Seqsphere software version 7

High-throughput WGS and subsequent data analysis were performed using a MiSeq instrument (Illumina, San Diego, CA, USA), as recently described [19 ]. For the library preparation, we used the Nextera DNA Flex Kit and Nextera DNA CS Indexes (Illumina, San Diego, CA, USA). Genomic DNA was paired-end sequenced with a MiSeq Reagent kit v2 250 bp (Illumina) with an average insertion size of 300 bp. The resulting reads were quality-trimmed and de novo assembled using the Velvet algorithm integrated in the Ridom Seqsphere⁺ software version 7 (Ridom GmbH, Muenster, Germany). For core genome multi-locus sequence typing (cgMLST), we used species-specific public cgMLST scheme for a gene-by-gene comparison on an allelic level [19 ,20 (link),21 (link)]. To illustrate the clonal relationships between different isolates, minimum-spanning tree analyses were performed based on the determined allelic profiles using the Ridom Seqsphere⁺ software with the parameter “pairwise ignore missing values”. We defined a clonal transmission event if the isolates differing ≤6 alleles for S. aureus, ≤10 alleles for E. coli, and ≤5 alleles for E. faecalis [19 ,22 (link)]. This whole genome shotgun project was deposited at DDBJ/ENA/GenBank under the accession JAINWQ000000000-JAINZL000000000 and JAIOGN000000000-JAIOGP000000000. The version described in this paper is version PRJNA759098.

Only ESBL-E were subjected to whole-genome sequencing (WGS) as described recently (21 (link)). Subsequently, we performed multilocus sequence typing (MLST) and core genome MLST (cgMLST) if a species-specific scheme was available at https://www.cgmlst.org (22 (link)). Based on the allelic profiles of the cgMLST scheme, we constructed a neighbor-joining tree to display the clonal relationship among the ESBL-E and, if applicable, additional reference strains using Ridom SeqSphere+ software version 7 (Ridom GmbH, Münster, Germany) (23 (link)). For extraction of genomic determinants related to the ESBL phenotype, we used the AMRFinder (24 (link)) that is implemented in SeqSphere+. The genome sequences determined here were available at https://www.cgmlst.org.