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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 1

Maximum-likelihood tree of Staphylococcus saprophyticus isolates recovered from human infections and colonization globally, 1997–2017. The tree was constructed by using 9,134 SNPs without recombination. Among analyzed isolates, 321 were recovered from UTIs, 12 from blood, and 4 from colonization. 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). Polymorphic sites resulting from recombination events in the single-nucleotide polymorphism (SNP) alignments were filtered out by using Gubbins version 2.3.4 (12). Maximum likelihood tree was reconstructed by using RAxML version 8.2.4 (https://github.com/stamatak/standard-RAxML). We performed generalized time-reversible nucleotide substitution model with gamma correction with 100 bootstraps random resampling for support. We visualized the tree by using Interactive Tree of Life (iTOL; https://itol.embl.de). Black triangles represent isolates fully sequenced by using the long-read nanopore technologies and used as reference to estimate r/m in the respective lineage. Cream color represents clusters G1, G2, G3, G4, and S1, which had dissemination and transmission in same country and in different countries. The outer ring represents isolates’ country of origin; blocks with identical color represent isolates from the same country. Of note, cluster G4 contains a pair of isolates collected in 2016 that had only 10 SNPs difference; one is a blood isolate from Barcelona, Spain (KS266) and the other is a UTI isolate recovered in Lisbon, Portugal (KS135). Scale bar indicates number of substitutions per site. UTI, urinary tract infection; r/m, recombination to mutation ratio.

Figure 1. Maximum-likelihood tree of Staphylococcus saprophyticus isolates recovered from human infections and colonization globally, 1997–2017. The tree was constructed by using 9,134 SNPs without recombination. Among analyzed isolates, 321 were recovered from UTIs, 12 from blood, and 4 from colonization. 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). Polymorphic sites resulting from recombination events in the single-nucleotide polymorphism (SNP) alignments were filtered out by using Gubbins version 2.3.4 (12). Maximum likelihood tree was reconstructed by using RAxML version 8.2.4 (https://github.com/stamatak/standard-RAxML). We performed generalized time-reversible nucleotide substitution model with gamma correction with 100 bootstraps random resampling for support. We visualized the tree by using Interactive Tree of Life (iTOL; https://itol.embl.de). Black triangles represent isolates fully sequenced by using the long-read nanopore technologies and used as reference to estimate r/m in the respective lineage. Cream color represents clusters G1, G2, G3, G4, and S1, which had dissemination and transmission in same country and in different countries. The outer ring represents isolates’ country of origin; blocks with identical color represent isolates from the same country. Of note, cluster G4 contains a pair of isolates collected in 2016 that had only 10 SNPs difference; one is a blood isolate from Barcelona, Spain (KS266) and the other is a UTI isolate recovered in Lisbon, Portugal (KS135). Scale bar indicates number of substitutions per site. UTI, urinary tract infection; r/m, recombination to mutation ratio.

Main Article

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