Commensal Rats Research Articles

Identification of rodent species confirmed as the cause of leptospirosis disease, along with ecosystem distribution and environmental factors

Background: Leptospirosis outbreaks have been reported in various parts of the world, classifying it as a re-emerging infectious disease. Rats act as the main reservoir for Leptospira spp. bacteria. The Indonesian Ministry of Health reported 1,170 cases of leptospirosis with 106 deaths Case Fatality Rate (CFR 9.1%) in 2020, obtained from 8 provinces. Additionally, in 2021, there was a decrease in cases by 734, but with an increased CFR of 11.4%, with the largest contributors being Central Java and East Java. Objective: To determine the most dominant rodent species confirmed to cause leptospirosis and the distribution of ecosystems and environmental factors that are the dominant causes of leptospirosis. Method: This paper is a narrative literature review study. Articles were searched through online databases such as Google Scholar and PubMed using keywords leptospirosis, rats, ecosystem, and environmental factors, published within the last 5 years. Findings: The identification results showed that Bandicota indica was the most dominant rodent species infected with leptospirosis. This type of rat is a commensal species. Leptospirosis cases occurred in non-forest ecosystems near settlements and coastal areas near settlements. The dominant environmental factors associated with leptospirosis incidence were poor sanitation conditions, indiscriminate waste disposal behavior, and stagnant water. Conclusion: The identification results indicate that Bandicota indica is the most dominant rodent species infected with leptospirosis, being a commensal rat species in non-forest ecosystems near settlements and coastal areas near settlements. The dominant environmental factors associated with leptospirosis incidence include poor sanitation conditions, indiscriminate waste disposal behavior, and stagnant water. Novelty/Originality of this Study: The study's findings confirmed that non-forest and coastal ecosystems near settlements are significant reservoirs for Leptospira bacteria. Additionally, it highlighted the critical role of poor sanitation, indiscriminate waste disposal, and stagnant water as environmental factors contributing to the transmission of leptospirosis.

A replacement name for the endemic Rattus (Muridae, Mammalia) of the island of Obi, Indonesia

A replacement name for the endemic Rattus (Muridae, Mammalia) of the island of Obi, Indonesia

Viral diversity in wild and urban rodents of Yunnan Province, China

ABSTRACT Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. R. tanezumi in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. R. tanezumi was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with R. tanezumi as an important reservoir for zoonotic viruses.

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.

Investigation of Zoonotic Bacterial Pathogens Associated with Rodents in Rural Areas of Nellore, India

Rodent species are known to harbour and host various zoonotic pathogens, including bacterial, viral, fungal, and protozoal species. Several investigations proved that commensal rats (Rattus spp.) are potential to transmit drug-resistant and hyper-virulent bacterial pathogens to humans. India's rapid urbanization and developmental activities facilitated rats to live near the human population. However, few information was known about bacterial species associated with rodents and their role in zoonotic risk to humans in India. The present study aimed to (i) investigate the presence of bacterial pathogens associated with rodents and (ii) infer the prevalence and diversity of potential bacterial pathogens in Nellore district, India. Bacterial prevalence was determined by isolation and identification techniques. The isolated bacterial cultures were submitted for phenotypic observation, biochemical identification using the VITEK 2 compact automated system, and molecular detection by DNA extraction and amplification of the 16S rRNA gene. A diversified bacterial community belonging to 14 species was detected from all collected animals. Bacterial species' prevalence was comparatively higher in black rats (n=66) than brown rats (n=27). 46 rats out of 93 were found to be positive (49.4%) for bacterial presence. A significant variation was found in the prevalence of bacterial species between both rodent species. The highest bacterial prevalence was recorded for Bacillus spp. (36%) followed by E. coli (29%). The prevalence of Klebsiella pneumoniae was found as 17%, of which 18% in black rats and 14% in brown rats. Listeria spp.'s prevalence was 23.6%, but a higher prevalence was observed in black rats (25.7%). Surprisingly, an uncommon pathogen, Sphingomonas paucimobilis, was detected in both rodent species. These results suggest that Rattus rats in Nellore were suspected to be potential carriers of transmitting zoonotic bacterial species to humans.

