Unraveling the Global Phylodynamic and Phylogeographic Expansion of Mycoplasma gallisepticum: Understanding the Origin and Expansion of This Pathogen in Ecuador

Abstract

Mycoplasma gallisepticum (MG) is among the most significant problems in the poultry industry worldwide, representing a serious threat to international trade. Despite the fact that the mgc2 gene has been widely used for diagnostic and molecular characterization purposes, there is a lack of evidence supporting the reliability of this gene as a marker for molecular epidemiology approaches. Therefore, the current study aimed to assess the accuracy of the mgc2 gene for phylogenetic, phylodynamic, and phylogeographic evaluations. Furthermore, the global phylodynamic expansion of MG is described, and the origin and extension of the outbreak caused by MG in Ecuador were tracked and characterized. The results obtained strongly supported the use of the mgc2 gene as a reliable phylogenetic marker and accurate estimator for the temporal and phylogeographic structure reconstruction of MG. The phylodynamic analysis denoted the failures in the current policies to control MG and highlighted the imperative need to implement more sensitive methodologies of diagnosis and more efficient vaccines. Framed in Ecuador, the present study provides the first piece of evidence of the circulation of virulent field MG strains in Ecuadorian commercial poultry. The findings derived from the current study provide novel and significant insights into the origin, diversification, and evolutionary process of MG globally.

Keywords: Mycoplasma gallisepticum; mgc2 gene; phylodynamic expansion; phylogeographic approach; temporal diversification.

Figure 1

Phylogenetic, phylodynamic, and temporal assessment and application of mgc2 gene of Mycoplasma gallisepticum. (A) Evaluation of phylogenetic noise (left), phylodynamic signal (center), and temporal signal (right) of the mgc2 marker used. Left panel represents the likelihood mapping of mgc2 sequences; the dots inside the triangles represent the posterior probabilities of the possible unrooted topologies for each quartet (LQM). Numbers indicate the percentage of dots in the center of the triangle corresponding to phylonetic noise. The center panel represents the node distribution based on the genetic distance and the proportion of residuals; violin plots were generated using the Graphpad Prism software 8.4.1 (1992–2020, Graphpad Prism Software Inc., San Diego, CA, USA). The right panel represents the regression of root-to-tip genetic divergence. Representation created with Biorender.com. (B) Phylogenetic tree based on mgc2 sequences using all no-redundant genomes available at GenBank and maximum likelihood (ML) method; the GenBank IDs for all the sequences, with country and year of isolation, are shown. The main two lineages related to virulence are denoted by designations and colors (virulent: red, non-virulent: blue): the taxa names of the Ecuadorian MG strains are denoted in red, and the bootstrap values are denoted. In addition, to facilitate the host source information for each strain/isolate, a color code was included (chicken: dark yellow, duck: blue, wild bird: green, and turkey: purple). (C) Evolutionary history reconstruction of MG strains globally. Maximum clade credibility (MCC) tree based on mgc2 sequences from all the field strains of MG, the estimation of the most probable year for the MRCA for the ancestor and the emergence of MG, as well as the 95% highest probability density (HPD) are denoted. (D) Bayesian skyline plot (BSP) using an exponential, uncorrelated clock model. The x-axis is in units of year, and the y-axis represents the logarithmic scale of Neτ (where Ne is the effective population size and τ is the generation time). The x-axis is in units of year, and the y-axis represents the logarithmic scale of Neτ (where Ne is the effective population size and τ is the generation time). The period from the development of the commercial poultry to the starting use of the antibiotics in poultry is highlighted by blue shadow.

Figure 2

Global spatiotemporal dispersal of Mycoplasma gallisepticum. (A) Dispersal patterns inferred using discrete phylogeographic analysis of the mgc2 dataset are shown for four time slices; the map was reconstructed using Google Earth from the SpreaD3 software output. (B) Most probable route for the transmission of MG values of BF are denoted, the connection map was directly taken from out file of the spreaD3 software. Country code was used based on two letters representation following ISO3166. Representation created with Biorender.com.

Figure 3

Distribution and pathological characterization of the Mycoplasma gallisepticum outbreak in Ecuador. (A) Ecuador map showing the geographic distribution of samples collected. Pie chart representing proportion of samples negative and positive are shown. Map was built using QGIS 3.10 (https://www.qgis.org.) (B–E) Representative pathologic lesions in the selected chicken: (B,D) gross observations; (B) tracheitis; (D) airsacculitis; (C,E) histopathological analysis; (C) trachea; (E) air sacs.