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.

Prevalence of Diarrheagenic Escherichia coli (DEC) and Salmonella spp. with zoonotic potential in urban rats in Salvador, Brazil.

Studies evaluating the occurrence of enteropathogenic bacteria in urban rats (Rattus spp.) are scarce worldwide, specifically in the urban environments of tropical countries. This study aims to estimate the prevalence of diarrhoeagenic Escherichia coli (DEC) and Salmonella spp. with zoonotic potential in urban slum environments. We trapped rats between April and June 2018 in Salvador, Brazil. We collected rectal swabs from Rattus spp., and cultured for E. coli and Salmonella spp., and screened E. coli isolates by polymerase chain reaction to identify pathotypes. E. coli were found in 70% of Rattus norvegicus and were found in four Rattus rattus. DEC were isolated in 31.3% of the 67 brown rats (R. norvegicus). The pathotypes detected more frequently were shiga toxin E. coli in 11.9%, followed by atypical enteropathogenic E. coli in 10.4% and enteroinvasive E. coli in 4.5%. From the five black rats (R. rattus), two presented DEC. Salmonella enterica was found in only one (1.4%) of 67 R. norvegicus. Our findings indicate that both R. norvegicus and R. rattus are host of DEC and, at lower prevalence, S. enterica, highlighting the importance of rodents as potential sources of pathogenic agents for humans.

Evidence of multiple intraspecific transmission routes for Leptospira acquisition in Norway rats (Rattus norvegicus).

Infectious diseases frequently have multiple potential routes of intraspecific transmission of pathogens within wildlife and other populations. For pathogens causing zoonotic diseases, knowing whether these transmission routes occur in the wild and their relative importance, is critical for understanding maintenance, improving control measures and ultimately preventing human disease. The Norway rat (Rattus norvegicus) is the primary reservoir of leptospirosis in the urban slums of Salvador, Brazil. There is biological evidence for potentially three different transmission routes of leptospire infection occurring in the rodent population. Using newly obtained prevalence data from rodents trapped at an urban slum field site, we present changes in cumulative risk of infection in relation to age-dependent transmission routes to infer which intra-specific transmission routes occur in the wild. We found that a significant proportion of animals leave the nest with infection and that the risk of infection increases throughout the lifetime of Norway rats. We did not observe a significant effect of sexual maturity on the risk of infection. In conclusion, our results suggest that vertical and environmental transmission of leptospirosis both occur in wild populations of Norway rats.

Factors affecting carriage and intensity of infection of Calodium hepaticum within Norway rats (Rattus norvegicus) from an urban slum environment in Salvador, Brazil.

Urban slum environments in the tropics are conducive to the proliferation and the spread of rodent-borne zoonotic pathogens to humans. Calodium hepaticum (Brancroft, 1893) is a zoonotic nematode known to infect a variety of mammalian hosts, including humans. Norway rats (Rattus norvegicus) are considered the most important mammalian host of C. hepaticum and are therefore a potentially useful species to inform estimates of the risk to humans living in urban slum environments. There is a lack of studies systematically evaluating the role of demographic and environmental factors that influence both carriage and intensity of infection of C. hepaticum in rodents from urban slum areas within tropical regions. Carriage and the intensity of infection of C. hepaticum were studied in 402 Norway rats over a 2-year period in an urban slum in Salvador, Brazil. Overall, prevalence in Norway rats was 83% (337/402). Independent risk factors for C. hepaticum carriage in R. norvegicus were age and valley of capture. Of those infected the proportion with gross liver involvement (i.e. >75% of the liver affected, a proxy for a high level intensity of infection), was low (8%, 26/337). Sixty soil samples were collected from ten locations to estimate levels of environmental contamination and provide information on the potential risk to humans of contracting C. hepaticum from the environment. Sixty percent (6/10) of the sites were contaminated with C. hepaticum. High carriage levels of C. hepaticum within Norway rats and sub-standard living conditions within slum areas may increase the risk to humans of exposure to the infective eggs of C. hepaticum. This study supports the need for further studies to assess whether humans are becoming infected within this community and whether C. hepaticum is posing a significant risk to human health.

Effects of height and load weight on shoulder muscle work during overhead lifting task.

