Early evaluation of the Food and Drug Administration (FDA) guidance on antimicrobial use in food animals on antimicrobial resistance trends reported by the National Antimicrobial Resistance Monitoring System (2012-2019).

Antimicrobial resistance (AMR) is one of the biggest challenges to global public health. To address this issue in the US, governmental agencies have implemented system-wide guidance frameworks and recommendations aimed at reducing antimicrobial use. In particular, the Food and Drug Administration (FDA) prohibited the extra-label use of cephalosporins in food animals in 2012 and issued the guidance for industry (GFI) #213 about establishing a framework to phase out the use of all medically relevant drugs for growth promotion in 2012. Also in 2015, the FDA implemented veterinary feed directive (VFD) drug regulations (GFI# 120) to control the use of certain antimicrobials. To assess the potential early effects of these FDA actions and other concurrent antimicrobial stewardship actions on AMR in the food chain, we compared the patterns of the phenotypic (minimum inhibitory concentration (MIC) and percentage of resistance) and genotypic resistances for selected antimicrobials before and after 2016 across different enteric pathogen species, as reported by the National Antimicrobial Resistance Monitoring System (NARMS). Most of the antimicrobials analyzed at the phenotypic level followed a downward trend in MIC after implementing the guidance. Although, most of those changes were less than one 1-fold dilution. On the other hand, compared to MIC results, the results based on phenotypic resistance prevalence evidenced higher differences in both directions between the pre- and post-guidance implementation period. Also, we did not find relevant differences in the presence of AMR genes between pre- and post-VFD drug regulations. We concluded that the FDA guidance on antimicrobial use has not led to substantial reductions in antimicrobial drug resistance yet.

Corrigendum: The Potential Distribution of Pythium insidiosum in the Chincoteague National Wildlife Refuge, Virginia.

[This corrects the article DOI: 10.3389/fvets.2021.640339.].

A review of epidemiological models of Clostridioides difficile transmission and control (2009-2021).

Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021. Models have underscored the importance of asymptomatic colonized patients in maintaining transmission in health-care settings. Infection control, antimicrobial stewardship, active testing, and vaccination have often been evaluated in models. Despite active testing and vaccination being not currently implemented, they are the most commonly evaluated interventions. Some aspects of C. difficile transmission, such community transmission and interventions in health-care settings other than in acute-care hospitals, remained less evaluated through modeling.

Whole Genome or Single Genes? A Phylodynamic and Bibliometric Analysis of PRRSV.

Diversity, ecology, and evolution of viruses are commonly determined through phylogenetics, an accurate tool for the identification and study of lineages with different pathological characteristics within the same species. In the case of PRRSV, evolutionary research has divided into two main branches based on the use of a specific gene (i.e., ORF5) or whole genome sequences as the input used to produce the phylogeny. In this study, we performed a review on PRRSV phylogenetic literature and characterized the spatiotemporal trends in research of single gene vs. whole genome evolutionary approaches. Finally, using publicly available data, we produced a Bayesian phylodynamic analysis following each research branch and compared the results to determine the pros and cons of each particular approach. This study provides an exploration of the two main phylogenetic research lines applied for PRRSV evolution, as well as an example of the differences found when both methods are applied to the same database. We expect that our results will serve as a guidance for future PRRSV phylogenetic research.

Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia.

Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010-2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.

Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus.

Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.

Impact of changes of horse movement regulations on the risks of equine infectious anemia: A risk assessment approach.

Equine infectious anemia virus (EIAV) is a transboundary disease affecting a large number of equines worldwide. In this study, we assessed the transmission risk of EIAV in Rio Grande do Sul, Brazil. Serum samples from 1010 animals from 341 farms were initially analyzed using agar gel immunodiffusion to detect viral antibodies, and no antibody-positive animals were found. A risk assessment stochastic model was applied to generate the expected number of potential infections per month and to estimate the time to new infections. Our results estimated 6.5 months as the interval for new infections in the worst-case scenario. Among the variables evaluated, the number of transported animals and the test sensitivity influenced the model the most. These results were then used to revisit the impact of EIAV control regulations, which triggered a change in the diagnostic testing required for animal movement, in which the validity of a negative test for EIAV was extended from 60 to 180 days. Finally, revisiting the annual average of infected farms before and after the new regulation, the number of infected farms increased pre-implementation, and then, the number of culled animals increased, which should impact future EIAV incidence in this region. Our results demonstrated the importance of constant reviews of disease control programs and provided quantitative-based knowledge for decision-makers in official veterinary services.

The Potential Distribution of Pythium insidiosum in the Chincoteague National Wildlife Refuge, Virginia.

