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Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids

Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who jus...

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Autores principales: Vázquez, Xenia, Fernández, Javier, Rodríguez-Lozano, Jesús, Calvo, Jorge, Rodicio, Rosaura, Rodicio, M. Rosario
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9219668/
https://www.ncbi.nlm.nih.gov/pubmed/35740192
http://dx.doi.org/10.3390/antibiotics11060786
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author Vázquez, Xenia
Fernández, Javier
Rodríguez-Lozano, Jesús
Calvo, Jorge
Rodicio, Rosaura
Rodicio, M. Rosario
author_facet Vázquez, Xenia
Fernández, Javier
Rodríguez-Lozano, Jesús
Calvo, Jorge
Rodicio, Rosaura
Rodicio, M. Rosario
author_sort Vázquez, Xenia
collection PubMed
description Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [bla(CTX-M-65), aph(4)-Ia, aac(3)-IVa, aph(3′)-Ia, floR, dfrA14, sul1, tet(A), aadA1 ± fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacEΔ1). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to bla(CTX-M-65)-positive ± fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis bla(CTX-M-65) ± fosA3 MDR clone has been reported in Spain.
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spelling pubmed-92196682022-06-24 Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids Vázquez, Xenia Fernández, Javier Rodríguez-Lozano, Jesús Calvo, Jorge Rodicio, Rosaura Rodicio, M. Rosario Antibiotics (Basel) Article Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [bla(CTX-M-65), aph(4)-Ia, aac(3)-IVa, aph(3′)-Ia, floR, dfrA14, sul1, tet(A), aadA1 ± fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacEΔ1). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to bla(CTX-M-65)-positive ± fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis bla(CTX-M-65) ± fosA3 MDR clone has been reported in Spain. MDPI 2022-06-09 /pmc/articles/PMC9219668/ /pubmed/35740192 http://dx.doi.org/10.3390/antibiotics11060786 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vázquez, Xenia
Fernández, Javier
Rodríguez-Lozano, Jesús
Calvo, Jorge
Rodicio, Rosaura
Rodicio, M. Rosario
Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title_full Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title_fullStr Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title_full_unstemmed Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title_short Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the bla(CTX-M-65) Gene with or without fosA3 in pESI-like Plasmids
title_sort genomic analysis of two mdr isolates of salmonella enterica serovar infantis from a spanish hospital bearing the bla(ctx-m-65) gene with or without fosa3 in pesi-like plasmids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9219668/
https://www.ncbi.nlm.nih.gov/pubmed/35740192
http://dx.doi.org/10.3390/antibiotics11060786
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