Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023.

Continued investigation into the bacteria associated with non-domestic animals provides important information for recognizing normal flora, assessing the health status of these unique species of animals, and identifying new or emerging pathogens of concern. In this summary of novel taxa and taxonomic revisions, considerable additions have been made toward understanding fecal and mucosal flora in multiple wild animal species. In addition, novel pathogenic bacteria are discussed, including multiple Chlamydia spp. causing disease in a hawk and crocodile, two Corynebacterium spp. causing oral lesions in penguins and a lesser-known genus, Mergibacter within Family Pasteurellaceae, causing disease in multiple wild bird species. Finally, a few revisions to bacteria isolated from normal non-domestic animal body sites are mentioned.

Protective immune response against Rhodococcus equi: An innate immunity-focused review.

Rhodococcus equi causes pyogranulomatous pneumonia in foals and immunocompromised people. Despite decades of research efforts, no vaccine is available against this common cause of disease and death in foals. The purpose of this narrative review is to summarise the current understanding of interactions between R. equi and the host innate immune system, to describe features of the immune response that are associated with resistance or susceptibility to R. equi infection, and help guide strategies for developing novel approaches for preventing R. equi infections. Virulence of R. equi in foals has been attributed to the virulence associated protein A which allows intracellular survival in macrophages by preventing acidification of R. equi-containing vacuole. Additionally, foal susceptibility to R. equi infection is associated with immaturity and naivety of innate and adaptive immune systems, while adult horses with fully functional immune system are resistant to pneumonia. Specific interaction between R. equi and innate immune cells can result in bacterial survival or death; learning how to manipulate these responses to control infection is critical to prevent pneumonia in foals. Administration of live vaccines and stimulation of innate immune responses appears to improve foals' immune response and has the potential to overcome the challenges of foal active vaccination and elicit protection against pneumonia.

Causal Agent Investigation and Treatment of Dogs Diagnosed with Discospondylitis in a Brucella canis Endemic Region.

Discospondylitis is a well-recognized disease in dogs, but the relative prevalence of causal infectious agents and efficiency of relevant diagnostic tests are not well-established. Medical record review identified 117 dogs diagnosed with discospondylitis in our clinic over a 5-year period. In 32 dogs, discospondylitis was diagnosed as an incidental imaging finding; 24 of these dogs had concomitant neoplasia. A likely causal infection was identified in 45 of the remaining 85 dogs in which blood and urine cultures, serology for Brucella spp., and galactomannan fungal antigen testing were recommended. Ten dogs were diagnosed with Brucella canis, and ten were diagnosed with suspected fungal infection. Brucella suis serology was negative in all 35 dogs that were tested. Blood cultures were positive in 28 of 71 (39%) tested dogs, and urine culture was positive in 12 of 79 (15%). Cultures were positive from the lesion site of four of eight dogs that underwent surgery and one of the five dogs that underwent image-guided lesion sample collection. Subluxation secondary to discospondylitis was stabilized with metallic implants in four dogs. A similar proportion of known satisfactory treatment outcomes at last follow-up were recorded in dogs that had suspected fungal disease, other bacterial infections, or were Brucella-positive and in those dogs with imaging diagnosis only, although some individuals continued to receive anti-microbial agents or showed recurrent signs. These data support the value of blood culture in discospondylitis and suggest a relatively high prevalence of infection with Brucella spp. and suspected fungal infection.

Optimizing the Glass Bead Sterilization Protocol Focusing on Removal of Organic and Bacterial Intraoperative Contamination.

Validated glass bead sterilization protocols to effectively sterilize rodent surgical instruments after bacterial exposure (for example, cecal contamination) are lacking. To refine current approaches, we added either a multienzyme detergent, neutral pH detergent, or chlorhexidine scrub step before glass bead sterilization of forceps or needle drivers exposed to cecal contents. We exposed sets of forceps and needle drivers to cecal contents, which were then air dried for 3 min. Immediately after, the instruments were wiped several times with a clean, dry paper towel. The contaminated tips were soaked in either a multienzyme or neutral pH detergent (t = 5 min), chlorhexidine scrub (t = 2 min), or no pretreatment solution. To further increase debris removal, instruments (from all groups) were brushed using a clean toothbrush. The nonpretreatment instruments were briefly soaked in saline before brushing. After being rinsed with sterile water, all instruments were exposed to a glass bead sterilizer for 60 s at 500 °F (260 °C). Sets were then swabbed for bacterial culturing. Swabs were plated onto either sheep blood agar (n = 23) or chocolate agar (n = 20) for aerobic culturing or Brucella agar (n = 20) for anaerobic culturing. A subset of instruments was sampled to determine organic material presence after treatment using an ATP luminometer (n = 21). Multiple agar types and bioluminescence were used to more deeply evaluate tool sterility and to differentiate the relative effectiveness of each protocol. From the saline group, only one pair of forceps yielded growth on Brucella agar, and 2 pairs yielded growth on chocolate agar. No other bacterial growth was observed. The use of a pretreatment agent also lowered overall organic contamination levels in needle drivers compared with using only saline. These results indicate that brushing instruments to mechanically remove debris from instruments is paramount to ensure sterility. However, a best practice would be to also use one of the pretreatment options used in this study.

