copies for adaptation to rapidly changing environments, like resistance against deadly diseases or strong toxins. Since the 1950s, resistance to anticoagulant rodenticides in several rodents has emerged through single nucleotide mutations in the vitamin-K-epoxid-reductase-complex-subunit-1 (VKORC1) gene, often located in its exon 3. Detection of high prevalence and concentrations of anticoagulant rodenticides in non-target vertebrates, including carnivorous Mustelidae, let us assume that secondary exposure by feeding on poisoned prey may also cause selection along the food chain and we hypothesized that VKORC1-based resistance might also have evolved in rodents’ predators. Using newly-developed mustelid-specific primers for direct sequencing of genomic DNA, we studied VKORC1-DNA-polymorphisms in 115 mustelids of five species (Martes martes, M. foina, Mustela nivalis, M. erminea, M. putorius), obtained from northern Denmark, yielding six sites with nonsynonymous and several synonymous amino acid polymorphisms in exon 3. Comparison of these VKORC1-genotypes with hepatic rodenticide residues (obtained by HPLC combined with fluorescence or mass spectrometry) in 83 individuals (except M. martes), using generalized linear models, suggested that anticoagulant levels depended on species and specific polymorphisms. Although most VKORC-1 polymorphisms may present standing genetic variation, some are situated in resistance-mediating membrane parts of the VKORC1-encoded protein, and might be a result of selection due to exposure to anticoagulant poisons. Our new molecular markers might allow detecting indirect effects of anticoagulant rodenticides on rodent predator populations in the future.

Leptospira infection in rats: A literature review of global prevalence and distribution

Background

The role of rodents in Leptospira epidemiology and transmission is well known worldwide. Rats are known to carry different pathogenic serovars of Leptospira spp. capable of causing disease in humans and animals. Wild rats (Rattus spp.), especially the Norway/brown rat (Rattus norvegicus) and the black rat (R. rattus), are the most important sources of Leptospira infection, as they are abundant in urban and peridomestic environments. In this study, we compiled and summarized available data in the literature on global prevalence of Leptospira exposure and infection in rats, as well as compared the global distribution of Leptospira spp. in rats with respect to prevalence, geographic location, method of detection, diversity of serogroups/serovars, and species of rat.

Methods

We conducted a thorough literature search using PubMed without restrictions on publication date as well as Google Scholar to manually search for other relevant articles. Abstracts were included if they described data pertaining to Leptospira spp. in rats (Rattus spp.) from any geographic region around the world, including reviews. The data extracted from the articles selected included the author(s), year of publication, geographic location, method(s) of detection used, species of rat(s), sample size, prevalence of Leptospira spp. (overall and within each rat species), and information on species, serogroups, and/or serovars of Leptospira spp. detected.

Findings

A thorough search on PubMed retrieved 303 titles. After screening the articles for duplicates and inclusion/exclusion criteria, as well as manual inclusion of relevant articles, 145 articles were included in this review. Leptospira prevalence in rats varied considerably based on geographic location, with some reporting zero prevalence in countries such as Madagascar, Tanzania, and the Faroe Islands, and others reporting as high as >80% prevalence in studies done in Brazil, India, and the Philippines. The top five countries that were reported based on number of articles include India (n = 13), Malaysia (n = 9), Brazil (n = 8), Thailand (n = 7), and France (n = 6). Methods of detecting or isolating Leptospira spp. also varied among studies. Studies among different Rattus species reported a higher Leptospira prevalence in R. norvegicus. The serovar Icterohaemorrhagiae was the most prevalent serovar reported in Rattus spp. worldwide. Additionally, this literature review provided evidence for Leptospira infection in laboratory rodent colonies within controlled environments, implicating the zoonotic potential to laboratory animal caretakers.

