Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Abstract

Background: M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity. Results: Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC betalactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, betalactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations. Conclusions: In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.

A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes

“…There are few reports on characterizing ARGs in individual Morganella isolates or a small collection of Morganella isolates ( n ≤ 22 in each study) ( 31 – 33 ). This study provides a genomic and bioinformatics view of the classification and evolution of Morganella species and the global prevalence of AGEs and associated ARGs in Morganella , based on a collection of 166 sequenced isolates, including 60 sequenced in this study.…”

Genetic and Phenotypic Diversity of Morganella morganii Isolated From Cheese

“…genomes retrieved from GenBank and the cheese isolates confirm that M. morganii and M. psychrotolerans can be distinguished using genomic analysis. Palmieri et al (2020) showed that the trehalose operon negative (subsp. morganii ) and the trehalose operon positive (subsp.…”

“…The existence of more Morganella species would also explain why the trehalose operon positive H1R strain does not cluster together with the other subsp. sibonii strains ( Palmieri et al, 2020 ). DNA-DNA hybridization experiments of Emborg et al (2006) also revealed that two trehalose positive strains analyzed in their study did not group together with the strains from subsp.…”

“…morganii (no trehalose fermenter) (Jensen et al, 1992). This phenotype is also linked to the presence of the trehalose operon (treR, treB, and treP) (Palmieri et al, 2020). This operon is present in the genome of all cheese isolates.…”

Diagnosing Infectious Diseases in Poultry Requires a Holistic Approach: A Review

“…Sequence analysis of rRNA has been used for example for species identification of Campylobacter jejuni and Campylobacter coli [93], or Avibacterium paragallinarum [94]. NGS/WGS proved valuable in gaining more data regarding characterization of Morganella morganii [95], Ornithobacterium rhinotracheale [96], E. coli [97] and Salmonella Infantis [98]. These methods can also be applied for direct identification of bacterial communities as shown for samples from poultry carcasses in slaughterhouses [99].…”