Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada.

BACKGROUND: Antimicrobial resistance (AMR) of bacterial pathogens is an emerging public health threat. This threat extends to pets as it also compromises our ability to treat their infections. Surveillance programs in the United States have traditionally focused on collecting data from food animals, foods, and people. The Veterinary Laboratory Investigation and Response Network (Vet-LIRN), a national network of 45 veterinary diagnostic laboratories, tested the antimicrobial susceptibility of clinically relevant bacterial isolates from animals, with companion animal species represented for the first time in a monitoring program. During 2017, we systematically collected and tested 1968 isolates. To identify genetic determinants associated with AMR and the potential genetic relatedness of animal and human strains, whole genome sequencing (WGS) was performed on 192 isolates: 69 Salmonella enterica (all animal sources), 63 Escherichia coli (dogs), and 60 Staphylococcus pseudintermedius (dogs). RESULTS: We found that most Salmonella isolates (46/69, 67%) had no known resistance genes. Several isolates from both food and companion animals, however, showed genetic relatedness to isolates from humans. For pathogenic E. coli, no resistance genes were identified in 60% (38/63) of the isolates. Diverse resistance patterns were observed, and one of the isolates had predicted resistance to fluoroquinolones and cephalosporins, important antibiotics in human and veterinary medicine. For S. pseudintermedius, we observed a bimodal distribution of resistance genes, with some isolates having a diverse array of resistance mechanisms, including the mecA gene (19/60, 32%). CONCLUSION: The findings from this study highlight the critical importance of veterinary diagnostic laboratory data as part of any national antimicrobial resistance surveillance program. The finding of some highly resistant bacteria from companion animals, and the observation of isolates related to those isolated from humans demonstrates the public health significance of incorporating companion animal data into surveillance systems. Vet-LIRN will continue to build the infrastructure to collect the data necessary to perform surveillance of resistant bacteria as part of fulfilling its mission to advance human and animal health. A One Health approach to AMR surveillance programs is crucial and must include data from humans, animals, and environmental sources to be effective.

Performance of commercial PCR assays to detect toxigenic Clostridioides difficile in the feces of puppies.

Clostridioides difficile is an important enteric pathogen that causes significant morbidity and mortality in humans. With community-acquired infections on the rise, it is important to identify reservoirs of the pathogen. Companion animals can be asymptomatic carriers of C. difficile and may therefore represent a reservoir, but epidemiological studies of C. difficile within the pet-owner unit are needed, along with validated methods to detect C. difficile in both people and animals. The goal of this study was to assess the performance of commercial qPCR assays and a multiplex PCR for C. difficile compared to toxigenic culture. These assays were tested on up to 103 fecal samples from puppies, a population in which the prevalence of C. difficile is the highest. The sensitivities, specificities, positive predictive values and negative predictive values were respectively 84.2%, 87.7%, 61.5%, and 95.9% for the Cepheid GeneXpert; 66.7%, 66.7%, 29.6%, and 90.9% for the DiaSorin Simplexa; and 94.4%, 85.0%, 65.4%, and 98.1%, for the multiplex qPCR. The agreement was highest between the GeneXpert and the multiplex PCR (90.1% agreement, with a kappa statistic of 0.77). For diagnostic purposes, the positive predictive values of the assays were low. However, the high sensitivities of the assays could render them useful for epidemiologic purposes.

Complete Genome Sequences of Seven Avibacterium paragallinarum Isolates from Poultry Farms in Pennsylvania, USA.

Avibacterium paragallinarum, the causative agent of infectious coryza, causes significant economic losses to the poultry industry due to increased culling rates in growing chickens and decreased egg production in layers. We present the complete genome sequences of seven strains of Avibacterium paragallinarum isolated from poultry farms in Pennsylvania during 2019.

Gut microbiota features associated with Clostridioides difficile colonization in puppies.

In people, colonization with Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, has been shown to be associated with distinct gut microbial features, including reduced bacterial community diversity and depletion of key taxa. In dogs, the gut microbiota features that define C. difficile colonization are less well understood. We sought to define the gut microbiota features associated with C. difficile colonization in puppies, a population where the prevalence of C. difficile has been shown to be elevated, and to define the effect of puppy age and litter upon these features and C. difficile risk. We collected fecal samples from weaned (n = 27) and unweaned (n = 74) puppies from 13 litters and analyzed the effects of colonization status, age and litter on microbial diversity using linear mixed effects models. Colonization with C. difficile was significantly associated with younger age, and colonized puppies had significantly decreased bacterial community diversity and differentially abundant taxa compared to non-colonized puppies, even when adjusting for age. C. difficile colonization remained associated with decreased bacterial community diversity, but the association did not reach statistical significance in a mixed effects model incorporating litter as a random effect. Even though litter explained a greater proportion (67%) of the variability in microbial diversity than colonization status, we nevertheless observed heterogeneity in gut microbial community diversity and colonization status within more than half of the litters, suggesting that the gut microbiota contributes to colonization resistance against C. difficile. The colonization of puppies with C. difficile has important implications for the potential zoonotic transfer of this organism to people. The identified associations point to mechanisms by which C. difficile colonization may be reduced.

Gram-negative multi-drug resistant bacteria influence survival to discharge for horses with septic synovial structures: 206 Cases (2010-2015).

Bacterial colonization of synovial structures can cause infections that are difficult to treat. Systemic and local antimicrobials and repeated joint lavages are the mainstays of therapy. However, despite aggressive treatments, infection may persist, leading to significant tissue damage or death of the patient. In order to investigate the impact of bacterial culture and antimicrobial resistance on survival to discharge, we reviewed medical records of horses admitted to the University of Pennsylvania's large animal teaching hospital from 2010-2015. Two-hundred and six cases with a definitive diagnosis of septic synovitis and a synovial fluid sample submitted for microbiological culture were included in the study. Of these horses, 48% were culture negative and 52% were positive for any bacterial growth, of which 66% were gram-positive and 28% were gram-negative aerobic organisms with 4% anaerobic and 2% fungal organisms. Overall survival to discharge from hospital was 86%. Horses that had negative growth on culture were more likely to survive until discharge (p < 0.02). Multivariable analyses revealed that the likelihood of euthanasia was significantly associated with identification of coagulase positive Staphylococcus spp. (OR 7.66, 5.46-10.74, p < 0.0001), ß-hemolytic Streptococcus spp. (OR 5.18, 3.56-7.55, p < 0.0001), Enterococcus spp. (OR 18.38, 11.45-29.52, p = 0.002), Enterobacteriaceae (OR 31.37, 22.28-44.17, p < 0.0001), Pseudomonas aeruginosa (OR 9.31, 5.30-16.34, p = 0.0004) or other gram-negative species (OR 3.51, 2.07-5.94, p = 0.001). Multi-drug resistance and gram-negative bacteria species were associated with significantly decreased survival rates (OR 119.24, 70.57-201.46, p < 0.0001). In conclusion, prognosis for survival to discharge was poor for horses that were infected with gram-negative organisms, particularly those with MDR phenotypes.

A Clinical Synthesis of the "Late Talker" Literature: Implications for Service Delivery.

"Late talkers" are most often differentiated from their normally developing peers by their limited expressive lexicons. In the majority of the studies conducted on late talkers, these children are described as producing fewer than 50 words and/or producing limited word combinations by 24 months of age. The expressive language of some of the late talkers will eventually resemble their same-age peers; however, a substantial number of these children will continue to evidence difficulties with their expressive language acquisition. This article provides a review of the literature on late talkers in order to assist speech-language pathologists as they tackle those issues that are specific to service provision with this population of children.