Stowaways: Maritime ecology of the oldest commensal ship rats (Rattus rattus) found on a Mediterranean shipwreck

Ship rats (Rattus rattus) have successfully colonized six continents and 80% of islands worldwide by stowing-away on anthropogenic vessels. Numerous zooarchaeological and metagenomic studies have contributed to tracing the western dispersal of ship rats out of the Indian subcontinent and into the Mediterranean Basin, North Africa, and Europe. This has increased understanding of historical maritime mobility, trade contacts, and the spread of pandemic disease such as the plague. Moreover, considerable research has been conducted on the behavior, ecology, and population dynamics of ship rats in invaded areas, which supports conservation and eradication efforts. However, few studies have shed light on the mode of travel in between the geographic origins and destinations of ship rats, such as ships and boats, which act as mobile, commensal habitat for this cosmopolitan species. We address this lacuna here, by analyzing an assemblage of ship rat remains from an early Islamic period shipwreck, the Ma‘agan Mikhael B, located on the Carmel coast of modern Israel. Using zooarchaeological, biometrical, and palaeogenetic (aDNA) methodologies, we investigated the maritime ecology of ship rats regarding dispersal behavior, habitat selection, source–sink dynamics, and relative body size. The results of this study suggest that ship rats actively inhabited the Ma‘agan Mikhael B as part of their habitat selection processes, that conditions onboard provided high-quality habitat (adequate food and harborage, likely absence of predators and disease), and that they appear to have exhibited a degree of gigantism, possibly due to ‘island rule’. This study has implications for future metapopulation genetic studies on ship rats, as well as shows the value of zooarchaeological analysis in understanding the ecological circumstances of the maritime mobility of ship rats in the Mediterranean region.

Abundance and Dynamics of Small Mammals in New Zealand: Sequential Invasions into an Island Ecosystem Like No Other.

New Zealand had no people or four-footed mammals of any size until it was colonised by Polynesian voyagers and Pacific rats in c. 1280 AD. Between 1769 and 1920 AD, Europeans brought three more species of commensal rats and mice, and three predatory mustelids, plus rabbits, house cats hedgehogs and Australian brushtail possums. All have in turn invaded the whole country and many offshore islands in huge abundance, at least initially. Three species are now reduced to remnant populations, but the other eight remain widely distributed. They comprise an artificial but interacting and fully functional bottom-up predator-prey system, responding at all levels to interspecific competition, habitat quality and periodic resource pulsing.

Activity and movement of small mammal tick hosts at the urban fringes of Sydney, Australia

Context Small mammals may traverse the urban fringe and use both natural and anthropogenic resources. In Australia, human commensal black rats (Rattus rattus) and native long-nosed bandicoots (Perameles nasuta) are important tick hosts, which can be found persisting at the urban fringe, leading to human–wildlife conflict. Aims We aimed to (1) determine the relative activity of small mammals in yards and associations with yard attributes, (2) compare activity of black rats and long-nosed bandicoots in bushland with activity in yards and (3) determine the proportion of black rats and long-nosed bandicoots that crossed the urban fringe. We predicted that native bandicoots would be more active in bushland habitats and that black rats would be more active in yards. Methods We used camera trapping in 56 residential yards, 18 of which were paired with adjacent bushland to measure small mammal activity in the two habitats. We recorded yard attributes and examined these associations using generalised linear models. We used isodar analysis to investigate black rat preferences of bushland habitat compared with yards, and we used Rhodamine B baiting to investigate movement at the urban fringe. Key results We found that black rats were the most active small mammal in residential yards and were detected in more yards than other small mammals, followed by bandicoots. Black rat activity was greater in yards adjacent to bushland, but no other yard attributes were associated with black rat and bandicoot activity. Overall, activity tended to be higher in bushland than in yards at paired locations. Conclusions Our findings suggest residential yards likely provide high-quality resources for long-nosed bandicoots. Low rates of movement at the urban fringe (6%), and a preference for bushland at low densities suggests that black rats may be synanthropic rather than commensal, occupying an urban niche but not depending on anthropogenic resources as expected. Implications Residential properties located adjacent to bushland may be exposed to increased black rat activity in yards. Future work should consider how introduced rats may be controlled in bushland to assist urban rat control efforts and avoid non-target impacts. Residential yards are likely to be important habitat for the persistence of long-nosed bandicoots in urban environments.

