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. 2023 Jan;9(1):234-241.
doi: 10.1002/vms3.1015. Epub 2022 Nov 29.

Aspergillus flavus genetic structure at a turkey farm

Ghaya Cherif  1   2 , Ines Hadrich  3 , Myriam Harrabi  2   4 , Aicha Kallel  1   2 , Nejla Fakhfekh  1   2 , Mariem Messaoud  1   2 , Hajer Ben Abdallah  5 , Ons Azeiz  6 , Kalthoum Kallel  1   2 , Stéphane Ranque  7   8
Affiliations

Aspergillus flavus genetic structure at a turkey farm

Ghaya Cherif et al. Vet Med Sci. 2023 Jan.

Abstract

Background: The ubiquitous environmental fungus Aspergillus flavus is also a life-threatening avian pathogen.

Objectives: This study aimed to assess the genetic diversity and population structure of A. flavus isolated from turkey lung biopsy or environmental samples collected in a poultry farm.

Methods: A. flavus isolates were identified using both morphological and ITS sequence features. Multilocus microsatellite genotyping was performed by using a panel of six microsatellite markers. Population genetic indices were computed using FSTAT and STRUCTURE. A minimum-spanning tree (MST) and UPGMA dendrogram were drawn using BioNumerics and NTSYS-PC, respectively.

Results: The 63 environmental (air, surfaces, eggshells and food) A. flavus isolates clustered in 36 genotypes (genotypic diversity = 0.57), and the 19 turkey lung biopsies isolates clustered in 17 genotypes (genotypic diversity = 0.89). The genetic structure of environmental and avian A. flavus populations were clearly differentiated, according to both F-statistics and Bayesian model-based analysis' results. The Bayesian approach indicated gene flow between both A. flavus populations. The MST illustrated the genetic structure of this A. flavus population split in nine clusters, including six singletons.

Conclusions: Our results highlight the distinct genetic structure of environmental and avian A. flavus populations, indicative of a genome-based adaptation of isolates involved in avian aspergillosis.

Keywords: Aspergillus flavus; Bayesian model; F-statistics; Meleagris gallopavo; aspergillosis; avian aspergillosis; environment; genetic structure; microsatellite markers; population genetics; typing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Estimated population structure of Aspergillus flavus in a commercial poultry farm in Sfax (Tunisia) as inferred by the STRUCTURE software on the basis of the data on six microsatellite markers obtained from 82 isolates from environment (ENV‐A. flavus; n = 63) or turkey lung biopsy (AVI‐A. flavus; n = 19) samples. (a) Plot of the mean posterior probability (Ln P(D)) values per clusters (K), based on 10 replicates per K, generated by the STRUCTURE software, and (b)  ΔK analysis of Ln P(K). (c) STRUCTURE plots grouped by Q‐matrix (estimated membership coefficient for each sample) showing the distribution of genetic variation (c) at K = 2. Each strain is represented by a vertical line, which is partitioned into the coloured segments that represent the fungi estimated membership fractions in K. The same colour indicates that the isolates belong to the same group. Different colours for the same isolate indicate the percentage of the genotype shared with each group. An asterisk ‘*’ marks isolates that appear misclassified by STRUCTURE, which identifies them as a possible migrant or a descendent of a recent immigrant from another population.
FIGURE 2
FIGURE 2
Minimum spanning tree showing the genotypic diversity of Aspergillus flavus isolates based on microsatellite data. Each circle shows a unique genotype and its size, the number of strains belonging to the same genotype. Connecting lines and number between circles show the similarity between genotypes: (1.00) indicates only one marker difference, (2.00) indicates difference in two in two markers, and (3.00) difference in three markers. ‘*’ shows singletons.
FIGURE 3
FIGURE 3
UPGMA dendrogram based on the Dice similarity coefficient upon analysis of six microsatellites markers obtained from 82 environmental (ENV‐Aspergillus flavus; n = 63) and avian (AVI‐A. flavus; n = 19) isolates. Two main clusters are identified. Each cluster encompasses both environmental (red dots) and avian isolates (green dots) without any strict partition according to sampling origin. The three migrants isolates (lung biopsy) appear with triple stars ‘*’.
See this image and copyright information in PMC

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