Conclusions

Reports on global distribution of Leptospira infection in rats varies widely, with considerably high prevalence reported in many countries. This literature review emphasizes the need for enhanced surveillance programs using standardized methods for assessing Leptospira exposure or infection in rats. This review also demonstrated several weaknesses to the current methods of reporting the prevalence of Leptospira spp. in rats worldwide. As such, this necessitates a call for standardized protocols for the testing and reporting of such studies, especially pertaining to the diagnostic methods used. A deeper understanding of the ecology and epidemiology of Leptospira spp. in rats in urban environments is warranted. It is also pertinent for rat control programs to be proposed in conjunction with increased efforts for public awareness and education regarding leptospirosis transmission and prevention.

The role of rodents in the transmission of many diseases, including leptospirosis, is widely known. Rats abundant in urban and peridomestic environments are the most important reservoirs and sources of Leptospira infection in humans and animals. Leptospirosis is a significant but neglected disease of humans and animals that is increasing in incidence in regions affected by natural disasters. This paper summarizes the global prevalence and distribution of Leptospira infection in rats and will add to the literature that supports research, education, and public awareness regarding leptospirosis transmission and prevention.

House Mice as a Real Sanitary Threat of Human and Animal Leptospirosis: Proposal for Integrated Management

Leptospirosis is a reemerging zoonosis and ranges in severity from benign to sometimes fatal. In cattle, infection may be responsible for abortion and infertility cases causing economic losses. Humans may be contaminated through direct contact with urine of infected animals or indirectly though interaction with urine-contaminated environment. Many wildlife species living close to cattle, especially commensal rodents may play a role in the transmission of leptospires. Because little is known on the epidemiology of nonmaintenance Leptospira serovars, appropriate management is still limited. On a French farm where human and cattle leptospirosis were detected, the transmission cycle was explored to propose appropriate mitigation measures. For that, commensal rodents present on the farm were trapped and their leptospires carriage was studied by molecular methods. Trapped mice were shown to carry two pathogenic Leptospira species (L. interrogans and L. kirschneri). Since these 2 serogroups were simultaneously detected in the trapped mice and in the cows of this farm, we suspected an initial Leptospira transmission from mice to cows requiring an effective management of mice on this farm. Because resistance to anticoagulant rodenticides due to Vkorc1 mutations has been largely described in rodents and first-generation anticoagulant rodenticides seemed to be inefficient in controlling mice on this farm, susceptibility of these mice to anticoagulants has been characterized by Vkorc1 sequencing. 50% of the trapped mice carried mutations in the Vkorc1 gene leading to severe resistance to first-generation anticoagulants. The management of such mice that are a real sanitary threat can be achieved only by using the most toxic second-generation anticoagulants or nonanticoagulant solutions.

Bacterial isolation from internal organs of rats (Rattus rattus) captured in Baghdad city of Iraq

Aim

Rats are accused in disseminating many zoonotic diseases. This study aimed to isolate and identify bacteria from internal organs of rats captured in Baghdad City, Iraq.

Materials and Methods

A total of 120 black rats (R. rattus) were trapped from different areas in Baghdad city. Rats were kept in individual plastic cages for 3 h before euthanizing. Deep pharyngeal swab, intestinal content, urine, and pieces of the liver and spleen, lung, kidney, and brain were obtained aseptically. The specimens were inoculated into peptone water and incubated at 37°C for 24 h for enrichment. A loopful of each specimen was then subcultured onto MacConkey Agar, Blood Agar, and Mannitol Salt Agar. CHROMagar O157 H7 and CHROMagar Listeria were used to detect Escherichia coli 157:7 and Listeria spp., respectively. Biochemical tests on analytical profile index, microscopic examination, and commercial kit for latex agglutination test for serotyping E. coli O157:H7 were used.

