Fig. 2

HDA-mNGS increases both microbial and TB reads in Xpert positive samples. A Boxplot of host reads rates from three methods suggest that HDA steps reduced human DNA percentage rates to thereby dramatically increase the Pathogen Reads rate, as confirmed using the Wilcoxon test. B Metagenomics sequencing methods that incorporate steps to substantially remove host DNA were associated with increased Pathogen Reads rates. C The Ct value of Xpert indicated a negative correlation with the number of normalised reads obtained by metagenomic sequencing. D According to Ct value cutoffs (< 22, 22–28, > 28), the detection performance of metage-nomic sequencing gradually decreased with decreasing MTB DNA content. Moreover, HDA-mNGS results were more robust as compared to results obtained using mNGS and HDA-Nanopore: Coverage of the M. tuberculosis genome obtained using metagenomic sequencing, based on Ct values for different patient groups (non-PTB versus PTB groups). The results indicated that HDA-mNGS provided excellent coverage depth that exceeded the coverage depths obtained using the other two methods