Exploring Klebsiella pneumoniae in Healthy Poultry Reveals High Genetic Diversity, Good Biofilm-Forming Abilities and Higher Prevalence in Turkeys Than Broilers

Abstract

<i>Klebsiella pneumoniae</i> is a well-studied human pathogen for which antimicrobial resistant and hypervirulent clones have emerged globally. <i>K. pneumoniae</i> is also present in a variety of environmental niches, but currently there is a lack of knowledge on the occurrence and characteristics of <i>K. pneumoniae</i> from non-human sources. Certain environmental niches, e.g., animals, may be associated with high <i>K. pneumoniae</i> abundance, and these can constitute a reservoir for further transmission of strains and genetic elements. The aim of this study was to explore and characterize <i>K. pneumoniae</i> from healthy broilers and turkeys. A total of 511 cecal samples (broiler <i>n</i> = 356, turkey <i>n</i> = 155), included in the Norwegian monitoring program for antimicrobial resistance (AMR) in the veterinary sector (NORM-VET) in 2018, were screened for <i>K. pneumoniae</i> by culturing on SCAI agar. <i>K. pneumoniae</i> was detected in 207 (40.5%) samples. Among the broiler samples, 25.8% were positive for <i>K. pneumoniae</i>, in contrast to turkey with 74.2% positive samples (<i>p</i> < 0.01). Antibiotic susceptibility testing was performed, in addition to investigating biofilm production. Whole genome sequencing was performed on 203 <i>K. pneumoniae</i> isolates, and analysis was performed utilizing comparative genomics tools. The genomes grouped into 66 sequence types (STs), with ST35, ST4710 and ST37 being the most prevalent at 13.8%, 7.4%, and 5.4%, respectively. The overall AMR occurrence was low, with only 11.3% of the isolates showing both pheno- and genotypic resistance. Genes encoding aerobactin, salmochelin or yersiniabactin were detected in 47 (23.2%) genomes. Fifteen hypervirulent genomes belonging to ST4710 and isolated from turkey were identified. These all encoded the siderophore virulence loci <i>iuc5</i> and <i>iro5</i> on an IncF plasmid. Isolates from both poultry species displayed good biofilm-forming abilities with an average of OD₅₉₅ 0.69 and 0.64. To conclude, the occurrence of <i>K. pneumoniae</i> in turkey was significantly higher than in broiler, indicating that turkey might be an important zoonotic reservoir for <i>K. pneumoniae</i> compared to broilers. Furthermore, our results show a highly diverse <i>K. pneumoniae</i> population in poultry, low levels of antimicrobial resistance, good biofilm-forming abilities and a novel hypervirulent ST4710 clone circulating in the turkey population.