MLST Wolbachia
We conducted NGMLST analysis on DNA extracts of 128 female fleas: 96 were collected from field-trapped rodents and 32 from the laboratory colony (Supplementary Text S1). We targeted five housekeeping genes commonly used in Wolbachia phylogenetic analysis gatB, coxA, hcpA, ftsZ, fbpA.. These genes were amplified from each flea sample using PCR and were evenly pooled based on Qubit fluorometer measurements. The resulting 128 pooled samples were subjected to next-generation sequencing. Paired-end 2300 bp reads were generated on the Illumina MiSeq platform at the DNA services facility of the Research Resources Center at the University of Illinois Chicago.