Biology subjects

Shapiro, J. T.

Publications and source records attributed to Shapiro, J. T..

6 recordsLinked to original sources

bioRxiv2026

Case report of unusual mortality of Egyptian fruit bat (Rousettus aegyptiacus) in northern Cyprus

We report an unusual mortality event affecting the isolated Egyptian fruit bat (Rousettus aegyptiacus) population in northern Cyprus, combining clinical admissions, microbiological findings, and roost surveys to assess magnitude and potential drivers. From January to June 2025, the Cyprus Wildlife Research Institute (CWRI) Wildlife Hospital received an unprecedented surge in admissions with 12 individuals (versus sporadic admissions in prior years), with high acute mortality: most bats arrived moribund and died within 12-24 hours. Clinical records noted localized purulent lesions and abscesses in a substantial fraction of cases. Bacteriological culture and PCR assays recovered Staphylococcus aureus from abscesses and skin swab samples in multiple individuals; isolates exhibited susceptibility to tested antibiotics. Necropsy sampling confirmed viable S. aureus in several specimens despite prolonged storage. Concurrent targeted surveys of ten known roosts in Feb-Mar 2026 documented marked declines at multiple historical sites, including reductions from hundreds to single-digit counts at formerly large colonies and the complete absence of bats at multiple roosts. No clear evidence of recent human disturbance, extreme weather anomalies, or reduced food availability was found; shotgun cartridges from historical hunting were present, but no direct anthropogenic cause was apparent. While S. aureus infections--seasonally concentrated in winter--are consistent with observed lesions and may have contributed to morbidity and mortality, causality for the population-level declines remains unknown, and other factors (toxins, unassessed pathogens, multi-factor stressors) cannot be excluded. Given the genetic isolation and conservation significance of the Cyprus Egyptian fruit bat population, these findings are concerning. We recommend urgent, coordinated longitudinal population monitoring, expanded pathogen surveillance including whole-genome sequencing of S. aureus isolates, toxicological screening, and development of a species recovery plan incorporating emergency response, habitat protection, and public outreach.

ecology↗

bioRxiv2026

Potential for real-time health and welfare monitoring in experimental rabies infection in red fox (Vulpes vulpes) using implants

Monitoring and improving animal health and welfare is a pressing need. Technological advances are increasing our ability to do so in a range of settings but currently, there are limited uses in experimental settings for less common model animals. Red foxes (Vulpes vulpes) are maintained by the French National Agency for Food, Environmental, and Occupational Health and Safety (ANSES) for regulatory and research purposes, primarily related to its role as a European Union and French Reference Laboratory for rabies and Echinococcus spp. In 2022, four foxes were surgically fitted with internal implants that recorded body temperature and activity levels and subsequently inoculated with rabies virus (RABV). Retrospectively, we tested the potential of these two variables to provide an early warning for the onset of rabies symptoms. We applied two anomaly detection algorithms (Shewhart and EWMA) with varying confidence levels to the data sets and compared how early the different models could detect significant changes while limiting false alarms during the calibration period. We hypothesized that body temperatures would rise significantly and foxes would significantly alter their activity levels at the beginning of infection, both at an earlier stage than is detectable through direct observation. We found that foxes significantly changed their activity during infection. We were best able to detect these changes using the EWMA algorithm, in some cases producing consecutive alarms up to two weeks before the death of an animal, while limiting false alarms. We found no evidence of fever in any of the infected foxes and body temperature did not appear to be a reliable indicator of foxes health. While here we applied our methods to a particularly severe and rarely implemented model with a very small sample size, this proof of concept illustrates the potential of these methods for a wide range of other situations that would benefit from similar long-term monitoring, including experimental protocols with milder clinical signs and routine monitoring for unexpected declines in health or welfare.

