Molecular characterization of multi drug resistant Escherichia coli isolates at a tertiary hospital in Abuja, Nigeria

Abstract

Infections caused by multi-drug resistant Escherichia coli cause significant morbidity and mortality especially in developing countries. In this study, we describe the molecular characteristics of E. coli isolated from clinical specimens and the patients’ outcomes. Phenotypic methods were used in the identification and antimicrobial susceptibility testing of E. coli from clinical specimens from a tertiary hospital in Abuja, Nigeria. Whole genome sequencing was used to describe the antimicrobial resistance genes, serotypes, sequence types/clonal complexes, and mobile genetic elements. The mean age of the patients was 20.3 years with 70.1% females and majority of isolates 75% from urine, 21% from blood cultures, and 3% each from cerebrospinal fluid and endo-cervical swabs. Of the 107 non-duplicate E. coli isolates, 101 (94.3%) were resistant to ampicillin, 95 (88.8%) to trimethoprim/sulfamethoxazole, 86 (80.4%) to ceftriaxone, 60 (56.1%) to gentamicin, and eight (7.5%) to meropenem. There were 102 (95.3%) isolates that were multi-drug resistant (MDR). Expression of Extended Spectrum Beta Lactamase (ESBL) phenotype was detected in 54 (50%) and blaCTX-M-15 genes detected in 75 (70.1%) isolates. The carbapenemase genes blaNDM-1 and blaNDM-5 were detected in six (5.6%), while the AmpC gene- blaCMY-2, was detected in seven (6.5%) isolates. Two (1.9%) isolates simultaneously harboured the blaOXA-1, blaCMY-2, blaCTX-M-15, and blaNDM-5 genes. In total, 35 sequence types (STs) were found with the majority being ST131 (n = 23; 21.5%). The most common serotype was O25:H4 associated with all 23 strains of ST131, followed by O1:H6/ST648 (n = 6). The ST410, ST671, and ST101 strains displayed phenotypic resistance to wide array of antibiotic classes and harbored high numbers of antibiotic resistance genes via in-silico analysis. The ST410 strain in particular harbored a higher number of antibiotic resistance genes and was phenotypically resistant to a wider array of antibiotics. Four pairs of isolates were closely related with three isolates (ST131, ST38, ST652) having a pairwise SNP difference of zero. 71/72 75/76 52/14. The MDR E. coli lineages circulating in this setting pose a clinical and public health threat as they can hinder effective prevention and management of infections. The genetic diversity and MDR E. coli with the emergence of ST410 and ST101 clones is concerning because of the potential for rapid dissemination in hospitals and communities- further increasing the problems of antibiotic resistance. Continuous routine surveillance of E. coli infections for AMR in hospitals becomes imperative, aimed at development of effective antimicrobial stewardship programs, facilitating prudent use of antimicrobial agents, and limiting dissemination of resistant strains.

Molecular Characterization of Escherichia coli Causing Urinary Tract Infections Through Next-Generation Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes

“…Similar to the results of this study, plasmid Col8282 and bla CTX-M-15 resistance genes were observed [ 43 ]. ST-648 was the second most common ST identified with an O1:H6 serotype (5.6%) combination, second to ST-131 [ 44 ]. ST-648 was among the predominant STs noted from E .…”

Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers—A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016

“…On the regional deployments, high exposure had to be considered as likely due to local partnering during training missions such as in Mali [51][52][53] or due to living under local conditions as it was the case for the United Nations observers in South Sudan and Sudan [73]. The sequence types ST38, ST131, and ST648, which were repeatedly isolated from returnees from the Sahel region, are well known from other epidemiological assessments from various sub-Saharan regions [88][89][90][91][92][93][94][95][96][97][98][99].…”

Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection

“…The susceptibility of the E. coli isolates to antibiotics was assessed by the Vitek 2 system (bio-Mérieux, Inc., Durham, NC, USA) based on AST-GN69 and the AST-XN06 cards according to the manufacturer’s instructions. The antibiotics tested included ampicillin (AMP), amoxicillin-clavulanic acid (AMX-C), piperacillin/tazobactam, amikacin (AMK), gentamicin (GEN), meropenem (MEM), imipenem (IPM), ertapenem (ETP), ciprofloxacin (CIP), LEV, TG, trimethoprim-sulfamethoxazole, ceftazidime, cefepime (CFP), ceftriaxone (CFN), cefuroxime (CXM), and cefixime (CFX) [ 27 ].…”