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Vieira T, Dos Santos CA, de Jesus Bertani AM, Costa GL, Campos KR, Sacchi CT, Cunha MPV, Carvalho E, da Costa AJ, de Paiva JB, Rubio MDS, Camargo CH, Tiba-Casas MR. Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates. Antibiotics (Basel) 2024; 13:110. [PMID: 38391496 PMCID: PMC10885896 DOI: 10.3390/antibiotics13020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
Until 2015, polymyxin resistance was primarily attributed to chromosomal mutations. However, with the first report of mobile colistin resistance (mcr-1) in commensal Escherichia coli from food animals in China, the landscape has changed. To evaluate the presence of polymyxin resistance in Salmonella spp., a drop screening test for colistin and polymyxin B was carried out on 1156 isolates of non-human origin (animals, food, and the environment), received in Brazil, between 2016 and 2021. Subsequently, 210 isolates with resistant results in the drop test were subjected to the gold-standard test (broth microdilution) for both colistin and polymyxin B. Whole-genome sequencing (WGS) of 102 resistant isolates was performed for a comprehensive analysis of associated genes. Surprisingly, none of the isolates resistant to colistin in the drop test harbored any of the mcr variants (mcr-1 to mcr-10). WGS identified that the most common mutations were found in pmrA (n= 22; T89S) and pmrB (n = 24; M15T, G73S, V74I, I83A, A111V). Other resistance determinants were also detected, such as the aac(6')-Iaa gene in 72 isolates, while others carried beta-lactamase genes (blaTEM-1blaCTX-M-2, blaCMY-2). Additionally, genes associated with fluoroquinolone resistance (qnrB19, qnrS1, oqxA/B) were detected in 11 isolates. Colistin and polymyxin B resistance were identified among Salmonella from non-human sources, but not associated with the mcr genes. Furthermore, the already-described mutations associated with polymyxin resistance were detected in only a small number of isolates, underscoring the need to explore and characterize unknown genes that contribute to resistance.
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Affiliation(s)
- Thais Vieira
- Adolfo Lutz Institute, São Paulo 01246-000, SP, Brazil
| | | | | | | | | | | | | | | | | | | | - Marcela da Silva Rubio
- School of Agriculture and Veterinarian Sciences, University of the State of São Paulo, Jaboticabal 14884-900, SP, Brazil
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Braga PRC, Dos Santos CA, Bertani AMDJ, Vieira T, Amarante AF, Reis AD, Sacchi CT, Camargo CH, Ribeiro MG, Borges AS, Tiba-Casas MR. Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring bla CMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal. J Glob Antimicrob Resist 2023; 35:198-201. [PMID: 37805072 DOI: 10.1016/j.jgar.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023] Open
Abstract
OBJECTIVES This study reports the genomic characterization of the multidrug resistant Salmonella Newport strain 195_20 recovered from the diarrheic faeces of a foal in Brazil and co-harbouring the mcr-9, blaCMY-2 and qnrB19 antibiotic resistance genes. METHODS Bacterial isolate positive for mobile colistin resistance gene (mcr-9) was submitted to antimicrobial susceptibility testing by disk diffusion and broth microdilution for colistin and polymyxin B. The isolate was submitted to whole genome sequencing by Illumina technology and Nanopore Sequencing. Conjugation assays, plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinIon long reads sequencing. RESULTS Isolate 195_20 was identified as sequence type ST45, resistant to penicillin and cephalosporins (ampicillin, ceftazidime, ceftriaxone and cefotaxime), aminoglycosides (streptomycin and gentamicin), phenicol (chloramphenicol), quinolones and fluoroquinolones (nalidixic acid, ciprofloxacin, and pefloxacin), folate pathway antagonists (sulfonamides and trimethoprim-sulfamethoxazole), and tetracycline. A transferable IncHI2/IncHI2A plasmid sized ca. 262kb was found to carry the mcr-9 gene in a module consisting of IS903-mcr-9-wbuC-IS26. In addition, an 174kb IncC and a 48kb IncN plasmid were also identified in the 195_20 isolate, carrying blaCMY-2 and qnrB19, respectively. CONCLUSIONS Not surprisingly, isolate 195_20 was susceptible to polymyxins, possibly due to absence of qseBC regulatory operon. Presence of mobile colistin resistance (mcr-9), third-generation cephalosporins (blaCMY-2) and quinolone (qnrB19) resistance determinants in zoonotic pathogens from animals in close contact with humans alerts for the possible route of transmission between these different reservoirs.
