The complete genome sequence of five pre-2013 Escherichia coli sequence type (ST)1193 strains reveals insights into an emerging pathogen

Fluoroquinolone-resistant Escherichia coli sequence type (ST)1193 is a profound, emerging lineage associated with systemic, urinary tract and neonatal infections. Humans, companion animals and the environment are reservoirs for ST1193, which has been disseminated globally. Following its detection in 2007, ST1193 has been identified repeatedly amongst fluoroquinolone-resistant clones in Australia. However, despite the growing importance of ST1193, only three complete genomes are published in the literature, none of which are from Australia. Here we expand on the available ST1193 resources with the complete genomes of five ST1193 strains sequenced using Oxford Nanopore Technologies and Illumina. Using in silico genotyping, we found that all strains were multi-drug resistant, including resistances to fluoroquinolones and cephalosporins. In vitro antibiotic susceptibility testing mostly correlated with individual genotypes. The exception was MS8320, which had additional in vitro resistance to piperacillin/tazobactam, ampicillin/sulbactam, cefazolin and doripenem (carbapenem). Further investigation identified seven additional copies of an IS26 transposable unit carrying a bla TEM-1B beta-lactamase gene, suggesting this tandem amplification is associated with extended resistance phenotypes. Uropathogenicity factors, including three separate siderophore-encoding loci, were conserved in chromosomal and plasmid regions. Using all complete genomes, we further elucidated the recombination events surrounding the previously described K5/K1 capsular locus switch. Phenotypic confirmation of differing capsules in Australian ST1193 strains, coupled with genetic analysis revealing insertions downstream of the capsular locus, underscored the genetic distinctions between K5 and K1 capsule encoding strains. This study provides five new reference ST1193 genomes from Australia. These include the earliest complete K5-capsule ST1193 genomes on record (collected 2007), alongside our reference genome (MS10858), a clinical isolate obtained early during the ST1193 expansion and representative of the predominant K1-associated clade. These findings lay the foundations for further genomic and molecular analyses that may help understand the underlying reasons for the rapid global expansion of ST1193.

Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales

Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infections caused by E. coli ST131. From 2013-2014 blood culture surveillance in Wales, 142 E. coli ST131 genomes were studied alongside global data. All three major ST131 clades were represented across Wales, with clade C/H30 predominant (n = 102/142, 71.8%). Consistent with global findings, Welsh strains of clade C/H30 contain β-lactamase genes from the blaCTX-M-1 group (n = 65/102, 63.7%), which confer resistance to third-generation cephalosporins. Most Welsh clade C/H30 genomes belonged to sub-clade C2/H30Rx (58.3%). A Wales-specific sub-lineage, named GB-WLS.C2, diverged around 1996-2000. An introduction to North Wales around 2002 led to a localised cluster by 2009, depicting limited genomic diversity within North Wales. This investigation emphasises the value of genomic epidemiology, allowing the detection of genetically similar strains in local areas, enabling targeted and timely public health interventions.

High prevalence of extensively drug resistant and extended spectrum beta lactamases (ESBLs) producing uropathogenic Escherichia coli isolated from Faisalabad, Pakistan

Urinary tract infections (UTIs) are predominantly caused by uropathogenic Escherichia coli (E. coli). There is rapid increase in antimicrobial resistance in UTIs, also declared as a serious health threat by World Health Organization (WHO). Present study was designed to investigate the antimicrobial resistance status with specific focus on ESBLs and carbapenemases in local uropathogenic E. coli (UPEC) isolates. E. coli isolates were characterized from patients of all ages visiting diagnostic laboratories for urine examination. Demographic data was also recorded for each patient. Antibiograms were developed to observe antibiotic resistance in UPEC using Kirby Bauer disc diffusion technique. Double Disc Synergy test (DDST) was used for phenotypic ESBL test. ESBLs and carbapenemases genes were detected in UPEC using PCR. The PCR results were confirmed by sequencing. The UPEC isolates under study exhibited 78%, 77%, 74%, 72% and 55% resistance against cefotaxime, amoxicillin, erythromycin, ceftriaxone and cefixime, respectively. Resistance against colistin and meropenem was observed in 64% and 34% isolates, respectively. Phenotypic DDST identified 48% isolates as ESBLs producers. Genotypic characterization identified 70%, 74.4% and 49% prevalence of CTXM-1, TEM-1 and CTXM-15 genes respectively. One isolate was observed exhibiting co-existence of all ESBL genes. TEM-1 + CTXM-1 and TEM-1 + CTXM-1 + CTXM-15 + OXA-1 gene patterns were dominant among ESBLs. For carbapenem-resistance, 14% isolates indicated the presence of KPC whereas GES and VIM was detected in 7% and 3.4% isolates, respectively. In conclusion, our results present a high prevalence of extensively drug resistant UPEC isolates with a considerable percentage of ESBL producers. These findings propose the need of continuous surveillance for antimicrobial resistance and targeted antimicrobial therapy.

Progress and prospects of nanomaterials against resistant bacteria

Drug-resistant bacterial infections are increasingly heightening, which lead to more severe illness, higher cost of treatment and increased risk of death. Nanomaterials-based therapy, an "outrider", serving as a kind of innovative antimicrobial therapeutics, showing promise in replacing antimicrobial agents and enhancing the activity of antibiotics, generally bases on the various inorganic and/or organic materials. When the size of those materials is below to a certain nano-level and the content of nanomaterials is above a certain amount, they are lethal to the resistant bacteria, which bypass the traditional bacterial resistance mechanisms. This review highlights the effect of nanomaterials in combating extracellular/intracellular bacteria and eradicating biofilms. Based on the studies searched on the Web of Science through relevant keywords, this review article starts with analyzing the current situation, resistance mechanisms, and treatment difficulties of bacteria resistance. Then, the efficacy of nanomaterials against resistant bacteria and their mechanisms (e.g., physical impairment, biofilm lysis, regulating bacterial metabolism, protein and DNA replication as well as enhancing the antibiotics concentration in infected cells) are collected. Lastly, the factors affecting the antibacterial efficacy are argued from the side of nanomatrials and bacterium, which followed by the emerging challenges and recent perspectives of achieving higher targeting released nanomaterials as antibacterial therapeutics.