Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

Abstract

Bacterial plasmids play a large role in allowing bacteria to adapt to changing environments and can pose a significant risk to human health if they confer virulence and antimicrobial resistance (AMR). Plasmids differ significantly in the taxonomic breadth of host bacteria in which they can successfully replicate, this is commonly referred to as ‘host range’ and is usually described in qualitative terms of ‘narrow’ or ‘broad’. Understanding the host range potential of plasmids is of great interest due to their ability to disseminate traits such as AMR through bacterial populations and into human pathogens. We developed the MOB-suite to facilitate characterization of plasmids and introduced a whole-sequence-based classification system based on clustering complete plasmid sequences using Mash distances (https://github.com/phac-nml/mob-suite). We updated the MOB-suite database from 12 091 to 23 671 complete sequences, representing 17 779 unique plasmids. With advances in new algorithms for rapidly calculating average nucleotide identity (ANI), we compared clustering characteristics using two different distance measures – Mash and ANI – and three clustering algorithms on the unique set of plasmids. The plasmid nomenclature is designed to group highly similar plasmids together that are unlikely to have multiple representatives within a single cell. Based on our results, we determined that clusters generated using Mash and complete-linkage clustering at a Mash distance of 0.06 resulted in highly homogeneous clusters while maintaining cluster size. The taxonomic distribution of plasmid biomarker sequences for replication and relaxase typing, in combination with MOB-suite whole-sequence-based clusters have been examined in detail for all high-quality publicly available plasmid sequences. We have incorporated prediction of plasmid replication host range into the MOB-suite based on observed distributions of these sequence features in combination with known plasmid hosts from the literature. Host range is reported as the highest taxonomic rank that covers all of the plasmids which share replicon or relaxase biomarkers or belong to the same MOB-suite cluster code. Reporting host range based on these criteria allows for comparisons of host range between studies and provides information for plasmid surveillance.

Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 ‘superplasmids’ in clinical carbapenem-resistant Enterobacterales

“…Another strength of our study was extensive use of long-and short-read sequencing to construct high-quality hybrid plasmid assemblies. Combining these techniques with non-alignment methods of determining sequence similarity creates a powerful tool for detecting spread of mobile genetic elements with important implications for infection prevention [32,33]. By doing this, we J o u r n a l P r e -p r o o f demonstrated that in our institution IncHI2 plasmids likely were transmitted by both clonal and interspecies spread.…”

“…Finally, we used non-alignment-based approaches to cluster plasmid genomes but there are few current data which would help define similarity cutoffs to indicate plasmid transmission. Prior reports have assessed plasmid diversity within single J o u r n a l P r e -p r o o f patients [44] and outbreaks [45] but further data across diverse plasmids and host backgrounds are needed to inform infection prevention decisions [32,33].…”

“…For E. hormaechei ST93 and ST190 median pairwise single nucleotide variant (SNV) distance was 8 SNVs (IQR 2-16) and 2 SNVs (IQR 1-2), respectively (Figure S1). In contrast, E. hormaechei ST114 had a median pairwise SNV distance of 28 SNVs (IQR [23][24][25][26][27][28][29][30][31][32][33][34][35][36]. For all clones, the low SNV distances are suggestive of intra-institutional spread.…”

Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms

“…In this study, we investigated a total of 18 plasmid incompatibility groups in all E. coli isolates. We were able to identify several isolates that carry IncN, P, HI1, and I1 incompatibility groups that have been shown to be associated with a broad-host range [ 76 , 77 , 78 ]. Interestingly, in our study, all ESBL-producing E. coli in the CC environment carried IncK/B type plasmids.…”

Plasmids facilitate pathogenicity, not cooperation, in bacteria

“…We then tested another prediction of the cooperation hypothesis: cooperation is more likely to be favoured when coded for on more mobile plasmids [14][15][16][17][18] . We used data from the MOBsuite database to assign plasmids to one of three levels of mobility (Fig 3a) 44,45 . We classify: conjugative plasmids, which carry all genes necessary to transfer, as the most mobile; mobilizable plasmids, which are dependent upon conjugative plasmids' machinery to transfer, to have intermediate mobility; non-mobilizable plasmids, which cannot be transferred via conjugation, to be the least mobile (Fig 3a) 44,46 .…”