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Affiliation(s)
- Pollyana Rennó Campos Braga
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | | | | | | | | | | | | | | | - Marcio Garcia Ribeiro
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | - Alexandre Secorun Borges
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
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de Jesus Bertani AM, Vieira T, Reis AD, Dos Santos CA, de Almeida EA, Camargo CH, Casas MRT. Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil. Sci Rep 2023; 13:2299. [PMID: 36759682 PMCID: PMC9911770 DOI: 10.1038/s41598-023-29599-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
This study analyzes the genomic findings of the first report of Salmonella isolate carrying the blaCTX-M-55 gene, recovered from a bacteremic patient from Brazil. A bacterial isolate positive for the blaCTX-M-55 gene was submitted to antimicrobial susceptibility testing by disk diffusion and epsilometric test. Whole genome sequencing was performed using Illumina technology. Conjugation assay was performed; plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinION long reads sequencing. Isolate 288_18 was identified as sequence type ST13, resistant to ampicillin, cefotaxime, ceftazidime, cefepime, ceftriaxone, and aztreonam. A transferable IncFII plasmid sized approximately 67 kb was found to carry the blaTEM-1 and blaCTX-M-55 in a module consisting of IS26-blaTEM-1B-WbuC-blaCTX-M-55-IS26. In addition, an 117 kb IncI1plasmid was also identified in the 288_18 isolate, but without additional resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-55 in Salmonella isolated from human infection in Brazil. The occurrence of blaCTX-M-55 in the IncFII epidemic plasmid in a relevant clinical human isolate of Salmonella Agona underscores the urgent need for enhanced and effective continuous surveillance for controlling its dissemination.
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Affiliation(s)
| | - Thais Vieira
- Bacteriology Division, Instituto Adolfo Lutz, 351, Doutor Arnaldo Avenue, São Paulo, Brazil
| | - Alex Domingos Reis
- Bacteriology Division, Instituto Adolfo Lutz, 351, Doutor Arnaldo Avenue, São Paulo, Brazil
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Yamada AY, de Souza AR, Lima MDJDC, Reis AD, Campos KR, Bertani AMDJ, de Araujo LJT, Sacchi CT, Tiba-Casas MR, Camargo CH. Co-production of Classes A and B Carbapenemases BKC-1 and VIM-2 in a Clinical Pseudomonas Putida Group Isolate from Brazil. Curr Microbiol 2022; 79:250. [PMID: 35834136 DOI: 10.1007/s00284-022-02945-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 11/03/2022]
Abstract
Emergence of resistance to classical antimicrobial agents is a public health issue, especially in countries with high antimicrobial consumption rates. Carbapenems have been employed as first-choice option for empirical treatment complicated infections. However, in the last decades, frequency of carbapenemase-producing Gram-negative bacteria has rising, demanding the use of alternative antimicrobial agents. By sequencing the entire genomes with short and long reads technologies, we report the isolation and genomic characterization of a carbapenem-resistant Pseudomonas clinical isolate. The identification based on average nucleotide identity indicates a putative new species into the Pseudomonas putida Group, which carries both the blaBKC-1 and blaVIM-2 carbapenemase genes. The blaBKC-1 was found to be on a transferable IncQ plasmid backbone, whereas blaVIM-2 was found in a new integron, In2126 (intl1∆-blaVIM-2-aacA7-blaVIM-2∆-aacA27-3'CS), described in this study. Our findings indicate that co-occurrence of classes A and B carbapenemase enzymes underscores the evolving emergence of more complex antimicrobial resistance in opportunistic pathogens.
