Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring

Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance.

Lactococcus petauri sp. nov., isolated from an abscess of a sugar glider

A strain of lactic acid bacteria, designated 159469^T, isolated from a facial abscess in a sugar glider, was characterized genetically and phenotypically. Cells of the strain were Gram-stain-positive, coccoid and catalase-negative. Morphological, physiological and phylogenetic data indicated that the isolate belongs to the genus Lactococcus. Strain 159469^T was closely related to Lactococcus garvieae ATCC 43921^T, showing 95.86 and 98.08 % sequence similarity in 16S rRNA gene and rpoB gene sequences, respectively. Furthermore, a pairwise average nucleotide identity blast (ANIb) value of 93.54 % and in silico DNA–DNA hybridization value of 50.7  % were determined for the genome of strain 159469^T, when compared with the genome of the type strain of Lactococcus garvieae. Based on the data presented here, the isolate represents a novel species of the genus Lactococcus, for which the name Lactococcus petauri sp. nov. is proposed. The type strain is 159469^T (=LMG 30040^T=DSM 104842^T).

Diagnostic Evidence of Staphylococcus Warneri as a Possible Cause of Bovine Abortion

Following a routine necropsy of a bovine fetus aborted at 5 months of gestation, placenta, fetal tissue samples, and stomach contents were subjected to a number of laboratory tests. Staphylococcus warneri was isolated in pure culture from the lung, liver, and stomach contents, whereas the placenta yielded S. warneri and a number of contaminants. Gross evaluation of agar plates showed predominant colonies to be morphologically consistent with those of S. warneri and the identity of the agent was further confirmed on a Trek Diagnostic Systems Sensititre, gram-positive identification (GPID) plate. Microscopic evaluation of fetal tissue sections showed extensive necrotizing lesions of the tongue, lung, and placenta in which there were numerous coccoid shaped gram-positive bacteria with morphology consistent with Staphylococcus spp. These results provide strong diagnostic evidence of S. warneri as a possible cause of bovine abortion and suggest there should be further investigations into the abortivirulence of this agent.

An Outbreak of Chronic Pneumonia and Polyarthritis Syndrome Caused by Mycoplasma Bovis in Feedlot Bison (Bison Bison)

Mycoplasma bovis was identified by a specific lesion, conventional bacterial culture, immunohistochemistry, and polymerase chain reaction in 2 feedlot bison found dead with severe, chronic, caseonecrotic pneumonia; polyarthritis; and laryngitis. On microscopic examination, pulmonary lesions were characterized by prominent, well-defined areas of caseous necrosis and bronchiectasis. Immunohistochemical analysis of lung exhibited staining in bronchiolar epithelium and in random areas of caseous necrosis. On gross examination, the laryngeal lesion observed in 1 animal was typical of changes seen in cases of calf diphtheria. Nasal swabs taken from 6 clinically ill bison from the same feedlot revealed 1 animal shedding M. bovis by the nasal route. No other pathogens were recovered from the pulmonary or laryngeal lesions; however, Mannheimia haemolytica was cultured from the nasal swabs of 2 clinically ill bison, although not from the animal found to be shedding M. bovis. Several other affected bison had swollen joints and exhibited lameness and a reluctance to move. Changes observed in dead and clinically ill bison from this feedlot are similar to what has been described in the literature as chronic pneumonia and polyarthritis syndrome in feedlot cattle caused by M. bovis. Based on the severity of the lesions, and the number of dead and affected animals, bison in a feedlot setting appear to exhibit sensitivity to infection with M. bovis.