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Volume 27, Number 3—March 2021
Research

Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections

Opeyemi U. Lawal, Maria J. Fraqueza, Ons Bouchami, Peder Worning, Mette D. Bartels, Maria L. Gonçalves, Paulo Paixão, Elsa Gonçalves, Cristina Toscano, Joanna Empel, Małgorzata Urbaś, M. Angeles Domínguez, Henrik Westh, Hermínia de Lencastre, and Maria MiragaiaComments to Author 
Author affiliations: Universidade Nova de Lisboa, Oeiras, Portugal (O.U. Lawal, O. Bouchami, H. de Lencastre, M. Miragaia); Centre for Interdisciplinary Research in Animal Health (CIISA), Universidade de Lisboa, Lisbon, Portugal (M.J., Fraqueza); Hvidovre University Hospital, Hvidovre, Denmark (P. Worning, M.D. Bartels, H. Westh); SAMS Hospital, Lisbon (M.L. Gonçalves); Hospital da Luz, Lisbon (P. Paixão); Hospital Egas Moniz, Lisbon (E. Gonçalves, C. Toscano); Narodowy Instytut Leków, Warsaw, Poland (J. Empel, M. Urbaś); Hospital Universitari de Bellvitge, Barcelona, Spain (M.A. Domínguez); University of Copenhagen, Copenhagen, Denmark (H. Westh); The Rockefeller University, New York, New York, USA (H. de Lencastre)

Main Article

Figure 2

Phylogenomic analysis and distribution of Staphylococcus saprophyticus isolates collected from human infections and a slaughterhouse, Portugal, 2016–2017. A) Maximum-likelihood tree of 232 isolates from human infections or slaughterhouse contamination. The tree was constructed by using 14,110 single-nucleotide polymorphisms (SNPs) without recombination. Each node represents a strain; nodes with identical color belong to the same lineage. The assembled contigs were mapped to the reference genome S. saprophyticus ATCC 15305 (GenBank accession no. AP008934.1; black star). SNPs generated from each genome were concatenated to single alignment corresponding to position of the reference genome. Polymorphic sites resulting from recombination events in the SNP alignments were filtered out by using out by using Gubbins version 2.3.4 (12). Tree was reconstructed by using RAxML version 8.2.4 (https://github.com/stamatak/standard-RAxML). The generalized time-reversible nucleotide substitution model with gamma correction was performed with 100 bootstrap random re-samplings for support. The tree was visualized by using Interactive Tree of Life (iTOL; https://itol.embl.de). The clusters highlighted in cream represent admixture of isolates recovered from different sources that are closely related by SNPs in clusters G5–G11 and S2–S4. The inner ring (ring 1) represents genetic relatedness of isolates recovered from different sites inside the slaughterhouses and those recovered from infection in the community. The center ring (ring 2) identifies the isolates recovered from different hospitals. The outer rings (rings 3–8) represent the distribution of 6 genes that convey antimicrobial resistance. Scale bar indicates nucleotide substitutions per site. B) Source-based distribution of S. saprophyticus isolates in the lineage G and lineage S. Lineage G consisted isolates from infections, colonization, and contamination. Almost all (97%) isolates in lineage S are from human colonization and infection.

Figure 2. Phylogenomic analysis and distribution of Staphylococcus saprophyticus isolates collected from human infections and a slaughterhouse, Portugal, 2016–2017. A) Maximum-likelihood tree of 232 isolates from human infections or slaughterhouse contamination. The tree was constructed by using 14,110 single-nucleotide polymorphisms (SNPs) without recombination. Each node represents a strain; nodes with identical color belong to the same lineage. The assembled contigs were mapped to the reference genome S. saprophyticus ATCC 15305 (GenBank accession no. AP008934.1; black star). SNPs generated from each genome were concatenated to single alignment corresponding to position of the reference genome. Polymorphic sites resulting from recombination events in the SNP alignments were filtered out by using out by using Gubbins version 2.3.4 (12). Tree was reconstructed by using RAxML version 8.2.4 (https://github.com/stamatak/standard-RAxML). The generalized time-reversible nucleotide substitution model with gamma correction was performed with 100 bootstrap random re-samplings for support. The tree was visualized by using Interactive Tree of Life (iTOL; https://itol.embl.de). The clusters highlighted in cream represent admixture of isolates recovered from different sources that are closely related by SNPs in clusters G5–G11 and S2–S4. The inner ring (ring 1) represents genetic relatedness of isolates recovered from different sites inside the slaughterhouses and those recovered from infection in the community. The center ring (ring 2) identifies the isolates recovered from different hospitals. The outer rings (rings 3–8) represent the distribution of 6 genes that convey antimicrobial resistance. Scale bar indicates nucleotide substitutions per site. B) Source-based distribution of S. saprophyticus isolates in the lineage G and lineage S. Lineage G consisted isolates from infections, colonization, and contamination. Almost all (97%) isolates in lineage S are from human colonization and infection.

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