Mapping Antimicrobial Resistance in Escherichia coli and Klebsiella pneumoniae from Complicated Urinary Tract Infections in Oman: Phenotypic and Genotypic Insights

<b>Background:</b> Mapping the local etiology and susceptibility of common pathogens causing complicated urinary tract infection (cUTI) is important for promoting evidence-based antimicrobial prescribing. Evaluating the prevalence of extended-spectrum beta-lactamase (ESBL), AmpC beta-lactamase (AmpC), and carbapenemase-producing <i>Enterobacterales</i> (CPEs) is equally important as it informs treatment guidelines and empiric management. Whole genome sequencing (WGS) enhances antimicrobial resistance (AMR) surveillance by complementing phenotypic antimicrobial susceptibility testing, offering deeper insights into resistance mechanisms, transmissions, and evolutions. Integrating it into routine AMR monitoring can significantly improve global efforts to combat antimicrobial resistance. <b>Methods:</b> Antimicrobial susceptibility profiles of isolates from cUTI were collected from patients presenting with Sultan Qaboos University Hospital, Muscat and Suhar Hospital, Suhar, Oman. Automated systems as well as manual methods were used for detection of ESBL, AmpC, and CPE. ESBLs, AmpC β-lactamases, and CPEs were further detected by manual methods: double-disk synergy test for ESBL; disk approximation assay and D69C AmpC detection set for AmpC, and mCIM and <i>KPC/IMP/NDM/VIM/OXA-48</i> Combo test kit for CPE. WGS was carried out in 11 FOX-resistant <i>E. coli</i> and (22 carbapenem-resistant <i>K. pneumoniae</i>) isolates with varying susceptibilities to identify circulating clades, AMR genes, and plasmids. Bioinformatic analysis was performed using online tools. <b>Results:</b> The susceptibility patterns of <i>E. coli</i> from cUTI were as follows: nitrofurantoin (96%), fosfomycin (100%), fluoroquinolones (44%), aminoglycosides (93%), piperacillin-tazobactam (95%), and carbapenems (98%). In comparison, susceptibility rates of <i>K. pneumoniae</i> were far lower: nitrofurantoin (38%), fosfomycin (89%), aminoglycosides (82%), piperacillin-tazobactam (72%), and carbapenems (83%). <i>K. pneumoniae,</i> however, was more susceptible to fluoroquinolones at 47% in comparison to <i>E. coli.</i> The prevalence of ESBL among <i>E. coli</i> and <i>K. pneumoniae</i> was 37.2% and CRE was 6.2% while the estimated prevalence of AmpC was 5.4%. It was observed that <i>E. coli</i> was the predominant ESBL and AmpC producer, while <i>K. pneumoniae</i> was the major carbapenem-resistant <i>Enterobacterales</i> (CREs) producer. No predominant multi-locus sequence typing (MLST) lineage was observed in AmpC-producing <i>E. coli</i> with nine <i>E. coli</i> MLST lineages being identified from eleven isolates: <i>ST-10</i>, <i>ST-69</i>, <i>ST-77</i>, <i>ST-131</i>, <i>ST-156</i>, <i>ST-167</i>, <i>ST-361</i>, <i>ST-1125,</i> and <i>ST-2520</i>. On the other hand, a less diverse MLST spectrum (<i>ST-2096</i>, <i>ST-231</i>, <i>ST-147</i>, <i>ST-1770,</i> and <i>ST-111</i>) was observed in the CRE <i>K. pneumoniae</i>. Among the five MLST lineages, <i>ST-2096</i> (twelve isolates) and <i>ST-147</i> (seven isolates) predominated. WGS revealed that <i>DHA-1</i> was the predominant plasmid-mediated <i>AmpC</i> gene in <i>E. coli</i>, while <i>OXA-232</i> and <i>NDM-5</i> were the most common carbapenemase genes in <i>K. pneumoniae</i>. All <i>E. coli DHA-1</i>-positive isolates co-harbored the quinolone resistance gene <i>qnrB4</i> and the sulfonamide resistance gene <i>sul1</i> while no aminoglycoside resistance genes were detected. The majority of CPE CRE <i>K. pneumoniae</i> carried other β-lactamase genes, such as <i>blaCTX-M-15</i>, <i>blaSHV</i>, and <i>blaTEM</i>; all co-harbored the quinolone resistance gene <i>OqxAB;</i> and 77% carried the aminoglycoside resistance gene <i>armA</i>. <b>Conclusions:</b> Our results suggest that fosfomycin is an excellent empiric choice for treating complicated cystitis caused by both <i>E. coli</i> and <i>K. pneumoniae,</i> while nitrofurantoin is an appropriate choice for <i>E. coli</i> cystitis but not for <i>K. pneumoniae</i>. Aminoglycosides and piperacillin-tazobactam are excellent intravenous alternatives that spare carbapenems. <i>DHA-1</i> was the predominant AmpC in <i>E. coli,</i> while <i>OXA-232</i> and <i>NDM-5</i> were the predominant carbapenemases in <i>K. pneumoniae</i>. In AmpC-producing <i>E. coli,</i> no MLST predominated, suggesting a significant flux in <i>E. coli</i> with lack of stable clades in this region. In contrast, <i>ST-2096</i> and <i>ST-147</i> predominated in CRE <i>Klebsiella pneumoniae,</i> suggesting a stable circulation of these in Oman. WGS profiling provides a deeper understanding of the genetic basis of resistance and enhances surveillance and offers comprehensive insights into pathogen evolution and transmission patterns.