Foot health and prevalence of Dichelobacter nodosus in 11 ungulate species at Berne Animal Park.

INTRODUCTION: Dichelobacter nodosus (D. nodosus) is the etiological agent of ovine footrot affecting mainly sheep worldwide, but also free-ranging wild ungulates such as Alpine ibex (Capra ibex ibex) and mufflon (Ovis orientalis orientalis). A nationwide ovine footrot eradication program is planned for the years to come, based on polymerase chain reaction (PCR)-testing of interdigital swab samples and regular footbathing. In this cross-sectional study, we clinically evaluated the foot health and analysed presence of D. nodosus in 11 different even-toed ungulate species (mainly European species) during a 13 months (2018-2019) period in Berne Animal Park. The foot lesions were scored for any clinical signs of pathologies as described in cattle and simultaneously for clinical signs of footrot as described for sheep, using a scale from 0 to 5 (while 0 describes clinically healthy feet and 5 loss of the horn capsule). From a total of 53 animals, 4-feet swab samples were taken from the interdigital cleft and subjected to real-time PCR assays to detect D. nodosus at animal level. Foot lesions were detected in five different species. In 3/5 muskoxen (Ovibos moschatus wardi), 7/12 Cretan wild goats (Capra hircus cretica) and 2/3 dwarf goats (Capra hircus aegagrus), they mainly consisted of white line disease, whereas in 9/10 European bison, dermatitis of the interdigital cleft was diagnosed. 1/3 alpaca was diagnosed with chorioptic mange of the heel area. None of the examined animals showed clinical signs of footrot (score 0), and neither benign (aprB2-positive) nor virulent (aprV2-positive) D. nodosus were detected in any of the samples. This study provides additional information to facilitate an efficient ovine footrot control program in Switzerland and suggests that captive wild even-toed ungulates do not pose a risk to the planned footrot control program.

INTRODUCTION: Dichelobacter nodosus (D. nodosus) est l'agent étiologique du piétin chez les ruminants, qui affecte principalement les moutons dans le monde, mais aussi les ongulés sauvages en liberté tels que les bouquetins (Capra ibex ibex) et les mouflons (Ovis orientalis orientalis). Un programme d'éradication du piétin ovin à l'échelle Nationale, basé sur des tests PCR (réaction de polymérisation en chaîne) d'écouvillons de l'espace interdigité et des pédiluves réguliers, est prévu dans les années à venir en Suisse. Dans cette étude transversale, nous avons évalué cliniquement la santé des onglons et recherché la présence de D. nodosus chez 11 espèces différentes d'animaux biongulés (principalement des espèces européennes) pendant une période de 13 mois (2018­2019) au Parc animalier de Berne. Les lésions des onglons ont été notées pour tout signe clinique de pathologie et de présence de piétin, comme cela est décrit chez les bovins et les moutons et en utilisant une échelle de 0 à 5 (où 0 décrit des pieds cliniquement sains et 5 la perte de la boîte cornée). Des écouvillons ont été prélevés dans l'espace interdigité des 4 pieds sur un total de 53 animaux et soumis à des tests PCR en temps réel pour détecter D. nodosus. Des lésions aux onglons ont été détectées chez cinq espèces différentes. Chez 3 boeufs musqués (Ovibos moschatus wardi) sur 5, 7 chèvres sauvages crétoises (Capra hircus cretica) sur 12 et 2 chèvres naines (Capra hircus aegagrus) sur 3, il s'agissait principalement de lésions de la ligne blanche, alors que dans 9 bisons sur 10, le diagnostic était une dermatite interdigitale. Un alpaga sur 3 a été diagnostiqué avec une gale chorioptique de la zone du paturon. Aucun des animaux examinés n'a montré de signes cliniques de piétin (score 0) et aucun D. nodosus bénin (aprB2-positif) ou virulent (aprV2-positif ) n'a été mis en évidence dans les échantillons. Cette étude fournit des informations supplémentaires pour améliorer l'efficacité du programme d'éradication du piétin ovin et suggère que les biongulés sauvages détenus dans les parcs zoologiques ne présentent pas de risque pour le programme d'éradication prévu en Suisse.

From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. METHODS: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs. RESULTS: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most high-frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV. CONCLUSION: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.

Fatal Septicemia and Mastitis in Wild Sunda Colugos (Sunda Flying Lemurs; Galeopterus variegates) in Singapore.

Two free-ranging female Sunda colugos (Sunda flying lemur; Galeopterus variegates) were found dead in Singapore in November 2018 and February 2019. Septicemia and mastitis were diagnosed in both animals on postmortem examination. Infectious diseases have not previously been established as a cause of death in wild Sunda colugos.

Draft genome sequence of a multidrug-resistant CTX-M-65-producing Escherichia coli ST156 colonizing a giant anteater (Myrmecophaga tridactyla) in a Zoo.

OBJECTIVES: This study aimed to report the draft genome sequence of a multidrug-resistant (MDR) Escherichia coli colonizing a giant anteater (Myrmecophaga tridactyla) in a Brazilian Zoo. METHODS: The genome was sequenced using the Illumina MiSeq Platform and de novo genome assembly was performed using SPAdes v. 3.9. The draft genome sequence was annotated using NCBI Prokaryotic Genome Annotation Pipeline. Antibiotic resistance genes, virulence genes, sequence type, serotype and plasmid incompatibility groups were identified using tools from the Center for Genomic Epidemiology. RESULTS: The genome presented 4970 coding sequences and a GC content of 50.2%. Several antimicrobial resistance genes associated with resistance to ß-lactams (blaTEM-1A and blaCTX-M-65), aminoglycosides [aph(6)-ld, aph(3″)-lb, aph(4)-la, aac(3)-lVa, aadA1 and aadA2], tetracyclines (tetB), sulphonamides (sul2 and sul3), trimethoprim (dfrA8 and dfrA12) and phenicols (floR and cmlA1) were identified. Moreover, mutations in quinolone resistance-determining regions (QRDR) were found. This E. coli isolate also presented virulence genes and belonged to serotype ONT:H25 and ST156 (CC156). CONCLUSION: This is the first report of a draft genome sequence of a CTX-M-65-producing E. coli ST156 obtained from a zoo animal, which can be used by genomic surveillance platforms, in order to track transmission dynamics of extended-spectrum ß-lactamase (ESBL)-producing E. coli at the human-animal interface.