Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital

Abstract

This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013–2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried bla CTX -M- gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII–IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.

Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex

“…Most phylogenetically related ST131 isolates identified in this study tested positive for IncFII replicons and had identical resistance cargoes ( Figure 2 (B)). We, therefore, verified the presence of pSPRC_Ec234-FII within closely related ST131 genomes identified in our MrBayes phylogeny analysis ( Figure 3 (B)) and in ST131 isolates in our extended collection (Hastak et al Microbial Genomics, 2020 ). Only EC233 (the ST8196 representative) had an identical plasmid.…”

“…Based on branch distances between isolates in the subclade highlighted as Figure 2(A), the ST8196 representatives EC233 and EC234 were most closely related to ST131 isolate from Sydney (EC70 collected in 2013). EC70 was collected from Concord Hospital in Sydney in the course of sample collection for this study [23]. The other two Australian ST131 stains in the subclade, ESC_PA1114AA and ESC_CA5436AA were collected from Brisbane, Australia.…”

“…Here, we characterized two isolates, EC233 and EC234, that belong to a novel sequence type -ST8196, within the ST131CC. The two ST8196 isolates were collected from unrelated patients treated for bacteraemia at Concord Repatriation Hospital in Sydney in November 2014 [23]. They are both resistant to third-generation amino-penicillins (ampicillin and amoxicillin), second and third-generation cephalosporins (cefoxitin, ceftazidime and ceftriaxone), quinolones (ciprofloxacin and norfloxacin), and the aminoglycoside antibiotic gentamicin, which establishes their "extensively drug resistant" [24] status.…”

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

“…Antimicrobial resistance genes (ARGs) are most frequently part of class 1 integrons associated with various transposons, mostly belonging to the Tn 3 family. IS 26 plays an important role in the capture and assembly of ARGs and complex resistance locus (CRL) within transposons [ 19 , 23 , 25 ] and in shaping the structure of class 1 integrons [ 8 , 25 , 26 , 27 , 28 ].…”

Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

“…A total of 3479 E. coli isolates were sequenced of which 3278 passed in silico serotyping quality control. From these, 106 unique O-antigens were identified, though a relatively small number of these accounted for the majority of isolates (Fig.1) As the isolates from our study originated from a single region of the UK with a relatively low AMR burden, we compared our serotypes to those from recently published studies in the UK [12][13][14] and globally [15][16][17][18][19] . Overall, whilst there was some regional variation, findings Vaccines should also provide some protection against non-BSI infections which may evolve into BSIs, in particular urinary tract infections.…”