Pythium insidiosum is a widespread pathogen that causes pythiosis in mammals. Recent increase in cases reported in North America indicates a need to better understand the distribution and persistence of the pathogen in the environment. In this study, we reconstructed the distribution of P. insidiosum in the Chincoteague National Wildlife Refuge, located on Assateague Island, Virginia, and based on 136 environmental water samples collected between June and September of 2019. The Refuge hosts two grazing areas for horses, also known as the Chincoteague Ponies. In the past 3 years, 12 horses have succumbed to infection by P. insidiosum. Using an ecological niche model framework, we estimated and mapped suitable areas for P. insidiosum throughout the Refuge. We found P. insidiosum throughout much of the study area. Our results showed significant monthly variation in the predicted suitability, where the most influential environmental predictors were land-surface water and temperature. We found that June, July, and August were the months with the highest suitability for P. insidiosum across the Refuge, while December through March were less favorable months. Likewise, significant differences in suitability were observed between the two grazing areas. The suitability map provided here could also be used to make management decisions, such as monitoring horses for lesions during high risk months.

Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States.

Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production systems (external). Here, we examined the local and external dissemination dynamics of PRRSV and the processes facilitating its spread in three production systems. Overall, PRRSV genetic diversity has declined since 2018, while phylodynamic results support frequent external transmission. We found that PRRSV dissemination predominantly occurred mostly through transmission between farms of different production companies for several months, especially from November until May, a timeframe already established as PRRSV season. Although local PRRSV dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms), an important flux of PRRSV dissemination also occurred in the opposite direction, from finisher to sow and nursery farms, highlighting the importance of downstream farms as sources of the virus. Our results also showed that farms with pig densities of 500 to 1,000 pig/km2 and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to be infected by PRRSV, whereas farms at an elevation of 41 to 61 meters and surrounded by denser vegetation were less likely to be infected, indicating their role as dissemination barriers. In conclusion, our results demonstrate that external dissemination was intense, and reinforce the importance of farm proximity on PRRSV spread. Thus, consideration of farm location, geographic characteristics and animal densities across production systems may help to forecast PRRSV collateral dissemination.

Nairobi Sheep Disease Virus: A Historical and Epidemiological Perspective.

Nairobi Sheep Disease virus (NSDv) is a zoonotic and tick-borne disease that can cause over 90% mortality in small ruminants. NSDv has historically circulated in East Africa and has recently emerged in the Asian continent. Despite efforts to control the disease, some regions, mostly in warmer climates, persistently report disease outbreaks. Consequently, it is necessary to understand how environmental tolerances and factors that influence transmission may shed light on its possible emergence in other regions. In this study, we quantified the available literature of NSDv from which occurrence data was extracted. In total, 308 locations from Uganda, Kenya, Tanzania, Somalia, India, Sri Lanka and China were coupled with landscape conditions to reconstruct the ecological conditions for NSDv circulation and identify areas of potential disease transmission risk. Our results identified areas suitable for NSDv in Ethiopia, Malawi, Zimbabwe, Southeastern China, Taiwan, and Vietnam. Unsuitable areas included Democratic Republic of Congo, Zambia, and Southern Somalia. In summary, soil moisture, livestock density, and precipitation predispose certain areas to NSDv circulation. It is critical to investigate the epidemiology of NSDv in order to promote better allocation of resources to control its spread in regions that are more at risk. This will help reduce disease impact worldwide as climate change will favor emergence of such vector-borne diseases in areas with dense small ruminant populations.

Spatial distribution and spread potential of sixteen Leptospira serovars in a subtropical region of Brazil.

Leptospirosis is a bacterial disease that represents a major problem in animal and public health due to its high prevalence and widespread distribution. This zoonotic disease is most prevalent in tropical environments where conditions favour pathogen survival. The ecological preferences of Leptospira serovars are poorly understood, limiting our knowledge of where and when outbreaks can occur, which may result in misinformed prevention and control plans. While the disease can occur consistently in time and space in tropical regions, research on the ecology of leptospirosis remains limited in subtropical regions. This research gap regarding Leptospira ecology brings public and veterinary health problems, impacting local economies. To fill this gap of knowledge, we suggest to assess geographic and ecological features among Leptospira serovars in a subtropical area of Brazil where leptospirosis is endemic to (a) highlight environmental conditions that facilitate or limit Leptospira spread and survival and (b) reconstruct its geographic distribution. An ecological niche modelling framework was used to characterize and compare Leptospira serovars in both geographic and environmental space. Our results show that despite the geographic overlap exhibited by the different serovars assessed, we found ecological divergence among their occupied ecological niches. Ecological divergences were expressed as ranges of potential distributions and environmental conditions found suitably by serovar, Sejroe being the most asymmetric (<0.15). Most important predictors for the potential distribution of most serovars were soil pH (31.7%) and landscape temperature (24.2%). Identification of environmental preferences will allow epidemiologists to better infer the presence of a serovar based on the environmental characteristics of regions rather than inferences based solely on historical epidemiological records. Including geographic and ecological ranges of serovars also may help to forecast transmission potential of Leptospira in public health and the food animal practice.

