Diversity of Staphylococcus aureus associated with mastitis from dairy cows in Rwanda.

OBJECTIVES: The objective of the present study was to examine the diversity of Staphylococcus aureus from mastitis milk samples of cows in Rwanda. METHODS: A total of 1080 quarter milk samples from 279 dairy cows were collected in 80 different farms from all five provinces of Rwanda. In total, 135 S. aureus isolates were obtained and subjected to genotyping (spa typing, DNA microarray, whole-genome sequencing (WGS)), antimicrobial susceptibility testing (AST) and phenotypic profiling by Fourier Transform Infrared (FTIR) spectroscopy (including capsular serotyping). RESULTS: Resistance to penicillin and/or tetracycline was most frequently observed. Ten sequence types (STs) (ST1, ST151, ST152, ST5477, ST700, ST7110, ST7983, ST7984, ST8320, ST97) belonging to seven clonal complexes (CCs) (CC1, CC130, CC152, CC3591, CC3666, CC705, CC97) were detected. The Panton-Valentine leukocidin (PVL) genes (lukF-PV/lukS-PV), the bovine leukocidin genes (lukM/lukF-P83) and the human and bovine toxic shock syndrome toxin gene tst-1 variants were detected. FTIR-based capsular serotyping showed CC-specific differences. Most CC97 (cap5 allele) isolates were primarily nonencapsulated (82%), whereas isolates of CC3591 and CC3666 (cap8 allele) were mostly encapsulated (86.4% and 57.8%, respectively). Our results underline the widespread global distribution of cattle-adapted CC97. CONCLUSION: The presence of CC3591 and CC3666 in bovine mastitis suggests an important role in cattle health and dairy production in Rwanda. The results of the present study support the need for a rigorous One-Health Surveillance program of the bovine-human interface.

First isolation and genotyping of pathogenic Leptospira spp. from Austria.

Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2-6 h and a real-time PCR targeting the lipL32 gene was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.

Diversity of Staphylococcus aureus isolated from nares of ruminants.

AIMS: To examine the diversity of Staphylococcus aureus isolated from nasal swabs of ruminants in Rwanda. METHODS AND RESULTS: A total of 454 nasal swabs from 203 cows, 170 goats, and 81 sheep were examined for the presence of S. aureus, and 30 S. aureus isolates were detected and characterized pheno- and genotypically. Resistance to penicillin and/or tetracycline was observed. The isolates were assigned to eight different spa types (t21057 (novel), t10103, t18853, t20842, t318, t355, t458, and t9432) belonging to six clonal complexes (CCs) (CC152, CC30, CC3591, CC3666, CC522, and CC97). Panton-Valentine leukocidin (PVL) genes (lukF-PV/lukS-PV), the bovine leukocidin genes (lukM/lukF-P83), and the human and bovine variants of the toxic shock syndrome toxin gene tst-1 variants were detected. CONCLUSION: These findings demonstrate that the nares of ruminants in Rwanda are colonized with mastitis-associated S. aureus, including lineages that are also carried by humans, underscoring the zoonotic risk, especially for livestock keepers. These results highlight the crucial importance of hygiene measures when handling livestock.

Data on SARS-CoV-2 events in animals: Mind the gap!

Current research on SARS-CoV-2 has largely focused on the pandemic's impact on humans, with insufficient attention paid to monitoring, sharing, and communicating information about viral circulation and evolution in animal hosts. The objective of this study was to estimate and characterise the data gap between the number of SARS-CoV-2 cases and related deaths in animals officially notified to the World Organisation for Animal Health (WOAH) via its World Animal Health Information System (WAHIS) and known cases reported through two other data sources: ProMED-mail and scientific papers. We used the previously published dataset SARS-ANI to retrieve SARS-CoV-2 events in animals published through WAHIS and ProMED-mail. Additionally, we generated SARS-ANI SciLit v1.0, a novel structured dataset of SARS-CoV-2 events in animals published through scientific literature retrieved from PubMed. We evidenced that at least 52.8% of the SARS-CoV-2 animal cases and 65.8% of the deaths were not reported to WAHIS during 29/02/2020-16/08/2022. Combining information from three different data sources, we compiled a new comprehensive list of 35 animal species reported as susceptible to SARS-CoV-2 under natural conditions, representing a significant advance from the figures reported by the WOAH and the Food and Agriculture Organization of the United Nations. Furthermore, we identified animal species that were underreported to the WAHIS and found that dogs and cats garnered the most attention in research studies. We also showed that, compared to the official WAHIS reports, scientific papers generally experienced longer publication lags and demonstrated that national strategies regarding reporting/publishing of SARS-CoV-2 events in animals greatly differed among countries. This analysis provides valuable insights into the patterns of reporting animal infections with SARS-CoV-2. The study emphasises the need for improvements in data sharing regarding SARS-CoV-2 events in animals, as this is crucial for effective One Health surveillance, prevention, and control of emerging diseases of zoonotic origin.

