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Rat bite fever (RBF) is a zoonotic disease caused primarily by Streptobacillus ( S .) moniliformis . Norway or brown rats ( Rattus [ R. ] norvegicus ) are the natural host for S. moniliformis and carry the bacterium in the nasopharynx without clinical disease. Transmission to humans often occurs through rat bites or scratches, but also through contact with the excreta of infected rats. Although human infections with S. moniliformis occur worldwide, they are rarely diagnosed. For decades, S. moniliformis was the only known member of the genus Streptobacillus . In recent years, however, four additional species were identified, two of which being zoonotic pathogens capable of causing symptoms identical to RBF in humans. The aim of this study was to develop a serological assay covering all known Streptobacillus species. A bead-based multiplex fluorescence immunoassay for S. moniliformis detection has been used for years in routine diagnostics of laboratory rodents. Here, this assay was adapted to enable the detection of antibodies against all currently known Streptobacillus species and tested with sera from experimentally inoculated mice and rats, and with negative sera from laboratory rodents. Using this assay, we broadly examined the prevalence of Streptobacillus spp. reactive antibodies in wild rodents. Transudates from a total of 107 Norway rats, 81 black or roof rats ( Rattus rattus ) and 110 house mice ( Mus musculus ) from different husbandries and wildlife populations within Germany were tested. Antibody prevalences of 41% in R. norvegicus and 83% in R. rattus suggest that Streptobacillus spp. are widespread in wild and captive rats in Germany, whereas wild mice seem to be free of infection. Due to its high throughput capacity and multiplex format, the Streptobacillus multiplex serology is well suited for large seroprevalence studies in rodents and has the potential, after adaptation, for use in humans, thereby allowing for the assessment of Streptobacillus infection risk and risk of RBF.

The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5' region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.

Since 1814, when rubella was first described, the origins of the disease and its causative agent, rubella virus ( Matonaviridae : Rubivirus ), have remained unclear 1 . Here we describe ruhugu virus and rustrela virus in Africa and Europe, respectively, which are, to our knowledge, the first known relatives of rubella virus. Ruhugu virus, which is the closest relative of rubella virus, was found in apparently healthy cyclops leaf-nosed bats ( Hipposideros cyclops ) in Uganda. Rustrela virus, which is an outgroup to the clade that comprises rubella and ruhugu viruses, was found in acutely encephalitic placental and marsupial animals at a zoo in Germany and in wild yellow-necked field mice ( Apodemus flavicollis ) at and near the zoo. Ruhugu and rustrela viruses share an identical genomic architecture with rubella virus 2 , 3 . The amino acid sequences of four putative B cell epitopes in the fusion (E1) protein of the rubella, ruhugu and rustrela viruses and two putative T cell epitopes in the capsid protein of the rubella and ruhugu viruses are moderately to highly conserved 4 – 6 . Modelling of E1 homotrimers in the post-fusion state predicts that ruhugu and rubella viruses have a similar capacity for fusion with the host-cell membrane 5 . Together, these findings show that some members of the family Matonaviridae can cross substantial barriers between host species and that rubella virus probably has a zoonotic origin. Our findings raise concerns about future zoonotic transmission of rubella-like viruses, but will facilitate comparative studies and animal models of rubella and congenital rubella syndrome. Ruhugu virus and rustrela virus are the first close relatives of rubella virus, providing insights into the zoonotic origin of rubella virus and the epidemiology and evolution of all three viruses.

We tested 130 rats captured in Berlin for coronaviruses. SARS-CoV-2 antibodies were detected in 1 rat, but all animals were negative by reverse transcription PCR, suggesting SARS-CoV-2 was not circulating in the rat population. However, alphacoronaviruses were found. Monitoring rodent populations helps to determine coronavirus occurrence, transmission, and zoonotic potential.