New light on the introduction of ship-borne commensal rats and mice in Aotearoa New Zealand, 1790s–1830s

New light on the introduction of ship-borne commensal rats and mice in Aotearoa New Zealand, 1790s–1830s

Xenopsylla cheopis (rat flea)

The rat flea, Xenopsylla cheopis, is the primary vector of the bubonic plague bacterium, Yersinia pestis, and also serves as a vector of bacteria belonging to the genera Rickettsia and Bartonella. As a parasite of the commensal rat, Rattus ssp., it aligns with anthropogenic environments (i.e., sewer systems, human habitation, crop fields, etc.). Rats and fleas are often carried with cargo, and X. cheopis was associated with the spread of plague during the third pandemic from harbor to harbor via sea-trade routes. Fortunately, the environmental conditions required for X. cheopis development appear to have limited its persistence in many regions. Adult X. cheopis live on the host rather than in the nest. Both male and female fleas are hematophagous. They take sporadic blood meals to meet their nutritional requirements and promote egg maturation. Immature fleas live in rat nests and are sensitive to variation in temperature and relative humidity.

Genomic Analysis Reveals Subdivision of Black Rats (Rattus rattus) in India, Origin of the Worldwide Species Spread.

In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a genomic approach, we typed 27 R. rattus samples from Peninsular India using the genotyping-by-sequencing (GBS) method. Filtering and alignment of the FASTQ files yielded 1499 genome-wide SNPs. Phylogenomic tree reconstruction revealed a distinct subdivision in the R. rattus population, manifested as two clusters corresponding to the east and west coasts of India. We also identified signals of admixture between these two subpopulations, separated by an Fst of 0.20. This striking genomic difference between the east and west coast populations mirrors what has previously been described with mitochondrial DNA sequencing. It is notable that the west coast population of R. rattus has been spread globally, reflecting the origins of commensalism of the species in Western India and the subsequent transport by humans worldwide.

Spatial and Temporal Distribution of Rodents during the Epizootic and Enzootic Periods of Plague, with a Focus on Exu, Northeastern Brazil.

The plague caused by the Yersinia pestis bacterium is primarily a flea-transmitted zoonosis of rodents that can also be conveyed to humans and other mammals. In this work, we analyzed the spatial and temporal distribution of rodent populations during epizootic and enzootic periods of the plague in the municipality of Exu, northeastern Brazil. The geospatial analyses showed that all the rodent species appeared through the whole territory of the municipality, with different occurrence hotspots for the different species. Important fluctuations in the rodent populations were observed, with a reduction in the wild rodent fauna following the end of a plague epizootic period, mostly represented by Necromys lasiurus and an increase in the commensal species Rattus rattus. A higher abundance of rats might lead to an increased exposure of human populations, favoring spillovers of plague and other rodent-borne diseases. Our analysis highlights the role of wild rodent species as amplifier hosts and of commensal rats (R. rattus) as preserver hosts in the enzootic period of a specific transmission infection area.

Commensal Rodent Habitat Expansion Enhances Arthropod Disease Vectors on a Tropical Volcanic Island.

