Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids
<i>Salmonella enterica</i> serovar Infantis (<i>S</i>. 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 <i>S</i>. I...
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MDPI AG
2022-06-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/11/6/786 |
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| author | Xenia Vázquez Javier Fernández Jesús Rodríguez-Lozano Jorge Calvo Rosaura Rodicio M. Rosario Rodicio |
| author_facet | Xenia Vázquez Javier Fernández Jesús Rodríguez-Lozano Jorge Calvo Rosaura Rodicio M. Rosario Rodicio |
| author_sort | Xenia Vázquez |
| collection | DOAJ |
| description | <i>Salmonella enterica</i> serovar Infantis (<i>S</i>. 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 <i>S</i>. 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 <i>S. enterica</i> 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 [<i>bla</i><sub>CTX-M-65</sub>, <i>aph(4)-Ia</i>, <i>aac(3)-IVa</i>, <i>aph(3′)-Ia</i>, <i>floR</i>, <i>dfrA14</i>, <i>sul1</i>, <i>tet</i>(A), <i>aadA1</i> ± <i>fosA3</i>], as well as genes for resistance to heavy metals and disinfectants (<i>mer</i>, <i>ars</i> and <i>qacEΔ1</i>). 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 <i>nfsA</i> and <i>nsfB</i>, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two <i>S</i>. 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 <i>bla</i><sub>CTX-M-65</sub>-positive ± <i>fosA3</i> 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 <i>S</i>. Infantis <i>bla</i><sub>CTX-M-65</sub> ± <i>fosA3</i> MDR clone has been reported in Spain. |
| first_indexed | 2024-03-10T00:35:36Z |
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| spelling | doaj.art-a210fd82a8e94da099c88319991f7fad2023-11-23T15:17:17ZengMDPI AGAntibiotics2079-63822022-06-0111678610.3390/antibiotics11060786Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like PlasmidsXenia Vázquez0Javier Fernández1Jesús Rodríguez-Lozano2Jorge Calvo3Rosaura Rodicio4M. Rosario Rodicio5Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), 33006 Oviedo, SpainInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, SpainServicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, SpainServicio de Microbiología, Hospital Universitario Marqués de Valdecilla (IDIVAL), 39008 Santander, SpainInstituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, SpainÁrea de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), 33006 Oviedo, Spain<i>Salmonella enterica</i> serovar Infantis (<i>S</i>. 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 <i>S</i>. 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 <i>S. enterica</i> 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 [<i>bla</i><sub>CTX-M-65</sub>, <i>aph(4)-Ia</i>, <i>aac(3)-IVa</i>, <i>aph(3′)-Ia</i>, <i>floR</i>, <i>dfrA14</i>, <i>sul1</i>, <i>tet</i>(A), <i>aadA1</i> ± <i>fosA3</i>], as well as genes for resistance to heavy metals and disinfectants (<i>mer</i>, <i>ars</i> and <i>qacEΔ1</i>). 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 <i>nfsA</i> and <i>nsfB</i>, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two <i>S</i>. 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 <i>bla</i><sub>CTX-M-65</sub>-positive ± <i>fosA3</i> 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 <i>S</i>. Infantis <i>bla</i><sub>CTX-M-65</sub> ± <i>fosA3</i> MDR clone has been reported in Spain.https://www.mdpi.com/2079-6382/11/6/786<i>S</i>. Infantismultidrug-resistance<i>bla</i><sub>CTX-M-65</sub><i>fosA3</i>heavy-metal resistancepESI-like megaplasmid |
| spellingShingle | Xenia Vázquez Javier Fernández Jesús Rodríguez-Lozano Jorge Calvo Rosaura Rodicio M. Rosario Rodicio Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids Antibiotics <i>S</i>. Infantis multidrug-resistance <i>bla</i><sub>CTX-M-65</sub> <i>fosA3</i> heavy-metal resistance pESI-like megaplasmid |
| title | Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids |
| title_full | Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids |
| title_fullStr | Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids |
| title_full_unstemmed | Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids |
| title_short | Genomic Analysis of Two MDR Isolates of <i>Salmonella enterica</i> Serovar Infantis from a Spanish Hospital Bearing the <i>bla</i><sub>CTX-M-65</sub> Gene with or without <i>fosA3</i> in pESI-like Plasmids |
| title_sort | genomic analysis of two mdr isolates of i salmonella enterica i serovar infantis from a spanish hospital bearing the i bla i sub ctx m 65 sub gene with or without i fosa3 i in pesi like plasmids |
| topic | <i>S</i>. Infantis multidrug-resistance <i>bla</i><sub>CTX-M-65</sub> <i>fosA3</i> heavy-metal resistance pESI-like megaplasmid |
| url | https://www.mdpi.com/2079-6382/11/6/786 |
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