Human activities such as agriculturalization and domestication have led to the emergence of many new pathogens via host-switching events between humans, domesticated and wild animals. Staphylococcus aureus is a multi-host opportunistic pathogen with a global healthcare and economic burden. Recently, it was discovered that laboratory and wild rodents can be colonised and infected with S . aureus , but the origins and zoonotic potential of rodent S . aureus is unknown. In order to trace their evolutionary history, we employed a dataset of 1249 S . aureus genome sequences including 393 of isolates from rodents and other small mammals (including newly determined sequences for 305 isolates from 7 countries). Among laboratory mouse populations, we identified multiple widespread rodent-specific S . aureus clones that likely originated in humans. Phylogeographic analysis of the most common murine lineage CC88 suggests that it emerged in the 1980s in laboratory mouse facilities most likely in North America, from where it spread to institutions around the world, via the distribution of mice for research. In contrast, wild rodents (mice, voles, squirrels) were colonized with a unique complement of S . aureus lineages that are widely disseminated across Europe. In order to investigate the molecular basis for S . aureus adaptation to rodent hosts, genome-wide association analysis was carried out revealing a unique complement of bacteriophages associated with a rodent host ecology. Of note, we identified novel prophages and pathogenicity islands in rodent-derived S . aureus that conferred the potential for coagulation of rodent plasma, a key phenotype of abscess formation and persistence. Our findings highlight the remarkable capacity of S . aureus to expand into new host populations, driven by the acquisition of genes promoting survival in new host-species.

Three squirrel breeders had encephalitis and died. A careful examination with the use of metagenomic approaches and next-generation sequencing suggested a previously unknown bornavirus, which may have come from the squirrels, as the culprit. Beginning in late 2011, three men in succession (63, 62, and 72 years of age) from the state of Saxony-Anhalt, Germany, had a progressive encephalitis or meningoencephalitis that led to death within 2 to 4 months after the onset of clinical symptoms. The clinical course was characterized by fever, shivers, or both; progressive psychomotor slowing; confusion; unsteady gait; myoclonus, ocular paresis, or both; and finally, coma. All three patients had preexisting medical conditions (hypertension, diabetes, or obesity). In all three patients, the disease was also accompanied, at some point during the course of the illness, by bilateral crural-vein thrombosis, which . . .

Rotaviruses infect humans and animals and are a main cause of diarrhea. They are non-enveloped viruses with a genome of 11 double-stranded RNA segments. Based on genome analysis and amino acid sequence identities of the capsid protein VP6, the rotavirus species A to J (RVA-RVJ) have been defined so far. In addition, rotaviruses putatively assigned to the novel rotavirus species K (RVK) and L (RVL) have been recently identified in common shrews (Sorex araneus), based on partial genome sequences. Here, the complete genome sequence of strain KS14/0241, a prototype strain of RVL, is presented. The deduced amino acid sequence for VP6 of this strain shows only up to 47% identity to that of RVA to RVJ reference strains. Phylogenetic analyses indicate a clustering separated from the established rotavirus species for all 11 genome segments of RVL, with the closest relationship to RVH and RVJ within the phylogenetic RVB-like clade. The non-coding genome segment termini of RVL showed conserved sequences at the 5′-end (positive-sense RNA strand), which are common to all rotaviruses, and those conserved among the RVB-like clade at the 3′-end. The results are consistent with a classification of the virus into a novel rotavirus species L.

Outside Asia, Seoul virus (SEOV) is an underestimated pathogen. In Germany, autochthonous SEOV-associated hantavirus disease has not been unequivocally diagnosed. We found clinical and molecular evidence for SEOV infection in a young woman; her pet rat was the source of infection.