A systematic review on leptospirosis in cattle: A European perspective.

Leptospirosis is a zoonotic disease which is globally distributed and represents a classic One Health issue that demands a comprehensive understanding of the hosts, transmission paths, and risk factors of transmission. Bovine leptospirosis often results in economic losses through its severe impact on reproduction performance while it threatens human health at human-cattle-environment interfaces. However, a clear analysis of the disease characteristics in European cattle is currently lacking. The objective of this review was to summarise the current knowledge on the epidemiology of bovine leptospirosis in Europe. We conducted a systematic literature review, screening four electronic databases, and filtered articles published between 2001 and 2021, in English, German, and French. Sixty-two articles were ultimately included in the review. The seroprevalence of leptospirosis in cattle was remarkably variable among studies, probably reflecting local variations but also heterogeneity in the study designs, laboratory methods, and sample sizes. Risk factors positively associated with the disease were diverse, related to local, environmental, and climatic parameters as well as farming practices. The most reported circulating Leptospira serogroups in European cattle were Sejroe (58.5%), Australis (41.5%), Grippotyphosa (41.5%), Icterohaemorrhagiae (37.7%), and Pomona (26.4%), which have also been associated with human infections worldwide. Abortion (58.6%) and fertility disorders (24.1%) were the most frequently reported signs of leptospirosis in European cattle and were generally associated with chronic infections. This work highlights several research gaps, including a lack of harmonisation in diagnostic methods, a lack of large-scale studies, and a lack of molecular investigations. Given that predictions regarding the climatic suitability for leptospirosis in Europe suggest an increase of leptospirosis risk it is important to raise awareness among stakeholders and motivate an integrated One Health approach to the prevention and control of this zoonotic disease in cattle and humans.

Network analysis of pig movement data as an epidemiological tool: an Austrian case study.

Animal movements represent a major risk for the spread of infectious diseases in the domestic swine population. In this study, we adopted methods from social network analysis to explore pig trades in Austria. We used a dataset of daily records of swine movements covering the period 2015-2021. We analyzed the topology of the network and its structural changes over time, including seasonal and long-term variations in the pig production activities. Finally, we studied the temporal dynamics of the network community structure. Our findings show that the Austrian pig production was dominated by small-sized farms while spatial farm density was heterogeneous. The network exhibited a scale-free topology but was very sparse, suggesting a moderate impact of infectious disease outbreaks. However, two regions (Upper Austria and Styria) may present a higher structural vulnerability. The network also showed very high assortativity between holdings from the same federal state. Dynamic community detection revealed a stable behavior of the clusters. Yet trade communities did not correspond to sub-national administrative divisions and may be an alternative zoning approach to managing infectious diseases. Knowledge about the topology, contact patterns, and temporal dynamics of the pig trade network can support optimized risk-based disease control and surveillance strategies.

Detection of Pneumocystis and Morphological Description of Fungal Distribution and Severity of Infection in Thirty-Six Mammal Species.

