Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

Abstract

22The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, 23 which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been 24 associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is 25 a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes 26 enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-27 14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs).28 Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow 29 MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read 30 sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most 31 long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with 32 more fragmented assemblies created with short reads alone. The long read assemblies highlighted 33 diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one 34 and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal 35 blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the 36 adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple 37 different chromosomal and plasmid contexts even between closely-related isolates within a clonal 38 group such as E. coli ST131. 39 40 Importance 41 Drug-resistant bacteria are a major cause of illness worldwide and a specific subtype called 42 Escherichia coli ST131 cause a significant amount of these infections. ST131 become resistant to 43 treatment by modifying their DNA and by transferring genes among one another via large packages of 44 genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a 45 better understanding of what plasmids are being exchanged and their exact contents. To achieve this, 46we applied new high-resolution DNA sequencing technology to six ST131 samples from infected 47 patients and compared the output to an existing approach. A combination of methods shows that drug-48 resistance genes on plasmids are highly mobile because they can jump into ST131's chromosomes. We 49 found that the plasmids are very elastic and undergo extensive rearrangements even in closely related 50 samples. This application of DNA sequencing technologies illustrates at a new level the highly 51 dynamic nature of ST131 genomes. 52 53 54 55 56 57 Reported cases of bloodstream and urinary tract infections caused by extraintestinal pathogenic 58 Escherichia coli (ExPEC) are increasing globally at an alarming rate [1]. As a key source of ExPEC 59 isolates worldwide, E. coli sequence type 131 (ST131) is regarded as a serious threat to public health, 60 given its high level of a...

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

“…Within ST131, Clade C core genomes are highly conserved but accessory genomes have extensive differences in AMR gene content [50,52,61]. Here, this was supported by NCTC13441's repertoire of bla TEM and bla OXY genes, contrasting with EC958's variety of bla CMY ones.…”

“…Fluctuating antibiotic exposure, host type, anatomical niche and immunity mean that resistomes vary [51]. Conjugation, recombination and MGEs help shape ST131 resistome dynamics [2,11,[52][53][54][55]. ST131's plasmids typically are from incompatibility (Inc) groups F, I1, N and A/C [56][57][58].…”

Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

“…Long-read output can span repetitive regions either from bacteria, archaea or eukarya, thus facilitating the assembly of genomes and the characterization of plasmids, and the location and genomic context of resistance genes 13 . These strategies have been also applied for resistome and plasmidome characterization [14][15][16][17][18] since antimicrobial resistance has become a global concern.…”