Strong influence of livestock environments on the emergence and dissemination of distinct multidrug-resistant phenotypes among the population of non-typhoidal Salmonella

The problem of emergence and dissemination of multidrug resistance, especially among Gram-negative bacteria, has reached alarming levels. This increases the need to develop surveillance methods that more effectively and accurately provide information about the emergence and spread of multidrug-resistant organisms. In this study, using a well-defined population of non-typhoidal Salmonella (NTS) isolates associated with avian, bovine and porcine hosts, we found that the livestock environments had a specific (P < 0.005) and profound (P < 0.005) effect on the evolution of multidrug-resistant phenotypes among population of NTS isolates. The MDR pattern containing penicillins, tetracyclines and macrolides and the evolving counterparts (i.e., penicillins, tetracyclines and macrolides + other antibiotic classes) were significantly (P < 0.005) associated with NTS isolates of porcine origin. Similarly, MDR patterns containing folate pathway inhibitors, macrolides and aminocyclitol or containing penicillins, cephalosporins, tetracyclines, phenicols and macrolides were significantly associated with avian (P < 0.005) and bovine (P < 0.005) NTS isolates, respectively. Furthermore, STRUCTURE, an evolutionary analysis, clearly showed that the host origin (i.e., livestock environment), and not the genetic background of different NTS serovars, was the most determinative factor for acquisition and spread of MDR phenotypes. In addition, we described a novel non-synonymous mutation, located outside of the QRDR at position 864 of GyrA, that was likely associated with fluoroquinolone resistance.