Whole-genome sequences of Campylobacter coli and Campylobacter jejuni isolates from rhesus macaques (Macaca mulatta) with and without intestinal disease.

Campylobacter jejuni or Campylobacter coli infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (Macaca mulatta). We report the complete genomes of 8 C. jejuni isolates and 103 C. coli isolates obtained from rhesus macaques with and without intestinal disease.

Methicillin Resistance Elements in the Canine Pathogen Staphylococcus pseudintermedius and Their Association with the Peptide Toxin PSM-mec.

Staphylococcus pseudintermedius is a frequent cause of infections in dogs. Infectious isolates of this coagulase-positive staphylococcal species are often methicillin- and multidrug-resistant, which complicates therapy. In staphylococci, methicillin resistance is encoded by determinants found on mobile genetic elements called Staphylococcal Chromosome Cassette mec (SCCmec), which, in addition to methicillin resistance factors, sometimes encode additional genes, such as further resistance factors and, rarely, virulence determinants. In this study, we analyzed SCCmec in a collection of infectious methicillin-resistant S. pseudintermedius (MRSP) isolates from predominant lineages in the United States. We found that several lineages characteristically have specific types of SCCmec elements and Agr types and harbor additional factors in their SCCmec elements that may promote virulence or affect DNA uptake. All isolates had SCCmec-encoded restriction-modification (R-M) systems of types I or II, and sequence types (STs) ST84 and ST64 had one type II and one type I R-M system, although the latter lacked a complete methylation enzyme gene. ST68 isolates also had an SCCmec-encoded CRISPR system. ST71 isolates had a psm-mec gene, which, in all but apparently Agr-dysfunctional isolates, produced a PSM-mec peptide toxin, albeit at relatively small amounts. This study gives detailed insight into the composition of SCCmec elements in infectious isolates of S. pseudintermedius and lays the genetic foundation for further efforts directed at elucidating the contribution of identified accessory SCCmec factors in impacting SCCmec-encoded and thus methicillin resistance-associated virulence and resistance to DNA uptake in this leading canine pathogen.

Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.

Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.

An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022.

Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.

Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022.

Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the implications of those changes. Here, we describe additions of novel taxa from domestic animals published in 2022 that are validly published per the International Code of Nomenclature of Prokaryotes. These included new members of Staphylococcaceae, Moraxella nasovis sp. nov. in sheep with respiratory disease, three additions to Campylobacteraceae (including one from chickens with spotty liver disease), and multiple additions of organisms from the microbiota of dogs, pigs, and especially honeybees and other important pollinators. Noteworthy additions were associated with diseases of cattle, including mastitis, endocarditis, orchitis, and endometritis. Also described in 2022 was Pseudochrobactrum algeriense sp. nov., a member of the Brucellaceae family, isolated from the mammary lymph nodes of cows.

Tolerability and the effect on skin Staphylococcus pseudintermedius density of repeated diluted sodium hypochlorite (bleach) baths at 0.005% in healthy dogs.

BACKGROUND: Dilute sodium hypochlorite (bleach) baths at 0.005% concentration twice weekly have been shown to markedly reduce the severity of atopic dermatitis in children, yet no tolerability and efficacy data are available for this treatment in dogs. OBJECTIVES: To determine the local tolerability and the longitudinal effect on the density of Staphylococcus pseudintermedius of repeated diluted bleach baths on healthy dog skin. ANIMALS: Four healthy hound cross-bred dogs. METHODS: Bleach baths (0.005%; twice weekly for 15 min) were applied to four healthy hound cross-bred dogs over four weeks (eight baths). Local tolerability was assessed for axillae, abdomen and legs by an investigator before, immediately after and 24 h after each bath. The longitudinal effect on density of S. pseudintermedius from axillae and groin was analysed through quantitative PCR before treatment [at Day (D)-7 and -3], during treatment on D4, D11 and D25, and on D30. RESULTS: There was no erythema or scaling after the baths in any dog. Copy numbers of S. pseudintermedius in axillae, groin and both (axillae and groin together) were not significantly different at any time point during the study. CONCLUSIONS AND CLINICAL RELEVANCE: Repeated 0.005% hypochlorite bleach baths over four weeks were safe and well-tolerated in healthy dogs without significant changes in the density of S. pseudintermedius.