Alternative reproductive adaptations predict asymmetric responses to climate change in lizards.

Anthropogenic climate change ranks among the major global-scale threats to modern biodiversity. Extinction risks are known to increase via the interactions between rapid climatic alterations and environmentally-sensitive species traits that fail to adapt to those changes. Accumulating evidence reveals the influence of ecophysiological, ecological and phenological factors as drivers underlying demographic collapses that lead to population extinctions. However, the extent to which life-history traits influence population responses to climate change remains largely unexplored. The emerging 'cul-de-sac hypothesis' predicts that reptilian viviparity ('live-bearing' reproduction), a 'key innovation' facilitating historical invasions of cold climates, increases extinction risks under progressively warming climates compared to oviparous reproduction - as warming advances polewards/mountainwards, historically cold-climates shrink, leading viviparous species to face demographic collapses. We present the first large-scale test of this prediction based on multiple lizard radiations and on future projections of climate-based ecological niche models. Viviparous species were found to experience stronger elevational range shifts (and potentially increased extinctions) in coming decades, compared to oviparous lizards. Therefore, our analyses support the hypothesis's fundamental prediction that elevational shifts are more severe in viviparous species, and highlight the role that life-history adaptations play in the responses of biodiversity to ongoing climate change.

The Macroecology of Chemical Communication in Lizards: Do Climatic Factors Drive the Evolution of Signalling Glands?

Chemical communication plays a pivotal role in shaping sexual and ecological interactions among animals. In lizards, fundamental mechanisms of sexual selection such as female mate choice have rarely been shown to be influenced by quantitative phenotypic traits (e.g., ornaments), while chemical signals have been found to potentially influence multiple forms of sexual and social interactions, including mate choice and territoriality. Chemical signals in lizards are secreted by glands primarily located on the edge of the cloacae (precloacal glands, PG) and thighs (femoral glands), and whose interspecific and interclade number ranges from 0 to > 100. However, elucidating the factors underlying the evolution of such remarkable variation remains an elusive endeavour. Competing hypotheses suggest a dominant role for phylogenetic conservatism (i.e., species within clades share similar numbers of glands) or for natural selection (i.e., their adaptive diversification results in deviating numbers of glands from ancestors). Using the prolific Liolaemus lizard radiation from South America (where PG vary from 0 to 14), we present one of the largest-scale tests of both hypotheses to date. Based on climatic and phylogenetic modelling, we show a clear role for both phylogenetic inertia and adaptation underlying gland variation: (i) solar radiation, net primary productivity, topographic heterogeneity and precipitation range have a significant effect on PG variation, (ii) humid and cold environments tend to concentrate species with a higher number of glands, (iii) there is a strong phylogenetic signal that tends to conserve the number of PG within clades. Collectively, our study confirms that the inertia of niche conservatism can be broken down by the need of species facing different selection regimes to adjust their glands to suit the demands of their specific environments.

Interpopulational and seasonal variation in the chemical signals of the lizard Gallotia galloti.

Communicative traits are strikingly diverse and may vary among populations of the same species. Within a population, these traits may also display seasonal variation. Chemical signals play a key role in the communication of many taxa. However, we still know far too little about chemical communication in some vertebrate groups. In lizards, only a few studies have examined interpopulational variation in the composition of chemical cues and signals and only one study has explored the seasonal effects. Here we sampled three subspecies of the Tenerife lizards (Gallotia galloti) and analyze the lipophilic fraction of their femoral gland secretions to characterize the potential interpopulational variation in the chemical signals. In addition, we assessed whether composition of these secretions differed between the reproductive and the non-reproductive season. We analyzed variations in both the overall chemical profile and the abundance of the two main compounds (cholesterol and vitamin E). Our results show interpopulational and seasonal differences in G. gallotia chemical profiles. These findings are in accordance with the high interpopulational variability of compounds observed in lizard chemical signals and show that their composition is not only shaped by selective factors linked to reproductive season.

Macroevolutionary diversification of glands for chemical communication in squamate reptiles.