Few musculoskeletal models are available to assess shoulder deeper muscle demand during overhead lifting tasks. Our objective was to implement a musculoskeletal model to assess the effect of lifting height and load on shoulder muscle work. A musculoskeletal model scaled from 15 male subjects was used to calculate shoulder muscle work during six lifting tasks. Boxes containing three different loads (6, 12 and 18 kg) were lifted by the subjects from the waist to shoulder or eye level. After optimisation of the maximal isometric force of the model's muscles, the bio-fidelity of the model was improved by 19%. The latter was able to reproduce the subjects' lifting movements. Mechanical work of the rotator cuff muscles, upper trapezius and anterior deltoid was increased with lifting load and height augmentation. In conclusion, the use of a musculoskeletal model validated by electromyography enabled to evaluate the muscle demand of deep muscles during lifting tasks.

Host-parasite biology in the real world: the field voles of Kielder.

Research on the interactions between the field voles (Microtus agrestis) of Kielder Forest and their natural parasites dates back to the 1930s. These early studies were primarily concerned with understanding how parasites shape the characteristic cyclic population dynamics of their hosts. However, since the early 2000s, research on the Kielder field voles has expanded considerably and the system has now been utilized for the study of host-parasite biology across many levels, including genetics, evolutionary ecology, immunology and epidemiology. The Kielder field voles therefore represent one of the most intensely and broadly studied natural host-parasite systems, bridging theoretical and empirical approaches to better understand the biology of infectious disease in the real world. This article synthesizes the body of work published on this system and summarizes some important insights and general messages provided by the integrated and multidisciplinary study of host-parasite interactions in the natural environment.

The abundance threshold for plague as a critical percolation phenomenon.

Percolation theory is most commonly associated with the slow flow of liquid through a porous medium, with applications to the physical sciences. Epidemiological applications have been anticipated for disease systems where the host is a plant or volume of soil, and hence is fixed in space. However, no natural examples have been reported. The central question of interest in percolation theory, the possibility of an infinite connected cluster, corresponds in infectious disease to a positive probability of an epidemic. Archived records of plague (infection with Yersinia pestis) in populations of great gerbils (Rhombomys opimus) in Kazakhstan have been used to show that epizootics only occur when more than about 0.33 of the burrow systems built by the host are occupied by family groups. The underlying mechanism for this abundance threshold is unknown. Here we present evidence that it is a percolation threshold, which arises from the difference in scale between the movements that transport infectious fleas between family groups and the vast size of contiguous landscapes colonized by gerbils. Conventional theory predicts that abundance thresholds for the spread of infectious disease arise when transmission between hosts is density dependent such that the basic reproduction number (R(0)) increases with abundance, attaining 1 at the threshold. Percolation thresholds, however, are separate, spatially explicit thresholds that indicate long-range connectivity in a system and do not coincide with R(0) = 1. Abundance thresholds are the theoretical basis for attempts to manage infectious disease by reducing the abundance of susceptibles, including vaccination and the culling of wildlife. This first natural example of a percolation threshold in a disease system invites a re-appraisal of other invasion thresholds, such as those for epidemic viral infections in African lions (Panthera leo), and of other disease systems such as bovine tuberculosis (caused by Mycobacterium bovis) in badgers (Meles meles).

Mycobacterium microti tuberculosis in its maintenance host, the field vole (Microtus agrestis): characterization of the disease and possible routes of transmission.

The field vole (Microtus agrestis) is a known maintenance host of Mycobacterium microti. Previous studies have shown that infected animals develop tuberculosis. However, the disease is also known in cats and is sporadically reported from humans and other mammalian species. We examined trapped field voles from an endemic area, using a range of diagnostic approaches. These confirmed that a combination of gross and histological examination with culture is most appropriate to identify the true prevalence of the disease, which was shown to be more than 13% at times when older animals that have previously been shown to be more likely to develop the disease dominate the population. The thorough pathological examination of diseased animals showed that voles generally develop systemic disease with most frequent involvement of spleen and liver, followed by skin, lymph nodes, and lungs. The morphology of the lesions was consistent with active disease, and their distribution suggested skin wounds or oral and/or aerogenic infection as the main portal of entry. The demonstration of mycobacteria in open skin lesions, airways, and salivary glands indicated bacterial shedding from the skin and with sputum and saliva. This suggests not only the environment but also direct contact and devouring as likely sources of infection.

The interplay of fatigue dynamics and task achievement using optimal control predictive simulation.