Urban rats present a global public health concern as they are considered a reservoir and vector of zoonotic pathogens, including Escherichia coli. In view of the increasing emergence of antimicrobial resistant E. coli strains and the on-going discussion about environmental reservoirs, we intended to analyse whether urban rats might be a potential source of putatively zoonotic E. coli combining resistance and virulence. For that, we took fecal samples from 87 brown rats (Rattus norvegicus) and tested at least three E. coli colonies from each animal. Thirty two of these E. coli strains were pre-selected from a total of 211 non-duplicate isolates based on their phenotypic resistance to at least three antimicrobial classes, thus fulfilling the definition of multiresistance. As determined by multilocus sequence typing (MLST), these 32 strains belonged to 24 different sequence types (STs), indicating a high phylogenetic diversity. We identified STs, which frequently occur among extraintestinal pathogenic E. coli (ExPEC), such as STs 95, 131, 70, 428, and 127. Also, the detection of a number of typical virulence genes confirmed that the rats tested carried ExPEC-like strains. In particular, the finding of an Extended-spectrum beta-lactamase (ESBL)-producing strain which belongs to a highly virulent, so far mainly human- and avian-restricted ExPEC lineage (ST95), which expresses a serogroup linked with invasive strains (O18:NM:K1), and finally, which produces an ESBL-type frequently identified among human strains (CTX-M-9), pointed towards the important role, urban rats might play in the transmission of multiresistant and virulent E. coli strains. Indeed, using a chicken infection model, this strain showed a high in vivo pathogenicity. Imagining the high numbers of urban rats living worldwide, the way to the transmission of putatively zoonotic, multiresistant, and virulent strains might not be far ahead. The unforeseeable consequences of such an emerging public health threat need careful consideration in the future.

Background Ixodid ticks are important vectors for zoonotic pathogens, with Ixodes ricinus being the most important in Europe. Rodents are hosts of immature life stages of I. ricinus ticks and are considered main reservoirs for tick-borne pathogens, e.g. Borrelia burgdorferi . The aim of this study was to analyse the prevalence as well as genospecies and sequence type (ST) diversity of Borrelia burgdorferi sensu lato in ticks and small mammals from central Germany and to elaborate on the influence of environmental and/or individual host and vector factors on Borrelia prevalence. Methods After species identification, 1167 small mammal skin samples and 1094 ticks from vegetation were screened by B. burgdorferi sensu lato real-time polymerase chain reaction, and positive samples were characterized by multilocus sequence typing. Generalized linear (mixed) models were used to estimate how seasonality, small mammal species/tick life stage and habitat affect individual infection status. Results In total, 10 small mammal species and three tick species, Ixodes ricinus , Ixodes inopinatus (both considered members of the I. ricinus complex) and Dermacentor reticulatus , were investigated. Borrelia DNA was detected in eight host species, i.e. the striped field mouse ( Apodemus agrarius ), the yellow-necked field mouse ( Apodemus flavicollis ), the wood mouse ( Apodemus sylvaticus ), the water vole ( Arvicola amphibius ), the bank vole ( Clethrionomys glareolus ), the field vole ( Microtus agrestis ), the common vole ( Microtus arvalis ), and the common shrew ( Sorex araneus ). Two species were Borrelia negative, the greater white-toothed shrew ( Crocidura russula ) and the pygmy shrew ( Sorex minutus ). The average prevalence was 6.2%, with two genospecies detected, Borrelia afzelii and Borrelia garinii , and at least three STs that had not been previously reported in small mammals. Borrelia prevalence in small mammals did not differ between seasons. Six genospecies of Borrelia —Borrelia afzelii , Borrelia valaisiana , Borrelia garinii , Borrelia lusitaniae , Borrelia spielmanii , and Borrelia burgdorferi sensu stricto—and 25 STs of Borrelia , of which 12 have not been previously described at all and five have not been previously reported in Germany, were detected in 13% of I. ricinus complex ticks. Prevalence was highest in adult females (25.3%) and lowest in nymphs (11.4%). Prevalence was significantly higher in ticks from grassland (16.8%) compared to forests (11.4%). Conclusions The high level of small mammal diversity in this region of Germany seems to be reflected in a wide variety of genospecies and STs of B. burgdorferi . Graphical abstract