Chemical communication plays a central role in social, sexual and ecological interactions among animals. However, the macroevolutionary diversification of traits responsible for chemical signaling remains fundamentally unknown. Most research investigating evolutionary diversification of glands responsible for the production of chemical signals has focused on arthropods, while its study among vertebrates remains neglected. Using a global-scale dataset covering > 80% (7,904 species) of the living diversity of lizards and snakes (squamates), we investigate rates, trajectories and phylogenetic patterns of diversification of their follicular glands for chemical communication. We observed these glands in 13.66% of species, that their expression has varying phylogenetic signal among lineages, and that the crown squamate ancestor lacked follicular glands, which therefore originated and diversified subsequently during their evolutionary history. Additionally, our findings challenge the longstanding view that within squamates the Iguania are visually oriented while Scleroglossa are chemically-oriented, given that Iguania doubles Scleroglossa in the frequency of glands. Our phylogenetic analyses identified stabilizing selection as the best model describing follicular gland diversification, and revealed high rates of disparity. We provide the first global-scale analysis investigating the diversification of one of the main forms of communication among reptiles, presenting a macroevolutionary angle to questions traditionally explored at microevolutionary scale.

Heterogeneous tempo and mode of evolutionary diversification of compounds in lizard chemical signals.

Important part of the multivariate selection shaping social and interspecific interactions among and within animal species emerges from communication. Therefore, understanding the diversification of signals for animal communication is a central endeavor in evolutionary biology. Over the last decade, the rapid development of phylogenetic approaches has promoted a stream of studies investigating evolution of communication signals. However, comparative research has primarily focused on visual and acoustic signals, while the evolution of chemical signals remains largely unstudied. An increasing interest in understanding the evolution of chemical communication has been inspired by the realization that chemical signals underlie some of the major interaction channels in a wide range of organisms. In lizards, in particular, chemosignals play paramount roles in female choice and male-male competition, and during community assembly and speciation. Here, using phylogenetic macro-evolutionary modeling, we show for the very first time that multiple compounds of scents for communication in lizards have diversified following highly different evolutionary speeds and trajectories. Our results suggest that cholesterol, α-tocopherol, and cholesta-5,7-dien-3-ol have been subject to stabilizing selection (Ornstein-Uhlenbeck model), whereas the remaining compounds are better described by Brownian motion modes of evolution. Additionally, the diversification of the individual compounds has accumulated substantial relative disparity over time. Thus, our study reveals that the chemical components of lizard chemosignals have proliferated across different species following compound-specific directions.

The sexual signals of speciation? A new sexually dimorphic Phymaturus species of the patagonicus clade from Patagonia Argentina.

Evolution is a multivariate process which, therefore, is expected to leave multiple recognizable signals after episodes of speciation. These signals express in the genome regardless of the mechanism driving speciation, and in a few or in multiple phenotypic traits when divergent selection has been implicated. In lineages that have undergone adaptive radiations (i.e. speciation accompanied by ecological diversification), the phenotypic signals of speciation can be substantially pronounced. In contrast, within non-adaptive radiations (i.e. lineage diversification with minimal ecological diversification linked to allopatric or parapatric species distributions), phenotypic signals of speciation can be minimal. The South American lizard genus Phymaturus is regarded as a candidate non-adaptive radiation given the tendency for non-overlapping distributions among its phenotypically and ecologically similar (i.e. niche conservatism) species. Thus, limited phenotypic divergence has evolved among closely related species. Within the patagonicus clade of the genus, sexual monochromatism is highly conserved, while sexual dichromatism is rare, and mostly negligible when observed. In this paper, we provide the description of a new sexually dimorphic and dichromatic species of this clade (Phymaturus camilae sp. nov.). This species is substantially isolated spatially and phylogenetically separated from P. ceii, P. delheyi and P. zapalensis, the most sexually dichromatic members of the clade. In addition, the new taxon was recently identified as a 'candidate new species' based on molecular (nuclear) phylogenetic evidence.

Zonificación sísmica de ciudades en México

En este trabajo se describe la experiencia de la Univerisdada Autónoma Metropolitana de la zonificación sísmica de ciudades de importancia media en la República Mexicana. La falta de información sismológica y geodinámica, tipicas de esta clase de localidades, hace necesario el uso de técnicas y criterios alternativos para desarrollar propuestas racionales para la zonificación sísmica, tal como se expone. Especial énfasis se hace en la organización de proyectos que involucra a los investigadores y profesionistas de cada localidad, lo que facilita la adopción de los resultados en los reglamentos de construcción y la integración de grupos locales de investigación que continúen el trabajo para mejorar las propuestas iniciales (AU)