Data accessibility
All original fastq.gz sequencing files were deposited in the NCBI open-access sequence read archive (SRA) under accession numbers ERS3168383, ERS3168384, ERS3168414, ERS3168415, ERS3168569, ERS3168570, ERS3168460, ERS3168461, ERS3168762, ERS3168763 (MTB); and SRR13482776-SRR13482785 (CBH). All metadata associated with the samples, including detailed accession numbers, are given in Appendix 1 and are available at https://www.pangaea.de/ and BioSamples.