Pneumocystis spp. are thought to adapt to the lungs of potentially all mammals. However, the full host range, fungal burden and severity of infection are unknown for many species. In this study, lung tissue samples originating from 845 animals of 31 different families of eight mammal orders were screened by in situ hybridization (ISH) using a universal 18S rRNA probe for Pneumocystis, followed by hematoxylin and eosin (H&E) staining for determining histopathological lesions. A total of 216 (26%) samples were positive for Pneumocystis spp., encompassing 36 of 98 investigated mammal species, with 17 of them being described for the first time for the presence of Pneumocystis spp. The prevalence of Pneumocystis spp. as assessed by ISH varied greatly among different mammal species while the organism load was overall low, suggesting a status of colonization or subclinical infection. Severe Pneumocystis pneumonia seemed to be very rare. For most of the Pneumocystis-positive samples, comparative microscopic examination of H&E- and ISH-stained serial sections revealed an association of the fungus with minor lesions, consistent with an interstitial pneumonia. Colonization or subclinical infection of Pneumocystis in the lung might be important in many mammal species because the animals may serve as a reservoir.

Monitoring Urban Zoonotic Virus Activity: Are City Rats a Promising Surveillance Tool for Emerging Viruses?

Urban environments represent unique ecosystems where dense human populations may come into contact with wildlife species, some of which are established or potential reservoirs for zoonotic pathogens that cause human diseases. Finding practical ways to monitor the presence and/or abundance of zoonotic pathogens is important to estimate the risk of spillover to humans in cities. As brown rats (Rattus norvegicus) are ubiquitous in urban habitats, and are hosts of several zoonotic viruses, we conducted longitudinal sampling of brown rats in Vienna, Austria, a large population center in Central Europe. We investigated rat tissues for the presence of several zoonotic viruses, including flaviviruses, hantaviruses, coronaviruses, poxviruses, hepatitis E virus, encephalomyocarditis virus, and influenza A virus. Although we found no evidence of active infections (all were negative for viral nucleic acids) among 96 rats captured between 2016 and 2018, our study supports the findings of others, suggesting that monitoring urban rats may be an efficient way to estimate the activity of zoonotic viruses in urban environments.

Surveillance and Control of African Swine Fever in the Early Phase of the COVID-19 Pandemic, March-May 2020: A Multi-Country E-Survey.

Stringent COVID-19 public health and social measures (PHSMs) have challenged the work of animal health professionals, especially in the early phase of the pandemic. We aimed to qualitatively describe how COVID-19 PHSMs have affected the surveillance and control of African swine fever (ASF) in Europe, assess how professionals engaged in these activities perceived the impact of the COVID-19 crisis, and identify potential areas of improvement. An online questionnaire was proposed via email between 9 December 2020 and 22 January 2021 to professionals engaged in ASF-related activities in Europe and Eastern neighboring countries. The questionnaire contained questions pertaining to ASF surveillance and control activities between March and May 2020, respondent's perception of the impact of COVID-19 PHSMs on these activities, and respondent's opinion on potential improvements to prepare for future crises. Economic and sanitary variables were used to describe the national contexts over the study period. Twenty-seven respondents from 24 countries participated to the study. Essential activities related to surveillance and management of ASF were reduced and/or adapted but maintained in most surveyed countries. Communication was mentioned as the first area of improvement during crisis while maintenance of efficient veterinary services and surveillance activities were cited second and third top priorities. The need for the development of remote procedures was also recognized. Some respondents highlighted difficulties in ensuring biosecurity and biosafety of the field actors due to shortage in protective equipment. Only a small majority (52%) of the survey participants agreed that their institution/working group is better prepared to future lockdown-type situations. Our study emphasizes that short-term measures were globally successful to tackle the immediate impacts of the COVID-19 crisis on the routine duties of professionals involved in ASF surveillance and control. Our findings suggest that country-specific improvements are necessary to support and advance the preparedness of the actors involved in infectious animal disease surveillance and control in case lockdown-like measures are implemented. Overall, our results highlight the crucial importance of recognizing animal health services as essential activities during crisis.

SARS-ANI: a global open access dataset of reported SARS-CoV-2 events in animals.

The zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 in animal hosts. We used two major health databases to extract unstructured data and generated a global dataset of SARS-CoV-2 events in animals. The dataset presents harmonized host names, integrates relevant epidemiological and clinical data on each event, and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapting monitoring strategies, preventing the formation of animal reservoirs, and tailoring future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborations, to develop it further and expand its use.

