The diversity of antimicrobial resistance is different in Salmonella Typhimurium DT104 from co-located animals and humans

In our paper, we set out to examine antimicrobial resistinclude only human isolates [1–3], and therefore explicit ance patterns in animals and humans, using an existing extensive dataset of Salmonella Typhimurium DT104 in Scotland. We concluded, based on a variety of novel and statistically robust analyses, that the Scottish animal population was unlikely to be the major source of resistance diversity for DT104 in humans. Far from concluding that there was no association between antimicrobial-resistant Salmonella in animals and humans, we set out to dissect the nature of this association using new analytical tools and techniques applied to one of the largest datasets available. We summarize Professor Collignon’s criticisms of our paper as follows: (i) most isolates had a resistance profile that was common to both animals and humans; (ii) we over-emphasized the importance of rare profiles; (iii) we ignored the issue of imported food; and (iv) the passively sampled animal isolates in our study were biased in some way. Given the clonal nature of S. Typhimurium DT104, it is unsurprising that the majority of isolates exhibit the same phenotypic resistance profiles. This may well indicate an association between isolates from animals and humans, but no objective interpretation of this observation alone would conclude that it is informative of any predominance in the direction of transmission between the two populations. Second, and in Professor Collignon’s view, most importantly, he states that we have selectively given similar weights to rare profiles as to more common profiles. This is not the case. We examined the diversity of resistance profiles found in these two populations across a spectrum of ecological diversity measures that include all possible weightings of rare profiles from equal contribution to no contribution (fig. 2c,d in our original paper). For all of these possible weightings, the phenotypes found in the human population are more diverse than those found in the animal population. Third, we reiterate the important distinction between the food products consumed in Scotland (much of which is imported), and the focus of our study—the local animal population that might comprise the Salmonella reservoir, and of which our sample is much more representative. The previous research on DT104 we reference does not demonstrate that DT104 is predominantly spread from food animals to humans via food; many of these studies