TY - JOUR
T1 - Reply to Shaw
T2 - Challenges for enrichment analysis of AMR gene-bearing plasmids
AU - Che, You
AU - Yang, Yu
AU - Xu, Xiaoqing
AU - Břinda, Karel
AU - Polz, Martin F
AU - Hanage, William P
AU - Zhang, Tong
PY - 2021/5/25
Y1 - 2021/5/25
N2 - We thank Liam Shaw for his letter (1), “Null models for gene enrichment in plasmids,” and appreciate the detailed simulation regarding the enrichment analysis of AMR genes on different types of plasmids, which confirms our original conclusions that conjugative plasmids are enriched in these genes (2). We agree that considering the plasmid size is a good point when using a null model for the enrichment analysis as it tests for a completely neutral accumulation of genes. However, using a completely neutral model for all genes on plasmids does not capture the reality of gene content constraints. Conjugative plasmids contain a much larger portion of genes that are involved in transfer and maintenance than other plasmids. Hence, the proportion of genes that can be readily exchanged is much smaller than suggested by the entire genome size. Additionally, we note that different plasmid types have very different biology, and hence the plasmid type is an important category to test for.
AB - We thank Liam Shaw for his letter (1), “Null models for gene enrichment in plasmids,” and appreciate the detailed simulation regarding the enrichment analysis of AMR genes on different types of plasmids, which confirms our original conclusions that conjugative plasmids are enriched in these genes (2). We agree that considering the plasmid size is a good point when using a null model for the enrichment analysis as it tests for a completely neutral accumulation of genes. However, using a completely neutral model for all genes on plasmids does not capture the reality of gene content constraints. Conjugative plasmids contain a much larger portion of genes that are involved in transfer and maintenance than other plasmids. Hence, the proportion of genes that can be readily exchanged is much smaller than suggested by the entire genome size. Additionally, we note that different plasmid types have very different biology, and hence the plasmid type is an important category to test for.
KW - AMR genes
KW - plasmid size
KW - plasmid type
UR - http://www.scopus.com/inward/record.url?scp=85105772040&partnerID=8YFLogxK
U2 - 10.1073/pnas.2104557118
DO - 10.1073/pnas.2104557118
M3 - Short communication
C2 - 33975908
SN - 0027-8424
VL - 118
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 21
M1 - e2104557118
ER -