Surface Waters and Urban Brown Rats as Potential Sources of Human-Infective Cryptosporidium and Giardia in Vienna, Austria.

Cryptosporidium and Giardia are waterborne protozoa that cause intestinal infections in a wide range of warm-blooded animals. Human infections vary from asymptomatic to life-threatening in immunocompromised people, and can cause growth retardation in children. The aim of our study was to assess the prevalence and diversity of Cryptosporidium and Giardia in urban surface water and in brown rats trapped in the center of Vienna, Austria, using molecular methods, and to subsequently identify their source and potential transmission pathways. Out of 15 water samples taken from a side arm of the River Danube, Cryptosporidium and Giardia (oo)cysts were detected in 60% and 73% of them, with concentrations ranging between 0.3-4 oocysts/L and 0.6-96 cysts/L, respectively. Cryptosporidium and Giardia were identified in 13 and 16 out of 50 rats, respectively. Eimeria, a parasite of high veterinary importance, was also identified in seven rats. Parasite co-ocurrence was detected in nine rats. Rat-associated genotypes did not match those found in water, but matched Giardia previously isolated from patients with diarrhea in Austria, bringing up a potential role of rats as sources or reservoirs of zoonotic pathogenic Giardia. Following a One Health approach, molecular typing across potential animal and environmental reservoirs and human cases gives an insight into environmental transmission pathways and therefore helps design efficient surveillance strategies and relevant outbreak responses.

Seasonal diet-based resistance to anticoagulant rodenticides in the fossorial water vole (Arvicola amphibius).

Anticoagulant rodenticides (AR) resistance has been defined as "a major loss of efficacy due to the presence of a strain of rodent with a heritable and commensurately reduced sensitivity to the anticoagulant". The mechanism that supports this resistance has been identified as based on mutations in the Vkorc1 gene leading to severe resistance in rats and mice. This study evaluates the validity of this definition in the fossorial water vole and explores the possibility of a non-genetic diet-based resistance in a strict herbivorous rodent species. Genetic support was explored by sequencing the Vkorc1 gene and the diet-based resistance was explored by the dosing of vitamins K in liver of voles according to seasons. From a sample of 300 voles, only 2 coding mutations, G71R and S149I, were detected in the Vkorc1 gene in the heterozygous state with low allele frequencies (0.5-1%). These mutations did not modify the sensitivity to AR, suggesting an absence of genetic Vkorc1-based resistance in the water vole. On the contrary, vitamin K1 was shown to be 5 times more abundant in the liver of the water vole compared to rats. This liver concentration was shown to seasonally vary, with a trough in late winter and a peak in late spring/early summer related to the growth profile of grass. This increase in concentration might be responsible for the increased resistance of water voles to AR. This study highlights a non-genetic, diet-related resistance mechanism in rodents to AR. This diet-based resistance might explain the different evolution of the Vkorc1 gene in the fossorial water vole compared to rats and mice.

Ranking the effectiveness of worldwide COVID-19 government interventions.

Assessing the effectiveness of non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 is critical to inform future preparedness response plans. Here we quantify the impact of 6,068 hierarchically coded NPIs implemented in 79 territories on the effective reproduction number, Rt, of COVID-19. We propose a modelling approach that combines four computational techniques merging statistical, inference and artificial intelligence tools. We validate our findings with two external datasets recording 42,151 additional NPIs from 226 countries. Our results indicate that a suitable combination of NPIs is necessary to curb the spread of the virus. Less disruptive and costly NPIs can be as effective as more intrusive, drastic, ones (for example, a national lockdown). Using country-specific 'what-if' scenarios, we assess how the effectiveness of NPIs depends on the local context such as timing of their adoption, opening the way for forecasting the effectiveness of future interventions.

Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia.

Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake's adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.

A structured open dataset of government interventions in response to COVID-19.