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Affiliation(s)
- Amanda Yaeko Yamada
- Bacteriology Division, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 9º floor, Sao Paulo, 01246-902, Brazil.,Faculdade de Medicina, Universidade de São Paulo, Doutor Arnaldo Avenue, 455, São Paulo, 01246-000, Brazil
| | - Andreia Rodrigues de Souza
- Bacteriology Division, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 9º floor, Sao Paulo, 01246-902, Brazil
| | | | - Alex Domingos Reis
- Strategic Laboratory, Rapid Response Center, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 10º floor, Sao Paulo, 01246-902, Brazil
| | - Karoline Rodrigues Campos
- Strategic Laboratory, Rapid Response Center, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 10º floor, Sao Paulo, 01246-902, Brazil
| | | | - Leonardo Jose Tadeu de Araujo
- Strategic Laboratory, Rapid Response Center, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 10º floor, Sao Paulo, 01246-902, Brazil
| | - Claudio Tavares Sacchi
- Strategic Laboratory, Rapid Response Center, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 10º floor, Sao Paulo, 01246-902, Brazil
| | - Monique Ribeiro Tiba-Casas
- Bacteriology Division, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 9º floor, Sao Paulo, 01246-902, Brazil
| | - Carlos Henrique Camargo
- Bacteriology Division, Instituto Adolfo Lutz, Doutor Arnaldo Avenue, 351, 9º floor, Sao Paulo, 01246-902, Brazil. .,Faculdade de Medicina, Universidade de São Paulo, Doutor Arnaldo Avenue, 455, São Paulo, 01246-000, Brazil.
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de Jesus Bertani AM, Cunha MPV, de Carvalho E, de Araújo LT, dos Santos CA, Amarante AF, Reis AD, de Almeida EA, Campos KR, Sacchi CT, Camargo CH, Tiba-Casas MR. Genomic characterization of a multi-drug resistant, CTX-M-65-producing clinical isolate of Salmonella Infantis isolated in Brazil. Microbes Infect 2022; 24:104972. [DOI: 10.1016/j.micinf.2022.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
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Bueno MS, Freire MP, Cunha MPV, de Barcellos TAF, Bertani AMDJ, Dos Santos CA, Chimara E, Nagamori FO, Takagi EH, Costa SF, Ito RKDL, Abdala E, de Carvalho E, Tiba-Casas MR, Camargo CH. Detection of pandrug-resistant ST15 Acinetobacter baumannii causing bloodstream infection in an HSCT patient in Brazil. J Antimicrob Chemother 2021; 75:2691-2693. [PMID: 32544227 DOI: 10.1093/jac/dkaa218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mariana Sardinha Bueno
- Instituto Adolfo Lutz, São Paulo, SP, Brazil.,Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Edson Abdala
- Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Carlos Henrique Camargo
- Instituto Adolfo Lutz, São Paulo, SP, Brazil.,Universidade de São Paulo, São Paulo, SP, Brazil
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Dos Santos CA, Cunha MPV, Bertani AMDJ, de Almeida EA, Gonçalves CR, Sacchi CT, de Paiva JB, Camargo CH, Tiba-Casas MR. Detection of multidrug- and colistin-resistant Salmonella Choleraesuis causing bloodstream infection. J Antimicrob Chemother 2021; 75:2009-2010. [PMID: 32155258 DOI: 10.1093/jac/dkaa076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Camargo CH, Cunha MPV, de Barcellos TAF, Bueno MS, Bertani AMDJ, dos Santos CA, Nagamori FO, Takagi EH, Chimara E, de Carvalho E, Tiba-Casas MR. Genomic and phenotypic characterisation of antimicrobial resistance in carbapenem-resistant Acinetobacter baumannii hyperendemic clones CC1, CC15, CC79 and CC25. Int J Antimicrob Agents 2020; 56:106195. [DOI: 10.1016/j.ijantimicag.2020.106195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/29/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022]
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Soares FB, Camargo CH, Cunha MPV, de Almeida EA, Bertani AMDJ, Carvalho ED, de Paiva JB, Fernandes SA, Tiba-Casas MR. Co-occurrence of qnrE1 and blaCTX-M-8 in IncM1 transferable plasmids contributing to MDR in different Salmonella serotypes. J Antimicrob Chemother 2020; 74:1155-1156. [PMID: 30541085 DOI: 10.1093/jac/dky516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tavares LCB, Cunha MPV, de Vasconcellos FM, Bertani AMDJ, de Barcellos TAF, Bueno MS, Santos CA, Sant'Ana DA, Ferreira AM, Mondelli AL, Montelli AC, Sadatsune T, Sacchi CT, Gonçalves CR, Tiba-Casas MR, Camargo CH. Genomic and Clinical Characterization of IMP-1-Producing Multidrug-Resistant Acinetobacter bereziniae Isolates from Bloodstream Infections in a Brazilian Tertiary Hospital. Microb Drug Resist 2020; 26:1399-1404. [PMID: 32155381 DOI: 10.1089/mdr.2019.0210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Acinetobacter baumannii is the main species of the Acinetobacter genus; however, non-baumannii