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Salmonella enterica isolated from dairy cattle in Uruguay presents a diversity of antibiotic resistance genes and mobile genetic elements
Casaux, M.L., D’Alessandro, B...
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Objectives
The objective of this work is to study the presence and distribution of antibiotic resistance genes, plasmids and integrons in Salmonella enterica of bovine origin from Uruguay.
Materials and methods
In total 75 isolates from the collection of Plataforma de Investigación en Salud Animal-INIA-Uruguay collection were included. Forty-two isolates were obtained between 2016 and 2020 from 33 outbreaks of neonatal diarrhea and/or mortality due to bovine salmonellosis in calves that presented or succumbed to the disease with bacteriological and histopathological diagnosis. The remaining 33 isolates were obtained between 2019 and 2020 from one dairy farm with a history of bovine salmonellosis. Isolate sources included calves and cows’ feces, water and food for animal consumption.
The genome of this isolates' set was obtained using Illumina MiSeq in MicrobesNG (UK). The sequence reads were uploaded to EnteroBase. The isolates' serovar was determined using the SISTR1+SEqSero2 scheme, and the sequence type (ST) using the Achtman scheme. The assembled genomes were then further analyzed using the tools ResFiinder 4.1, PointFinder, PlasmidFinder 2.1 and IntFinder 1.0 from the Center for Genomic Epidemiology (CGE) for identifying acquired resistance genes, chromosomal mutations, plasmids and integrons.
Results
In total, 31 isolates were typed as S. Typhimurium (STy, 41.3%), 24 as S. Newport (SNw; 32.0%), 11 as S. Anatum (SAn; 14.6%), 6 as S. Dublin (SDb; 8.0%), one S. Agona (SAg; 1.3%); one S. Montevideo (SMv; 1.3%) and one as IIIb61:i:z53 (1.3%).
For every serovar identified, only a single ST was present. Every STy isolate was classified as ST19, SNw isolates as ST45, ST64 for the SAn isolates and SDb isolates were typed as ST10. Less frequent isolates SAg, SMv and IIIb61:i:z53 were typed as ST13, ST138 and ST430 respectively.
There was a high diversity of antibiotic resistance genes in the isolates collection. Every isolate carries the aac(6')-Iaa gene that confers resistance to aminoglycosides. Within this group, aph(3'')-Ib and aph(6)-Id were also frequently present. Fifty-one isolates presented resistance genes for tetracyclines, tet(A) was detected in 47 isolates while four carried tet(B). The sul2 gene was present in 29 isolates conferring resistance to sulfonamides. Interestingly some genes like aadA1, aadA2, aadA17, floR and cmlA1 that generally are present in genetic mobile elements were detected. The blaTEM-1B gene related to penicillin was detected only in 7 isolates of SA and ST isolates. Plasmidic qnr gene was carried by 5 isolates while 37 isolates had the parC_T57S mutation both conferring resistance to quinolones. One SD isolated showed the mutation acrB_R717Q to confer resistance to azithromycin.
Considering the presence of antibiotic resistance in all the genomes, twenty-four were multi drug resistant (MDR). This characteristic was only detected in STy, SA and SAg serotypes. Among these, one presented antibiotic resistance genes for 4 groups of antibiotics and five for 6 groups of antibiotics.
All except five isolates carried at least one plasmid. The most frequent plasmids were IncFII(pHN7A8), IncFII(S), IncFIB(S), Col440I and IncI1. Forty-nine strains had 1 plasmid, 17 strains had 2 plasmids, and 4 strains had 3 plasmids. All STy carried plasmids and the most frequent combination of plasmids was Col440/ IncFIB(S).
Two class 1 integrons were detected in the collection. In705, carrying aadA1 gene, was detected in two STy isolates while In1363, carrying aac(3)-IId and intI1, was detected in one SAn isolate and in one STy. These 4 isolates were MDR and carried at least one plasmid.
Conclusions
The evaluation of the genome allowed us to detect serotypes involved in the outbreaks with STy as the most frequent. A wide distribution of MDR isolates was found in the farm's outbreaks and environment. There was a high number of isolates carrying genes that confer resistance to aminoglycosides, tetracyclines and sulfonamides, antibiotics that are widely used in veterinary practice in Uruguay. Most of the serotypes detected in the collection could have an impact on human health. This work represents one of the first studies assessing the MDR genes in Salmonella from dairy cattle in South America.
Keywords: Salmonellosis, dairy cattle, antimicrobial resistance, genome, South America.
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