On volcanic islands, the release of animals from predators and competitors can lead to increased body size and population density as well as the expanded habitat use of introduced animals relative to their mainland counterparts. Such alterations might facilitate the spread of diseases on islands when these exotic animals also carry pathogenic agents; however, this has rarely been investigated. The commensal Asian house rat (Rattus tanezumi) is confined to human residential surroundings in mainland Taiwan but can be observed in the forests of nearby Orchid Island, which is a tropical volcanic island. Orchid Island is also a hot spot for scrub typhus, a lethal febrile disease transmitted by larval trombiculid mites (chiggers) that are infected primarily with the rickettsia Orientia tsutsugamushi (OT). We predicted an increase in chigger abundance when rodents (the primary host of chiggers) invade forests from human settlements since soils are largely absent in the latter habitat but necessary for the survival of nymphal and adult mites. A trimonthly rodent survey at 10 sites in three habitats (human residential, grassland, and forest) found only R. tanezumi and showed more R. tanezumi and chiggers in forests than in human residential sites. There was a positive association between rodent and chigger abundance, as well as between rodent body weight and chigger load. Lastly, >95% of chiggers were Leptotrombidium deliense and their OT infection rates were similar among all habitats. Our study demonstrated potentially elevated risks of scrub typhus when this commensal rat species is allowed to invade natural habitats on islands. Additionally, while the success of invasive species can be ascribed to their parasites being left behind, island invaders might instead obtain more parasites if the parasite requires only a single host (e.g., trombiculid mite), is a host generalist (e.g., L. deliense), and is transferred from unsuitable to suitable habitats (i.e., human settlements on the mainland to forests on an island).

Analysis of different factors contributing the rodent infestations in urban areas in Faisalabad, Pakistan

In the last decade there is a huge increase in the human population that has witnessed the important changes in the ecology, climate and human behaviour which ultimately favours the survival and increase in the population of urban pests. More alarmingly, a dramatic expansion in the rodent’s populations is a growing threat to the humans living in different urban settings. It is supposed that several socio-economic issues, environmental factors and type of housing facilities are contributing towards this higher increase in the rodent’s population in these areas. However, urban rat control programs are still ineffective as very little is known about their ecology. This study sought to investigate the type of housing and environment factors that provide food, water, shelter and harborage to rats and mice and risk factors of rodent infestations in three of the housing systems i.e. in squatter’s settlements, departmental colonies and posh residences including bungalows in Faisalabad. A total of 720 structures (240 each) were selected from these three housing systems. Snap and live trapping of commensal rats and mice (Rattus rattus, Rattus norvegicus,Mus musculus) was carried out fortnightly from November, 2017 to October, 2018 suspecting the rats and mice population as variable as different structured housing systems. The removal data were used to estimate the size of the population of rats and mice per system. For rat and mice population estimation, Change-in-ratio (CIR) and Regression of daily capture on cumulative captures (RR) were employed. The higher number of rats/mice (814 specimens) were collected in squatter’ settlements. Among these 560, 184 and 70 specimens were of Mus musculus, Rattus rattus and Suncus murinus, respectively. The number of rodents captured from departmental colonies and posh residences/bungalows was 210 specimens (129 of M. musculus, 71 of R. rattus and 10 specimens of S. murinus) and 30 specimens of M. musculus, respectively. The major socio-economic factors contributing to these higher rodent infestations were low-grade residences with inadequate or no building maintenance measures and higher housing densities along with heterogenous breeding sites. These higher densities of rats and mice may pose a serious disease threats to human populations as they are carriers of a number of pathogens. The findings of the present study provide the specific features of rats and mice population in concern to human residences and may help to formulate controlling strategies against these culprits.

Stable Isotopic Evidence for Nutrient Rejuvenation and Long-Term Resilience on Tikopia Island (Southeast Solomon Islands)

Tikopia Island, a small and relatively isolated Polynesian Outlier in the Southeast Solomon Islands, supports a remarkably dense human population with minimal external support. Examining long-term trends in human land use on Tikopia through archaeological datasets spanning nearly 3000 years presents an opportunity to investigate pathways to long-term sustainability in a tropical island setting. Here, we trace nutrient dynamics across Tikopia’s three pre-European contact phases (Kiki, Sinapupu, Tuakamali) via stable carbon and nitrogen isotope analysis of commensal Pacific rat (Rattus exulans) and domestic pig (Sus scrofa) bone and tooth dentine collagen. Our results show a decline in δ15N values from the Kiki (c. 800 BC-AD 100) to Sinapupu (c. AD 100–1200) phases, consistent with long-term commensal isotope trends observed on other Polynesian islands. However, increased δ15N coupled with lower δ13C values in the Tuakamali Phase (c. AD 1200–1800) point to a later nutrient rejuvenation, likely tied to dramatic transformations in agriculture and land use at the Sinapupu-Tuakamali transition. This study offers new, quantifiable evidence for deep-time land and resource management decisions on Tikopia and subsequent impacts on island nutrient status and long-term sustainability.