Predictive simulation of human motion could provide insight into optimal techniques. In repetitive or long-duration tasks, these simulations must predict fatigue-induced adaptation. However, most studies minimize cost function terms related to actuator activations, assuming it minimizes fatigue. An additional modeling layer is needed to consider the previous use of muscles to reveal adaptive strategies to the decreased force production capability. Here, we propose interfacing Xia's three-compartment fatigue dynamics model with rigid-body dynamics. A stabilization invariant was added to Xia's model. We simulated the maximum repetition of dumbbell biceps curls as an optimal control problem (OCP) using direct multiple shooting. We explored three cost functions (minimizing torque, fatigue, or both) and two OCP formulations (full-horizon and sliding-horizon approaches). We adapted Xia's model by adding a stabilization invariant coefficients S=105 for direct multiple shooting. Sliding-horizon OCPs achieved 20 to 21 repetitions. The kinematic strategy slowly deviated from a plausible dumbbell lifting task to a swinging strategy as fatigue onset increasingly compromised the humerus to remain vertical. In full-horizon OCPs, the latter kinematic strategy was used over the whole motion, resulting in 32 repetitions. We showed that sliding-horizon OCPs revealed a reactive strategy to fatigue when only torque was included in the cost function, whereas an anticipatory strategy was revealed when the fatigue term was included in the cost function. Overall, the proposed approach has the potential to be a valuable tool in optimizing performance and helping reduce fatigue-related injuries in a variety of fields.

Is an ellipsoid surface suitable to model the scapulothoracic sliding plane?

Closed loop kinematic chain approaches are commonly used to assess scapular kinematics but with heterogeneous ellipsoid calibration procedures. This study aimed to assess whether an ellipsoid surface can model the scapulothoracic sliding plane and determine the optimal number of static poses to calibrate the ellipsoid parameters. An intracortical pin with a rigid cluster of four reflective markers was inserted into the left scapular spine of two healthy males (P1 and P2). They performed arm elevations, internal rotations, ball throwing, hockey shooting, and eating movements. Ellipsoid radii and center location were functionally calibrated for each participant and each movement, either based on all frames of a movement or based on a reduced number of frames (from 3 to 200 equally position-distributed frames). Across both participants and all movements, ellipsoid radii varied up to 10.2 cm, 3.9 cm, and 18.4 cm in the antero-posterior, medio-lateral, and cranio-caudal directions, respectively. When all frames of a movement were considered for calibration, the median scapula-to-ellipsoid distance was, on average, 0.52 mm and 0.38 mm for P1 and P2, respectively. When only five frames were considered for ellipsoid calibration, the scapula-to-ellipsoid median distance slightly increased with 0.57 mm and 0.47 mm for P1 and P2, respectively. To conclude, this study highlights that an ellipsoid surface may effectively be appropriate to model the scapulothoracic sliding plane, especially when the calibration is functional, participant- and movement-specific. Furthermore, the number of poses required for the ellipsoid calibration can be reduced to five, minimizing the experimental cost.

Increased migration in host-pathogen metapopulations can cause host extinction.

There are at least two potentially counteracting effects of migration in host-pathogen metapopulations. On the one hand increased migration leads to increased colonization of empty habitats by healthy hosts; on the other hand migrants can carry infectious diseases to susceptible populations. Earlier metapopulation models have found that the beneficial effects of increasing migration (reduced infection) are likely to dominate, and a general recommendation for managers of endangered metapopulations has been to increase connectivity between habitat patches. We extend the model framework to simultaneously allow for (1) Allee effects in host colonization rate, (2) spillover of pathogens from a second host species, and (3) differential colonization success by infected and healthy hosts. We find that the dynamics of a host-pathogen system can be highly sensitive to increased migration rates. Allee effects make host populations vulnerable to spillover of pathogens from other hosts, and metapopulation extinction can emerge from seemingly stable situations of endemic coexistence. Increasing connectivity in endangered metapopulations can be a risky management action unless the details of the biology of the host-pathogen system are known.

The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host.

AIMS: To investigate the prevalence and temporal patterns of antimicrobial resistance in wild rodents with no apparent exposure to antimicrobials. METHODS AND RESULTS: Two sympatric populations of bank voles and wood mice were trapped and individually monitored over a 2- year period for faecal carriage of antimicrobial-resistant Escherichia coli. High prevalences of ampicillin-, chloramphenicol-, tetracycline- and trimethoprim-resistant E. coli were observed. A markedly higher prevalence of antimicrobial-resistant E. coli was found in wood mice than in bank voles, with the prevalence in both increasing over time. Superimposed on this trend was a seasonal cycle with a peak prevalence of resistant E. coli in mice in early- to mid-summer and in voles in late summer and early autumn. CONCLUSIONS: These sympatric rodent species had no obvious contact with antimicrobials, and the difference in resistance profiles between rodent species and seasons suggests that factors present in their environment are unlikely to be drivers of such resistance. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that rodents may represent a reservoir of antimicrobial-resistant bacteria, transmissible to livestock and man. Furthermore, such findings have implications for human and veterinary medicine regarding antimicrobial usage and subsequent selection of antimicrobial-resistant organisms.

