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

Nicola Palmieri,Claudia Hess,Merima Alispahic,Michael Hess

doi:10.1186/s12864-020-07001-2

Nicola Palmieri, Claudia Hess + Show 2 more

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https://doi.org/10.1186/s12864-020-07001-2

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Abstract

BackgroundM. 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.ResultsTwo strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (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, beta-lactams, 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.ConclusionsIn 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.

Highlights

M. morganii is a bacterium frequently associated with urinary infections in humans
The bacterium is scarcely reported in poultry: in Nigeria and China, M. morganii was isolated from dead broilers and its pathogenicity confirmed by infecting day-old chicks [4, 5]
Escherichia coli was isolated from all cases investigated as reported by [7] who detected the same bacterium with M. morganii in liver and spleen of a broiler

Summary

Introduction

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. 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. In reported human cases the disease spectrum associated with M. morganii infections is broad and the mortality following an infection remains high [3]. The bacterium is scarcely reported in poultry: in Nigeria and China, M. morganii was isolated from dead broilers and its pathogenicity confirmed by infecting day-old chicks [4, 5]. A total of 47 complete genome sequences from M. morganii strains are currently available from NCBI database mainly isolated from humans, and one from a broiler, salamander, dolphin, plants and few where the host is unknown. These studies reported peculiar strainspecific innovations such as: i) acquisition of resistance genes from Acinetobacter spp. in the F675 strain [9], ii) introduction of toxins (hlyA) through lateral transfer from phages in the MM1, MM4 and MM190 strains [10], and iii) plasmid-mediated acquisition of quinolone resistance in the INSRALV892a strain [7]

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