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Volume 30, Number 4—April 2024
Research

Emergence of Poultry-Associated Human Salmonella enterica Serovar Abortusovis Infections, New South Wales, Australia

Michael Payne, Sarah Williamson, Qinning Wang, Xiaomei Zhang, Vitali Sintchenko, Anthony Pavic, and Ruiting LanComments to Author 
Author affiliations: University of New South Wales, Sydney, New South Wales, Australia (M. Payne, X. Zhang, R. Lan); Birling Laboratories, Bringelly, New South Wales, Australia (S. Williamson, A. Pavic); Institute of Clinical Pathology and Medical Research–NSW Health Pathology, Westmead Hospital, Westmead, New South Wales, Australia (Q. Wang, V. Sintchenko); University of Sydney, Sydney (V. Sintchenko)

Main Article

Figure 2

Phylogenetic relationships of isolates and associated metadata in a study of the emergence of poultry-associated human Salmonella enterica serovar Abortusovis infections, New South Wales, Australia. A maximum-likelihood phylogeny of all 56 isolates including subclade annotation and relevant metadata. Branches colors indicate subclades 1 (blue) and 2 (green) and bootstrap support values are indicated at tree nodes. Branch lengths for 5 international isolates were shortened for clarity (dashed lines). Red dots indicate complete genomes. Colors in columns indicate host species, source type, source details, year of isolation, and presence or absence of virulence genes. Virulence genes were predicted by using abricate (https://github.com/tseemann/abricate), KMA (23), and VFDB (25): a) pSAbAus; b) yersinia HPI (11 genes); c) ivy; d) cvaA; e) cdtB; f) cfaB; g) stfF; h) hdeB; i) eutEJGHABCLKR; j) astA; k) sodCI; l) ompN; m) hcp1; n) pSLT-like plasmid; o) spv toxin (3 genes); p) Fimbriae klf/fae (6 genes). *Some virulence genes or islands have the same presence and absence pattern in all genes; those data are collapsed into 1 column and the number of genes are indicated in parentheses in the list. Inconclusive gene presence was assigned when only KMA identified the gene and it had <20% of the normalized genome coverage. H, host species; S, source; SD, source details; Y, year.

Figure 2. Phylogenetic relationships of isolates and associated metadata in a study of the emergence of poultry-associated human Salmonella enterica serovar Abortusovis infections, New South Wales, Australia. A maximum-likelihood phylogeny of all 56 isolates including subclade annotation and relevant metadata. Branches colors indicate subclades 1 (blue) and 2 (green) and bootstrap support values are indicated at tree nodes. Branch lengths for 5 international isolates were shortened for clarity (dashed lines). Red dots indicate complete genomes. Colors in columns indicate host species, source type, source details, year of isolation, and presence or absence of virulence genes. Virulence genes were predicted by using abricate (https://github.com/tseemann/abricate), KMA (23), and VFDB (25): a) pSAbAus; b) yersinia HPI (11 genes); c) ivy; d) cvaA; e) cdtB; f) cfaB; g) stfF; h) hdeB; i) eutEJGHABCLKR; j) astA; k) sodCI; l) ompN; m) hcp1; n) pSLT-like plasmid; o) spv toxin (3 genes); p) Fimbriae klf/fae (6 genes). *Some virulence genes or islands have the same presence and absence pattern in all genes; those data are collapsed into 1 column and the number of genes are indicated in parentheses in the list. Inconclusive gene presence was assigned when only KMA identified the gene and it had <20% of the normalized genome coverage. H, host species; S, source; SD, source details; Y, year.

Main Article

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