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Title: Microarray-based analysis of IncA/C Plasmid-Associated genes from multidrug-resistant Salmonella enterica

Author
item Lindsey, Rebecca
item Frye, Jonathan
item Cray, Paula
item Meinersmann, Richard - Rick

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2011
Publication Date: 10/20/2011
Citation: Lindsey, R.L., Frye, J.G., Cray, P.J., Meinersmann, R.J. 2011. Microarray-based analysis of IncA/C Plasmid-Associated genes from multidrug-resistant Salmonella enterica. Applied and Environmental Microbiology. 77(19):6991-6999.

Interpretive Summary: Salmonella are food borne bacterial pathogens that can result in serious illness in humans and animals. Salmonella may be acquired by the oral ingestion of contaminated food or water. Approximately 600 people die each year in the U.S. after being infected. Salmonella carries assorted plasmids which are pieces of deoxyribonucleic acid (DNA) that can be easily transferred from one bacterial strain to another. There is a lot of interest in characterizing and tracking plasmids because they may carry genes or pieces of genes that contribute to disease. Some of these genes may confer resistance to antimicrobials. While antimicrobial treatment of salmonellosis is not typically recommended, in cases where it is necessary resistance to antimicrobials, and in particular multiple antimicrobials, may compromise treatment outcome. Inc A/C plasmids are of interest because they are associated with multidrug resistance. To study these plasmids we use DNA microarrays. Microarrays allow us to look at hundreds of genes at once and they are a powerful tool which enables us to get more information in a short period of time. Here we used a microarray to study Inc A/C plasmids from 59 Salmonella isolates collected from animal sources. From this data we can also study bacterial phylogeny which is useful for demonstrating how genes may move and how fast they move between bacteria. Our studies suggest that Inc A/C plasmids move antimicrobial resistance relatively slowly as compared to other mechanisms. Slow exchange decreases the rate at which Salmonella may develop resistance. These data are useful for physicians, veterinarians, scientists and epidemiologists as they develop models to better understand the evolution and transmission of antimicrobial resistance.

Technical Abstract: Bacteria plasmids are fragments of extra-chromosomal double stranded deoxyribonucleic acid (DNA) that can contain a variety of genes beneficial to the survival of the host bacteria. Classification and tracking of bacterial plasmids is valuable for the study of horizontal gene transfer of drug resistance. Plasmids can be classified according to incompatibility (Inc) types which are based on the inability of plasmids with the same replication mechanism to exist in the same cell. In Enterobacteriaceae there are 26 described Inc or replicon types. Certain replicon types such as Inc A/C are associated with multidrug resistance (MDR). We developed a hybridization microarray that contains 288 unique 70mer oligonucleotide probes based on sequence from five Inc A/C plasmids: pYR1 (Yersinia ruckeri str. YR71), pPIP1202 (Yersinia pestis biovar Orientalis str. IP275), pP990180 (Photobacterium damselae subsp. Piscicida), pSL254 (Salmonella enterica subsp. enterica serovar Newport str. SL254) and pP91278 (Photobacterium damselae subsp. Piscicida). DNA from 59 Salmonella enterica isolates was hybridized to the microarray and analyzed for the presence/absence of genes. These isolates represented 17 serovars from 14 different host sources and were geographically discrete throughout the United States. Qualitative cluster analysis was performed using CLUSTER 3.0 to group microarray hybridization results. We found Inc A/C plasmids occur in two lineages distinguished by a major insertion-deletion (indel) region that contains mostly hypothetical proteins. The most variable genes are represented by transposon associated genes (transposons, integrating and conjugative elements (ICEs) and insertion sequence common regions (ISCRs)) as well as four antimicrobial resistance genes (aminoglycoside 3’-phosphotransferase (aphA), mercuric transport protein periplasmic component (merP), mercuric reductase (merA,) and aminoglycoside adenylyltransferase (aadA). Three mercury resistance genes were identified that were heterogeneous, while another thirteen mercury resistance genes were highly conserved in these Inc A/C plasmids suggesting that mercury exposure is a stronger pressure than anticipated. Our studies suggest that the transfer of antimicrobial resistance determinants via complete or nearly complete Inc A/C plasmids is relatively slow compared to exchange orchestrated by transposable elements such as transposons, ICES and ISCRs and thus pose a lesser threat for exchange of antimicrobial resistance.