Impact of contraceptive hormones on the reproductive potential of male and female commensal black rats (Rattus rattus).

The black rat is considered one of the world's top pests. With increased restrictions on rodenticides, new alternatives to manage rats are urgently needed. Research on the use of contraceptive hormones, levonorgestrel (LE), and quinestrol (QU), have been evaluated against some rodent species, and this research is the first study to assess these on black rats. Hormones were incorporated into rodent bait at 10 and 50 ppm concentrations singly and in combination (EP-1). Groups of 10 animals of each sex were fed the baits over 7days. Lower bait consumption was observed with slight body mass reductions. On dissection, it was observed that the uterus was in a state of edema and male reproductive organs weighed less with reduced sperm counts/motility. The 2 most promising baits, 50 ppm QU and EP-1, were used to assess impact on pregnancy and litter size. Pregnancy was reduced from 70% success when both males and females consumed untreated bait, down to 30% when males had consumed contraceptive bait but females had not, and down to 0% when females had consumed contraceptive bait, regardless of whether they had paired with a treated or untreated male. Litter size in the untreated pairs was 8 pups, but only 4 pups in those cases where the male only had consumed the contraceptive. Further studies should investigate how long the effect lasts and its reversibility. Field studies at the population level may also shed light on the practicality of using contraceptive baits for black rats in different habitats.

The clock is ticking: Temporally prioritizing eradications on islands

Achieving conservation objectives is time critical, but the vast number of threats and potential actions means some form of ranking is necessary to aid prioritization. Objective methods for ranking conservation actions based on when they are differentially likely to become feasible, or to succeed, are currently unavailable within existing decision-making frameworks but are critical for making informed management decisions. We demonstrate how statistical tools developed for survival (or time-to-event) analysis can be used to rank conservation actions over time, through the lens of invasive mammal eradications on islands. Here we forecast the probability of eradicating commensal rat species (Rattus rattus, R. norvegicus, R. exulans) from the New Zealand archipelago by the government's stated target of year 2050. Our methods provide temporally ranked eradication trajectories for the entire country, thus facilitating meeting nationwide policy goals. This demonstration highlights the relevance and applicability of such an approach and its utility for prioritizing globally effective conservation actions.

Assessing the efficacy of oral intake of insecticides on mortality of fleas and ticks on commensal Rattus species

Many rodent-borne pathogens can be transmitted via their ectoparasites to humans and can cause severe zoonotic diseases (e.g. plague, tick-borne encephalitis, typhus). Managing relevant ectoparasites in rodents may reduce human infection risk. The purpose of this laboratory study was to screen potential insecticides for their palatability to commensal rat species and their efficacy against fleas and ticks feeding on rats. The preferences shown by Norway rats (Rattus norvegicus) for four insecticides (fipronil, cythioate, thiamethoxam and ivermectin) were assessed when presented as a choice in cereal-based pellets. Subsequently, specific doses of insecticide-containing cereal pellets were fed to rats to determine the ability of each insecticide, over time, to kill cat fleas (Ctenocephalides felis), stickfast fleas (Echidnophaga gallinacea) feeding on Norway rats, and possum ticks (Ixodes trichosuri) feeding on Norway rats and black rats (R. rattus). Fipronil, cythioate and thiamethoxam were similarly palatable to rats, but ivermectin was avoided at high concentration. Fipronil was the most effective in killing cat fleas, stickfast fleas and ticks feeding on rats. Cythioate and ivermectin performed similarly against two flea species, while the effects of ivermectin and fipronil were comparable against ticks. Cythioate was not efficacious against ticks at the doses tested. Fipronil should be tested as a systemic compound to minimise arthropod infestation in small mammals to reduce adverse effects of arthropod-borne disease on humans. This insecticide should also be tested in combination with a rodenticide to prevent migration of arthropods with zoonotic relevance from rodent carcasses to humans.