Acinetobacter (NBA) species causing infections have been described for the past years, as well as antimicrobial resistance. In this study, we describe the occurrence of two multidrug-resistant (MDR) IMP-1-producing Acinetobacter bereziniae isolates recovered from bloodstream infections in different patients but in the same intensive care unit among 134 carbapenem-resistant Acinetobacter screened. Antimicrobial susceptibility testing revealed resistance to carbapenems, extended spectrum, and antipseudomonad cephalosporins, amikacin, and trimethoprim-sulfamethoxazole. Both A. bereziniae isolates shared the same ApaI-pulsed-field gel electrophoresis (PFGE) pattern. Whole-genome sequencing of both isolates revealed that blaIMP-1 was embedded into an In86 Class I integron carrying also sul1, aac(6')-31, and aadA genes. A new sequence type (ST1309 Pasteur) was deposited. The virulence genes lpxC and ompA, seen in A. baumannii, were detected in the A. bereziniae strains. Recognition of A. bereziniae causing invasive MDR infection underscores the role of NBA species as human pathogens especially in at-risk patients.
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Affiliation(s)
- Lais Calissi Brisolla Tavares
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo, Brazil.,Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Thays Almeida Franco de Barcellos
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo, Brazil.,Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mariana Sardinha Bueno
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo, Brazil.,Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Terue Sadatsune
- Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | | | | | | | - Carlos Henrique Camargo
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo, Brazil.,Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Tiba-Casas MR, Sacchi CT, Gonçalves CR, Almeida EA, Soares FB, de Jesus Bertani AM, Fernandes SA, de Paula Eduardo MB, Camargo CH. Molecular analysis of clonally related Salmonella Typhi recovered from epidemiologically unrelated cases of typhoid fever, Brazil. Int J Infect Dis 2019; 81:191-195. [PMID: 30849581 DOI: 10.1016/j.ijid.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The primary method of molecular subtyping for the identification and investigation of outbreaks has been pulsed-field gel electrophoresis (PFGE). In some cases, this technique has not been able to show discrimination between the unrelated strains that can be achieved by whole genome sequencing (WGS). METHODS The aim of this study was to determine the strengths and drawbacks of WGS using different analytic approaches compared to traditional typing method, PFGE, for retrospectively typing clusters cases of 28 S. Typhi. RESULTS We evaluated three analytical approaches on the WGS data set (Nucleotide Difference (ND), (SNPs) and Whole genome multi locus sequence typing (wgMLST) that identically classified the clusters-related strains into two clusters, cluster A (with strains from 2017), and Cluster B (with strains from 2007). CONCLUSIONS In this study WGS based typing, was able to compete with PFGE for differentiation of the clusters of S. Typhi strains.
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Soares FB, Camargo CH, Cunha MPV, de Almeida EA, Bertani AMDJ, de Carvalho E, de Paiva JB, Fernandes SA, Tiba-Casas MR. Subtyping of plasmid-mediated quinolone resistance among Salmonella serotypes by whole genome sequencing. Diagn Microbiol Infect Dis 2019; 94:403-406. [PMID: 30955894 DOI: 10.1016/j.diagmicrobio.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/30/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022]
Abstract
Most known plasmids are identified by conferring virulence or antimicrobial resistance phenotypes and such characteristics aid in the success of the dispersion of different plasmid types between bacteria from different sources. This study aimed to perform the subtyping of the plasmid-mediated quinolone resistance, detected in Salmonella spp. A total of 34 Salmonella strains non-susceptible to ciprofloxacin were evaluated. Strains were selected based on the presence of PMQR determined by Polymerase Chain Reaction and further submitted to Next Generation Sequencing. Most of the strains presented the qnrB19 in small ColE-like plasmids and qnrB2 gene associated with IncN/ST5 plasmids also detected. Our results indicated the co-occurrence of PMQR and ESBLs in plasmids that are a lineage of epidemic plasmids circulating in Salmonella in which additional resistances were detected, highlighting the potential threat of resistance Salmonella to public health, particularly in infections in which antimicrobial therapy is needed.
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