Reply to Partridge et al. Complementary bioinformatics and experimental approaches to investigate the transfer of AMR genes

We would like to thank Sally R. Partridge et al. for the letter (1) and appreciate the opportunity to clarify our methods and thinking in relation to the concerns raised. We developed Plascad (2) for automated plasmid classification based on previously suggested schemes and standards (3⇓⇓–6) and extended the plasmid classification results in the existing database. We agree that the number of conjugative plasmids could be underestimated when the classification is relying on the presence of limited key genes. In fact, most of the misclassified plasmids in those Gram-positive bacteria mentioned by Partridge et al. are classified as mobilizable plasmids and also carry some genes related to conjugation based on our pipeline (Table 1), but do not meet the conserved criteria of the number of key indicators for conjugative plasmids previously proposed (5). Although mobilizable plasmids could exploit trans-acting conjugation apparatus and relaxases from coresident mobile genetic elements (MGEs) to increase the potential for transfer in some species, it’s difficult to estimate the compatibility of these elements and how common this phenomenon is, based on plasmid sequence analysis alone. Despite the limitations of our methods, they will lay the foundation of opportunities for achieving a more balanced specificity and sensitivity in the future when more experimentally verified plasmids, as well as diverse underappreciated mechanisms that may be related to plasmid transfer, are integrated for analysis.