Results

Mixed bacterial isolates were recorded as 116, 52, 36, 28, 18, 6, and 4 from intestinal contents, deep pharyngeal, liver and spleen, urine, lung, brain, and kidney, respectively. Microorganisms included E. coli, Staphylococcus aureus, Streptococcus spp., Bacillus spp., Pseudomonas aeruginosa, Citrobacter freundii, Proteus vulgaris, E. coli O157:H7, Enterobacter cloacae, Listeria spp., Klebsiella spp., Ochrobactrum anthropi, Aeromonas spp., Brucella spp., Pseudomonas fluorescens, Escherichia fergusonii, Micrococcus spp., Morganella spp., Proteus mirabilis, Pseudomonas luteola, and Streptobacillus spp. The highest bacterial prevalence (88; 73.33%) was recorded for E. coli, where 68 isolates were identified from the intestinal contents. Of these, four isolates were E. coli O157:H7.

Conclusion

Rats are important carriers and transmitters of a number of pathogens and can disseminate these microorganisms to humans and animals.

First survey on zoonotic helminthosis in urban brown rats (Rattus norvegicus) in Spain and associated public health considerations

The brown rat, Rattus norvegicus, with a worldwide distribution, is the most commensal species among synanthropic rodents, since its main habitat, in urban as well as in rural areas, is always linked to humans. Therefore, people living in close proximity to rodent populations can be exposed to infection. Whereas bacteria and viruses are the best known rat-associated zoonoses in urban environments, the role of brown rats as reservoirs for helminth parasites and the associated risk for humans are less well known. Specifically, this role has not been analyzed in Spain to date. A total of 100 R. norvegicus trapped in the sewage system (n = 85), and parks (n = 15) of Barcelona was examined. The overall prevalence of helminth infection was 85%. The helminths found were Hymenolepis nana (17%), H. diminuta (33%) (Cestoda), Calodium hepaticum (17%), Eucoleus gastricus (28%), Aonchotheca annulosa (12%), Trichosomoides crassicauda (7%), Nippostrongylus brasiliensis (46%), Heterakis spumosa (62%), Gongylonema neoplasticum (20%) (Nematoda) and Moniliformis moniliformis (6%) (Acanthocephala). Five of the ten helminth species are considered zoonotic parasites, with rats acting as reservoirs for human infection, i.e. H. nana, H. diminuta, C. hepaticum, G. neoplasticum and M. moniliformis. G. neoplasticum and M. moniliformis are reported for the first time in urban rats in Europe. H. nana, H. diminuta and C. hepaticum are the most widespread species in European cities. For H. nana and C. hepaticum, rats act as effective spreaders of the human infective stage (eggs). For H. diminuta, G. neoplasticum and M. moniliformis, rats act as indirect reservoirs of the zoonoses since the eggs shed by the rats are infective for their insect intermediate hosts only. Medical practitioners need to be made aware of the range of parasites carried by rats, as there is a realistic likelihood that ill health currently caused by rat infestations may be misdiagnosed.

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.

[The plague: An overview and hot topics]

Plague is a bacterial zoonosis caused by Yersinia pestis, usually found in fleas and small rodents that constitute the reservoir of the disease. It is transmitted to humans by flea bite, contact with rodents or inhalation of infected droplets. There are three clinical forms: bubonic plague, pulmonary plague and septicemic plague. The usual presentation is a flu-like syndrome possibly accompanied by an inflammatory lymphadenopathy which appears after 1 to 7days of incubation. Bubonic plague has a case fatality rate of about 50% while other forms of plague are almost always fatal without treatment. Diagnosis can be confirmed by usual bacteriological techniques (Gram examination, culture) but also by serological examination, use of rapid diagnostic tests or PCR. Although aminoglycosides are traditionally regarded as the most effective treatment, fluoroquinolones or cyclins are currently recommended in France. Plague is one of the re-emerging diseases according to the WHO and Madagascar suffered in 2017 the most important plague epidemic of the 21st century with more than 2000 cases and 200 deaths. Peru and the Democratic Republic of Congo are also considered endemic areas. Public health measures and a relentless fight against poverty are the cornerstone of the control of the disease. Vaccine improvement in endemic areas may also play an important role.