Closed-loop multibody kinematic optimization coupled with double calibration improves scapular kinematic estimates in asymptomatic population.

Non-invasive methods still need to better estimate scapular kinematics because of soft tissue artifact issue. This study aimed to develop and assess new procedures to estimate scapular kinematics by combining closed kinematic chain optimization and double calibration. Sixteen healthy volunteers performed static postures mimicking analytical and daily living movements. Scapulo-thoracic angles were computed either with a scapula locator (Ref), or with a closed-loop multibody kinematic optimization (Ell) or with double calibration involving linear (DClin), exponential (DCexp) or logarithmic (DClog) correction. Double calibration corrections enforced scapulo-thoracic angles to be the same than those measured with Ref at the end of the movement performed. DClin and DClog significantly (p < 0.01) reduced scapulo-thoracic misorientation for at least the second third of the movement with averaged improvement ranging from 9° to 32°. Moreover, for arm elevation in the sagittal plane, internal rotations and mimicking hair combing, the beneficial effect of DClin and DClog propagates up to half of the movement. To conclude, when a kinematic chain is required, coupling double calibration (using either linear or logarithmic correction), to a closed-loop multibody kinematic optimization is an efficient and fast method in regard with improvement in scapular kinematic estimates in healthy population.

Influence of glenohumeral joint muscle insertion on moment arms using a finite element model.

Accurate muscle geometry is essential to estimate moment arms in musculoskeletal models. Given the complex interactions between shoulder structures, we hypothesized that finite element (FE) modelling is suitable to obtain physiological muscle trajectory. A FE glenohumeral joint model was developed based on medical imaging. Moment arms were computed and compared to literature and MRI-based estimation. Our FE model produces moment arms consistent with the literature and with MRI data (max 17 mm differences). The inferior and superior fibres of a same muscle can have opposite action; predictions of moment arms are sensitive to muscle insertion (up to 20 mm variation).

Sensitivity of Shoulder Musculoskeletal Model Predictions to Muscle-Tendon Properties.

OBJECTIVE: While the sensitivity of estimated muscle forces to muscle-tendon properties is well documented for the lower limbs, little is known about the shoulder and upper limbs. The purpose of this study was to assess the sensitivity of estimated shoulder muscle forces and scapulohumeral joint force to muscle-tendon properties. METHODS: One healthy male participant performed arm flexions and simulated throwing maneuvers. Kinematics were recorded using intra-cortical pins. Muscle forces were estimated using static optimization with the generic delft shoulder and elbow in OpenSim, and scapulohumeral joint forces were calculated from the estimated forces. Then, variations from -25% to +25% of the nominal values of the tendon slack length, the optimal fiber length, the maximal isometric force, and the pennation angle were applied to the musculoskeletal model to compute affected muscle forces and scapulohumeral joint force. RESULTS: The variations in muscle-tendon properties led to changes up to 9.6 N or 174% in the muscle nominal forces. The more sensitive muscles were those that produced the greatest force: the rotator cuff muscles and the prime movers specific to the task. Among the four muscle-tendon properties, the maximal isometric force and the optimal fiber length had the greatest influence on the muscle force variability. Glenohumeral force was slightly influenced by muscle-tendon properties (<8%). CONCLUSION: Generic models (i.e., those without personalization of muscle-tendon properties) can lead to misinterpretations of muscle force. Efforts should focus on the maximal isometric force and the optimal fiber length of the rotator cuff muscles and prime movers.

Deterministic processes structure bacterial genetic communities across an urban landscape.

Land-use change is predicted to act as a driver of zoonotic disease emergence through human exposure to novel microbial diversity, but evidence for the effects of environmental change on microbial communities in vertebrates is lacking. We sample wild birds at 99 wildlife-livestock-human interfaces across Nairobi, Kenya, and use whole genome sequencing to characterise bacterial genes known to be carried on mobile genetic elements (MGEs) within avian-borne Escherichia coli (n = 241). By modelling the diversity of bacterial genes encoding virulence and antimicrobial resistance (AMR) against ecological and anthropogenic forms of urban environmental change, we demonstrate that communities of avian-borne bacterial genes are shaped by the assemblage of co-existing avian, livestock and human communities, and the habitat within which they exist. In showing that non-random processes structure bacterial genetic communities in urban wildlife, these findings suggest that it should be possible to forecast the effects of urban land-use change on microbial diversity.

Parasite interactions in natural populations: insights from longitudinal data.

