Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil

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.

Caracterização fenotípica e genotípica de cepas de Salmonella spp. e subtipagem molecular de plasmídeos carreando genes de beta-lactamases de espectro estendido e AmpC / Phenotypic and genotypic characterization of strains of Salmonella spp. and molecular subtyping of plasmids carrying extended-spectrum beta-lactamase and AmpC genes

Salmonella spp. são reconhecidas como um dos mais importantes patógenos que ocasionam doença entérica, sendo a terceira causa de morte entre as doenças transmitidas por alimentos (DTAs). A maior preocupação atual deve-se ao aumento da resistência aos beta-lactâmicos, e a produção de beta-lactamases mediadas por plasmídeos dentro do gênero. O objetivo deste trabalho foi caracterizar fenotipicamente e genotipicamente 44 isolados de Salmonella spp. produtores de beta lactamases além de, realizar a subtipagem dos plasmídeos de resistência aos beta lactâmicos de cepas de origem humana e não humana. Foi realizado o teste de sensibilidade aos antimicrobianos e a determinação da Concentração Inibitória Mínima (CIM). A PCR foi utilizada para a identificação dos genes blaESBL e blaAmpC, em seguida, confirmados por sequenciamento de Sanger. Para a subtipagem plasmídial dos isolados foram utilizadas as técnicas de PBRT e pMLST. Os resultados do teste de sensibilidade aos antimicrobianos mostrou que 97,7% dos isolados foram resistentes à cefotaxima, 86,3% resistentes à sulfonamida e tetraciclina, 81,9% resistentes ao ácido nalidíxico, 68,1% resistentes a ceftriaxona e 56,8% a estreptomicina. De acordo com a PCR, 24 isolados (54,5%) foram positivos para ESBLs (CTX-M), e 20 isolados (45,5%) positivos para beta-lactamase do tipo AmpC, CMY-2. A variante CTX-M-2 foi encontrada em 27,2% dos isolados, seguido da variante CTX-M-8 (22,7%). As variantes CTX-M-15 e CTX-M-65 foram detectadas em um isolado respectivamente. De acordo com a tipagem plasmidial foram encontrados os grupos de incompatibilidade IncI1/ST12 e IncA/C/ST2 em cepas positivas para blaCMY-2. Para as variantes de CTX-M foram detectados os grupos de incompatibilidade IncHI2 em cepas produtoras de CTX-M-2, IncI1, IncF e IncL/M identificados em cepas CTX-M-8, e dois isolados não tipáveis nas variantes CTX-M-15 e CTX-M-65. A análise do perfil genético dos isolados por PFGE sugerem a circulação de cepas geneticamente relacionadas entre fontes humanas e não humanas no sorotipo Muenchenn, e um perfil de similaridade de 82,3% no sorotipo Heidelberg, em cepas provenientes de fontes de origem e anos de isolamento diferentes. Os resultados encontrados neste estudo revelam o cenário atual da resistência aos beta-lactâmicos e reforçam a necessidade de intensificar o monitoramento de isolados portadores de plasmídeos epidêmicos carreadores de beta-lactamases (ESBL e AmpC) na clínica, ambiente e na cadeia produtiva. (AU)

Salmonella spp. are recognized as one of the most important pathogens that cause enteric disease, being the third leading cause of death among foodborne diseases. The greatest current concern should be the increase in resistance to beta-lactams and the production of plasmidmediated beta-lactamases within the genus. The objective of this work was to characterize phenotypically and genotypically 44 isolates of Salmonella spp. beta-lactamase producers, in addition to subtyping plasmids resistant to beta-lactams from human and non-human strains. The antimicrobial sensitivity test was performed and the Minimum Inhibitory Concentration (MIC) was determined. A PCR was used to identify the blaESBL and blaAmpC genes, followed by Sanger sequencing. For plasmid subtyping were used PBRT and pMLST techniques. The results of the antimicrobial sensitivity test showed that 97.7% of the strains were resistant to cefotaxime, 86.3% resistant to sulfonamide and tetracycline, 81.9% resistant to nalidic acid, 68.1% resistant to ceftriaxone and 56.8% streptomycin. According to the PCR, 24 (54.5%) were positive for ESBLs (CTX-M) and 20 (45.5%) positive for AmpC-type beta-lactamase, CMY-2. A CTX-M-2 variant was found in 27.2% of isolates followed by the CTX-M-8 variant (22.7%). The variants, CTX-M-15 and CTX-M-65 were detected in one isolate, respectively. According to plasmid typing, the incompatibility groups IncI1/ST12 and IncA/C/ST2 were found in positive strains for blaCMY-2. For the CTX-M variants, the IncHI2 incompatibility groups were detected in the CTX-M-2, IncI1, IncF and IncL/M were found in the CTX-M-8 strains, and CTX-M-15 and CTX-M-65 variants were not typeable. The analysis of the genetic profile by PFGE suggests the circulation of strains related between human and non-human sources in the Muenchen serotype, and a similarity index of 82.3% in the Heidelberg serotype, in strains from different sources and years. The results found in this study reveal the current scenario of resistance to betalactams and reinforce the need to intensify the monitoring of epidemic plasmids carrying beta-lactamases (ESBL and AmpC) in the clinic, environment and productive chain. (AU)