Transmission of Rat Hepatitis E Virus Infection to Humans in Hong Kong: A Clinical and Epidemiological Analysis.

Hepatitis E virus (HEV) variants causing human infection predominantly belong to HEV species A (HEV-A). HEV species C genotype 1 (HEV-C1) circulates in rats and is highly divergent from HEV-A. It was previously considered unable to infect humans, but the first case of human HEV-C1 infection was recently discovered in Hong Kong. The aim of this study is to further describe the features of this zoonosis in Hong Kong. We conducted a territory-wide prospective screening study for HEV-C1 infection over a 31-month period. Blood samples from 2,860 patients with abnormal liver function (n=2,201) or immunosuppressive conditions (n=659) were screened for HEV-C1 RNA. In addition, 186 captured commensal rats were screened for HEV-C1 RNA. Sequences of human-derived and rat-derived HEV-C1 isolates were compared. Epidemiological and clinical features of HEV-C1 infection were analyzed. HEV-C1 RNA was detected in 6/2,201 (0.27%) patients with hepatitis and 1/659 (0.15%) immunocompromised persons. Including the previously reported case, eight HEV-C1 infections were identified, including five in patients who were immunosuppressed. Three patients had acute hepatitis, four had persistent hepatitis, and one had subclinical infection without hepatitis. One patient died of meningoencephalitis, and HEV-C1 was detected in cerebrospinal fluid. HEV-C1 hepatitis was generally milder than HEV-A hepatitis. HEV-C1 RNA was detected in 7/186 (3.76%) rats. One HEV-C1 isolate obtained from a rat captured near the residences of patients was closely related to the major outbreak strain. HEV-C1 is a cause of hepatitis E in humans in Hong Kong. Immunosuppressed individuals are susceptible to persistent HEV-C1 infection and extrahepatic manifestations. Subclinical HEV-C1 infection threatens blood safety. Tests for HEV-C1 are required in clinical laboratories.

Epidemiology and genetic diversity of zoonotic pathogens in urban rats (Rattus spp.) from a subtropical city, Guangzhou, southern China

Commensal rats (Rattus spp.), which are globally distributed, harbour many pathogens responsible for significant human diseases. Despite this, we have a poor understanding of the epidemiology and genetic diversity of some recently neglected zoonotic pathogens, such as Leptospira spp., Bartonella spp. and hepatitis E virus (HEV), which constitute a major public health threat. Thus, we surveyed the occurrences, co-infection and genetic diversity of these pathogens in 129 urban rats from China. For Rattus tanezumi, the prevalences of Leptospira spp., Bartonella spp. and HEV infection were 6.67%, 0% and 46.67%, respectively. The prevalences of Leptospira spp., Bartonella spp. and HEV infection were 57.89%, 9.65% and 57.89% for Rattus norvegicus respectively. Leptospira spp. and HEV infections were more likely to occur in mature R.norvegicus. Phylogenetic analyses showed that pathogenic Leptospira interrogans and Leptospira borgpetersenii might exist. We also found that Bartonella spp. showed high similarity to Bartonella elizabethae, Bartonella rochalimae and Bartonella tribocorum, which are implicated in human disease. Dual and triple infections were both detected. Moreover, dual infections with Leptospira spp. and HEV represented the most frequent co-infection, and there was a significantly positive association between them. High genetic diversity was observed in genes segments from Leptospira, Bartonella and HEV. Our results first discover the occurrence of multiple co-infections and genetic diversity of Leptospira, Bartonella and HEV in commensal rats from China. Altogether, the present study provides an insight into evaluating the risk of rat-borne zoonoses in urban China.