In response to the COVID-19 pandemic, governments have implemented a wide range of non-pharmaceutical interventions (NPIs). Monitoring and documenting government strategies during the COVID-19 crisis is crucial to understand the progression of the epidemic. Following a content analysis strategy of existing public information sources, we developed a specific hierarchical coding scheme for NPIs. We generated a comprehensive structured dataset of government interventions and their respective timelines of implementation. To improve transparency and motivate collaborative validation process, information sources are shared via an open library. We also provide codes that enable users to visualise the dataset. Standardization and structure of the dataset facilitate inter-country comparison and the assessment of the impacts of different NPI categories on the epidemic parameters, population health indicators, the economy, and human rights, among others. This dataset provides an in-depth insight of the government strategies and can be a valuable tool for developing relevant preparedness plans for pandemic. We intend to further develop and update this dataset until the end of December 2020.

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

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

Urban brown rats (Rattus norvegicus) as possible source of multidrug-resistant Enterobacteriaceae and meticillin-resistant Staphylococcus spp., Vienna, Austria, 2016 and 2017.

BackgroundBrown rats (Rattus norvegicus) are an important wildlife species in cities, where they live in close proximity to humans. However, few studies have investigated their role as reservoir of antimicrobial-resistant bacteria.AimWe intended to determine whether urban rats at two highly frequented sites in Vienna, Austria, carry extended-spectrum ß-lactamase-producing Enterobacteriaceae, fluoroquinolone-resistant Enterobacteriaceae and meticillin-resistant (MR) Staphylococcus spp. (MRS).MethodsWe surveyed the presence of antimicrobial resistance in 62 urban brown rats captured in 2016 and 2017 in Vienna, Austria. Intestinal and nasopharyngeal samples were cultured on selective media. We characterised the isolates and their antimicrobial properties using microbiological and genetic methods including disk diffusion, microarray analysis, sequencing, and detection and characterisation of plasmids.ResultsEight multidrug-resistant Escherichia coli and two extensively drug-resistant New Delhi metallo-ß-lactamases-1 (NDM-1)-producing Enterobacter xiangfangensis ST114 (En. cloacae complex) were isolated from nine of 62 rats. Nine Enterobacteriaceae isolates harboured the bla CTX-M gene and one carried a plasmid-encoded ampC gene (bla CMY-2). Forty-four MRS were isolated from 37 rats; they belonged to seven different staphylococcal species: S. fleurettii, S. sciuri, S. aureus, S. pseudintermedius, S. epidermidis, S. haemolyticus (all mecA-positive) and mecC-positive S. xylosus.ConclusionOur findings suggest that brown rats in cities are a potential source of multidrug-resistant bacteria, including carbapenem-resistant En. xiangfangensis ST114. Considering the increasing worldwide urbanisation, rodent control remains an important priority for health in modern cities.

Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals.

The presence of the methicillin resistance gene mecC in coagulase-negative Staphylococcus spp. (CoNS) is scarce. The aim of this study was to characterize mecC-positive CoNS isolated from various wild and domestic animals. The presence of the mecC gene was screened in 4299 samples from wild animals and domestic animals. Fifteen coagulase-negative staphylococci, that displayed a cefoxitin-resistant phenotype, were tested mecC-positive by PCR. Antimicrobial susceptibility testing was performed for all isolates. The 15 isolates were genotyped by sequencing of the entire class E mec gene complex (blaZ-mecC-mecR1-mecI), the ccrA and ccrB recombinase genes and other determinants within the type XI SCCmec element. DNA microarray analysis was performed and five selected isolates were additionally whole genome sequenced and analyzed. S. stepanovicii (n = 3), S. caprae (n = 1), S. warneri (n = 1), S. xylosus (n = 1) and S. sciuri (n = 9) were detected. All but the S. sciuri isolates were found to be susceptible to all non-beta lactams. The entire class E mec gene complex was detected in all isolates but ccrA and ccrB genes were not identified in S. stepanovicii and S. xylosus. The genes erm(B) and fexA (n = 4, each) were the most predominant non-beta lactam resistance genes detected in the S. sciuri isolates. Even though the presence of the mecC gene among CoNS is a rare observation, this study further expands our knowledge by showing that the mecC gene, including its allotypes, are present in more staphylococcal species from different animal species than has been previously described.