The physiological and immunological state of an animal can be influenced by current infections and infection history. Consequently, both ongoing and previous infections can affect host susceptibility to another parasite, the biology of the subsequent infection (e.g. infection length) and the impact of infection on host morbidity (pathology). In natural populations, most animals will be infected by a succession of different parasites throughout the course of their lives, with probably frequent concomitant infections. The relative timing of different infections experienced by a host (i.e. the sequence of infection events), and the effects on factors such as host susceptibility and host survival, can only be derived from longitudinal data on individual hosts. Here we review some of the evidence for the impact of co-infection on host susceptibility, infection biology and pathology focusing on insights obtained from both longitudinal studies in humans and experiments that explicitly consider the sequence of infection. We then consider the challenges posed by longitudinal infection data collected from natural populations of animals. We illustrate their usefulness using our data of microparasite infections associated with field vole (Microtus agrestis) populations to examine impacts on susceptibility and infection length. Our primary aim is to describe an analytical approach that can be used on such data to identify interactions among the parasites. The preliminary analyses presented here indicate both synergistic and antagonistic interactions between microparasites within this community and emphasise that such interactions could have significant impacts on host-parasite fitness and dynamics.

Tuberculosis (Mycobacterium microti) in wild field vole populations.

Vole tuberculosis (TB; Mycobacterium microti) is an understudied endemic infection. Despite progressing slowly, it causes severe clinical pathology and overt symptoms in its rodent host. TB was monitored for 2 years in wild field voles in Kielder Forest, UK. The prevalence of characteristic cutaneous TB lesions was monitored longitudinally at 4 sites, with individuals live-trapped and repeatedly monitored. A prevalence of 5.2% of individuals with lesions was recorded (n=2791). In a cross-sectional study, 27 sites were monitored bi-annually, with TB assessed by post-mortem examination for macroscopic lesions, and by culture and histopathology. Seventy-nine voles (10.78%; n=733) were positive for mycobacteria, with the highest prevalence in spring (13.15%; n=327). TB prevalence varied, with between 0% and 50% of voles infected per site. Prevalence increased with age (mass), and apparent seasonality was due to a higher proportion of older animals in spring. Survival analysis supported this result, with cutaneous lesions only manifesting in the advanced stages of infection, and therefore only being found on older voles. The body condition of individuals with lesions declined at the time when the lesion was first recorded, when compared to individuals without lesions, suggesting there may be an acute phase of infection during its advanced stage. Although predicted survival following the appearance of a cutaneous lesion was lower than for uninfected individuals, this was not significant.

Empirical assessment of a threshold model for sylvatic plague.

Plague surveillance programmes established in Kazakhstan, Central Asia, during the previous century, have generated large plague archives that have been used to parameterize an abundance threshold model for sylvatic plague in great gerbil (Rhombomys opimus) populations. Here, we assess the model using additional data from the same archives. Throughout the focus, population levels above the threshold were a necessary condition for an epizootic to occur. However, there were large numbers of occasions when an epizootic was not observed even though great gerbils were, and had been, abundant. We examine six hypotheses that could explain the resulting false positive predictions, namely (i) including end-of-outbreak data erroneously lowers the estimated threshold, (ii) too few gerbils were tested, (iii) plague becomes locally extinct, (iv) the abundance of fleas was too low, (v) the climate was unfavourable, and (vi) a high proportion of gerbils were resistant. Of these, separate thresholds, fleas and climate received some support but accounted for few false positives and can be disregarded as serious omissions from the model. Small sample size and local extinction received strong support and can account for most of the false positives. Host resistance received no support here but should be subject to more direct experimental testing.

Effects of movement for estimating the hip joint centre.

Determination of the hip joint centre (HJC) using a functional approach requires access to the kinematics of various body postures. The present study aimed to determine the combined impact of the nature of the movement, its type and the number of cycles, on the accuracy of HJC estimation. Kinematics noise was modelled based on the deformation of hip and thigh clusters of seven subjects, while perfect ball-and-socket movements (used as reference) were calculated based on the movements of one of the subjects. The noise added to the reference kinematics allowed the simulation of 27 tests. Errors were defined as the Euclidean distance between the estimated and the reference HJC. A nested ANOVA and a multiple comparison procedures were performed on all errors. A test including 10 cycles of three different types of limited movements (flexion-extension, abduction-adduction and circumduction) yielded the greatest accuracy for estimating HJC (4.0+/-1.3 mm). Combining different types of movements allowed improving the accuracy. Given that noise increases as a function of the range of a motion, limited movements proved to be the most accurate; however, 10 cycles were required to achieve such results. For trials involving a single cycle, a large movement proved more efficient.