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Volume 29, Number 9—September 2023
Dispatch

Population Analysis of Escherichia coli Sequence Type 361 and Reduced Cefiderocol Susceptibility, France

Agnès B. JoussetComments to Author , Laura Bouabdallah, Aurélien Birer, Isabelle Rosinski-Chupin, Jean-François Mariet, Saoussen Oueslati, Cécile Emeraud, Delphine Girlich, Philippe Glaser, Thierry Naas, Rémy A. Bonnin, and Laurent Dortet
Author affiliations: Bicêtre Hospital Bacteriology Hygiene, Le Kremlin-Bicetre, France (A.B. Jousset, J.-F. Mariet, C. Emeraud, T. Naas, R.A. Bonnin, L. Dortet); Institut National de la Santé et de la Recherche Médicale, Paris, France (A.B. Jousset, L. Bouabdallah, S. Oueslati, C. Emeraud, D. Girlich, T. Naas, R.A. Bonnin, L. Dortet); Centre National de Référence de la Résistance aux Antibiotiques, Le Kremlin-Bicetre (A.B. Jousset, J.-F. Mariet, C. Emeraud, T. Naas, R.A. Bonnin, L. Dortet); Centre National de Référence de la Résistance aux Antibiotiques, Clermont-Ferrand, France (A. Birer); Institut Pasteur, Paris (I. Rosinski-Chupin, P. Glaser); Universite Paris-Sud, Paris (T. Naas)

Main Article

Figure 2

Phylogenetic analysis of 80 Escherichia coli ST361 isolates collected during 2015–2022 and used in a population analysis of E. coli ST361 and reduced cefiderocol susceptibility, France. Isolates were sent to the French National Reference Center for carbapenem-resistant Enterobacterales testing as part of routine surveillance. The phylogenetic tree was built by using SNIppy version 4.6.0 (https://github.com/tseemann/snippy) on whole-genome sequences. Data were visualized using iTOL 6.5.2 (https://itol.embl.de). The most ancient isolate, isolate no. 86J1 collected in 2015 (bold text, lower left of tree), was used as reference genome. A total of 4,957,882 nt positions were analyzed in the comparison. Colors indicate various outbreaks involving 13 OXA-244 producers (yellow) and 7 NDM-5 producers (blue). Two specific features are represented with filled circles: a YRIN(K) insertion in PBP3 (green) and chromosomal mutations within genes involved in siderophore-iron uptake (red). Genes investigated were cirA, fiu, fepA, fepB, fecA, fhuA, tonB, pcnB, exbB, exbD, baeS/baeR, and ompR/envZ. Scale bar indicates nucleotide substitutions per site. KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamase; OXA, oxacillinase; PBP3, penicillin-binding protein 3.

Figure 2. Phylogenetic analysis of 80 Escherichia coli ST361 isolates collected during 2015–2022 and used in a population analysis of E. coli ST361 and reduced cefiderocol susceptibility, France. Isolates were sent to the French National Reference Center for carbapenem-resistant Enterobacterales testing as part of routine surveillance. The phylogenetic tree was built by using SNIppy version 4.6.0 (https://github.com/tseemann/snippy) on whole-genome sequences. Data were visualized using iTOL 6.5.2 (https://itol.embl.de). The most ancient isolate, isolate no. 86J1 collected in 2015 (bold text, lower left of tree), was used as reference genome. A total of 4,957,882 nt positions were analyzed in the comparison. Colors indicate various outbreaks involving 13 OXA-244 producers (yellow) and 7 NDM-5 producers (blue). Two specific features are represented with filled circles: a YRIN(K) insertion in PBP3 (green) and chromosomal mutations within genes involved in siderophore-iron uptake (red). Genes investigated were cirA, fiu, fepA, fepB, fecA, fhuA, tonB, pcnB, exbB, exbD, baeS/baeR, and ompR/envZ. Scale bar indicates nucleotide substitutions per site. KPC, Klebsiella pneumoniae carbapenemase; NDM, New Delhi metallo-β-lactamase; OXA, oxacillinase; PBP3, penicillin-binding protein 3.

Main Article

Page created: July 14, 2023
Page updated: August 20, 2023
Page reviewed: August 20, 2023
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