animal behavior and cognition↗

bioRxiv2023

Urbanisation generates multiple trait syndromes for terrestrial taxa worldwide

Cities can host significant biological diversity. Yet, urbanisation leads to the loss of habitats and, potentially, to local extinctions. Understanding how multiple taxa respond to urbanisation globally is essential to promote and conserve biodiversity in cities and surrounding landscapes. Using a dataset with site-level occurrence and trait data of 5302 species from six terrestrial fauna taxonomic groups across 379 cities on 6 continents, we show that urbanisation produces taxon-specific changes in trait composition, with traits related to reproductive strategy consistently showing the strongest response. The effect of urbanisation on community trait composition is strongest at the largest spatial scale considered, and more closely linked to landscape composition (% urban) than arrangement (aggregation), although latitude and climatic variables remain a stronger influence. This study did not find evidence in support of a global urban taxa syndrome, but instead we suggest that there are four general urban trait syndromes, with resources associated with reproduction and diet likely to be driving patterns in traits associated with mobility and body size. Functional diversity measures showed a wide range of responses, leading to a shift in trait space that is most likely driven by the distribution and abundance of critical resources, and the urban trait syndrome displayed by individual species within a community. Further research is required to understand the interactions between the four general urban trait syndromes, resource distribution and abundance and changes in functional diversity of taxa at different spatial and temporal scales. Maximising opportunities to support species within taxa groups with different urban trait syndromes should be pivotal in conservation and management programmes within and among cities. This will reduce the likelihood of biotic homogenisation at the taxa level, and helps ensure that urban environments have the ecological capacity to respond to challenges such as climate change, further habitat fragmentation and loss, and other disruptions. These actions are critical if we are to reframe the role of cities in global biodiversity loss.

ecology↗

bioRxiv2022

Multilayer Networks of Plasmid Genetic Similarity Reveal Potential Pathways of Gene Transmission

Antimicrobial resistance (AMR) is a major threat to public health. Plasmids are principal vectors of antimicrobial resistance genes, greatly contributing to their spread and mobility across hosts. Nevertheless little is known about the dynamics of plasmid genetic exchange across animal hosts. The cow rumen ecosystem is an excellent model system because it hosts diverse plasmid communities which interact and exchange genes. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data-set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise genetic similarity between plasmids serving as a signature for past genetic exchange to identify potential routes and mechanisms of gene transmission within and between cows. The transmission network was dominated by links between cows. Modularity analysis unraveled a major cross-cow transmission pathway with additional small pathways. Plasmid functions influenced network structure: plasmids containing mobility genes were more connected; those with the same AMR genes formed their own modules. We find signatures of gene superspreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population is likely to reach all cows. Finally, we showed that link weights contain a non-random signature for the mechanisms of gene transmission allowing us to differentiate between dispersal and genetic exchange. These results provide insights into the mechanisms by which genes, including those providing AMR, spread across animal hosts.

ecology↗

bioRxiv2019

Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards

Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between ward patient transfers (or connectivity) impact hospital AMR can help optimize antibiotic stewardship and infection control strategies. Here, we used metapopulation ecology to explain variations in infection incidences of 17 ESKAPE pathogen variants in a network of 357 hospital wards. Multivariate models identified the strongest influence of ward-level antibiotic use on more resistant variants, and of connectivity on nosocomial species and carbapenem-resistant variants. Pairwise associations between infection incidence and the consumption of specific antibiotics were significantly stronger when such associations represented a priori AMR selection, suggesting that AMR evolves within the network. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data establish that both antibiotic use and connectivity measurably influence hospital AMR and provide a ranking of key antibiotics by their impact on AMR.

ecology↗

bioRxiv2019

Response of Bat Activity to Land-Cover and Land-Use Change in Savannas is Scale-, Season-, and Guild-Specific

Tropical savannas are biomes of global importance that are under severe pressure from anthropogenic change, including land-cover and land-use change. Bats, the second-most diverse group of mammals, are critical to ecosystem functioning, but may be vulnerable to such anthropogenic stresses. However, there is little information on the response of savanna bats to land-cover and land-use change, especially in Africa. This limits our ability to develop conservation strategies for bats and maintain the ecosystem functions and services they provide in this biome. Using acoustic monitoring, we measured how guild-specific (aerial, edge, and clutter forager) bat activity responded to both fine-scale metrics of vegetation structure and landscape-scale metrics of land-cover composition and configuration across the wet and dry seasons in a savanna in southern Africa undergoing rapid land-cover and land-use change. We found that all three guilds responded more strongly to landscape metrics than fine-scale vegetation structure, although the specific metrics varied between guilds. Aerial and edge bats responded most strongly to the percent savanna cover and savanna fragmentation in both seasons while clutter bats responded to percent rural cover in the wet season and percent water cover in the dry. All three guilds responded more strongly to the landscape in the dry season than the wet season. Our results show it is possible to conserve bats, and the ecosystem services they can provide, in savannas undergoing anthropogenic land-use and land-cover change but strategies to do so must consider foraging guild, large spatial scales, and seasonal variation in bat activity.\n\nHighlightsO_LIBats in savannas respond to land-cover and land-use change on large spatial scales\nC_LIO_LILandscape had a greater influence on bat activity in the dry season than the wet\nC_LIO_LIAerial and edge forager activity responded to savanna cover and fragmentation\nC_LIO_LIClutter forager activity was best explained by rural and water cover\nC_LIO_LIMinimizing fragmentation and maintaining water promotes bat activity in modified savannas\nC_LI

ecology↗