Phenotypic Detection and Antimicrobial Resistance of ESBL-Producing Escherichia coli Clinical Isolates Using VITEK 2

Escherichia coli is the most predominant Gram-negative bacteria that is associated with diverse infections, including urinary tract infections (UTIs), bloodstream infections, wound infections, and intra-abdominal infections [1,2]. Extraintestinal pathogenic Escherichia coli (ExPEC) contributes to various infections due to the presence of several virulence factors, which help its adherent properties [3]. The constant emergence of antibiotic-resistant E. coli strains, particularly those producing extended-spectrum β-lactamases (ESBLs) is a problem which should be counteracted nowadays as it limits the therapeutic choices, prolongs the duration of hospitalization, raises the expenditures of healthcare, and increases morbidity and mortality rates worldwide [4,5].

Extended-spectrum β-lactamases (ESBLs) are enzymes that can cleave penicillins, extended-spectrum cephalosporins, and monobactams, thus impairing the action of these antimicrobial drugs. Nevertheless, ESBLs’ actions are inhibited in the presence of β-lactamase inhibitors such as clavulanic acid, tazobactam, and sulbactam [5,6]. The principal ESBL families are represented by CTX-M, TEM, and SHV, which are mostly found on the transferable plasmids, which are capable of spreading germs quickly among Enterobacterales in terms of antimicrobial resistance. Besides, these plasmids  carry  extra  genes  that  give rise  to  resistance against aminoglycosides, fluoroquinolones, and sulfonamides and contribute to the emergence of multidrug-resistant (MDR) phenotype [7-10]. The issue is aggravated by the global spread of E. coli, which creates significant problems for clinical microbiology and health care systems since this bacterium is strongly linked to treatment failures, prolongation of hospital stay, and increased mortality [11,12].

Hence proper early screening as well as the accurate phenotype definition of ESBL production is essential in avoiding inappropriate empirical treatment and to control horizontal transmission of these resistant characteristics in wards of hospitals [13]. Although the DDST and CDT methods are both recommended by reference guidelines and very reliable the procedures for both testing methods are manual and require an incubation time of as much as 24 hours delaying essential clinical decisions [14, 15]. To remove these bottlenecks in the diagnostic process, modern clinical microbiology laboratories have utilized computerized automated susceptibility platforms such as the VITEK 2 system (bioMérieux) [16]. The VITEK 2 system provides an effective and reliable method of assessing the growth rate of the isolates against cephalosporin and cephalosporin + clavulanic acid(s) to obtain an accurate phenotype for detecting the presence of ESBL organisms and resistance mechanisms in hours; therefore, there is a significant improvement in infection control practice and antimicrobials stewardship due to the integration of the Advanced Expert System (AES) with the VITEK 2 system [17, 18].

The worldwide dissemination of Escherichia coli that produces extended-spectrum beta-lactamases (ESBLs) has emerged to be a significant concern to public health since these bacteria are linked with resistance to multiple drugs and have fewer treatments available. Increasing occurrence of bacteria that produce ESBLs has been a main contributing factor to treatment failure, prolonged hospitalization and raise of costs associated with treatment. Recent global surveys show that antimicrobial resistance is among the main cause of death associated with infections in humans and require more full time monitoring and application of effective treatment programs [19,20].In Iraq, getting current information on ESBL-producing E. coli is especially significant because of regional differences in antimicrobial resistance patterns, differences in how antibiotics are used, and the need to direct local empirical treatment and infection control guidelines.

Regardless, despite the growing incidence of ESBL-producing Escherichia coli, continuous tracking of antibiotic resistance is necessary, particularly on the regional level. Prior research in Iraq indicates the detection of ESBL-producing E. coli in clinical samples; however, there are still very few updated reports that include a typing and antibiotic susceptibility profile using automated methods like VITEK 2. Consequently, more studies are needed to provide current data regarding epidemiology and to support rational usage of antibiotics and infection control efforts [21,22]. Hence, this study sought to phenotypically identify and characterize the particular antimicrobial resistance profiles of clinical isolates of ESBL-producing Escherichia coli via the automated VITEK 2 system in order to expand regional epidemiological databases and to facilitate targeted prescribing guidelines.

Objectives of the Study

The primary objectives are:

To phenotypically distinguish between the clinical isolates of Escherichia coli that produced the extended-spectrum beta-lactamase (ESBL) enzyme, along with testing their antibacterial susceptibility patterns by making use of the automated system called VITEK® 2.

The secondary objectives are:

• To find out the prevalence of ESBL-producing coli clinical isolates found in the study population.
• To analyze the different kinds of antimicrobial susceptibility patterns of the ESBL-producing coli.
• To find out whether the VITEK® 2 Advanced Expert System (AES) is efficient in interpreting antimicrobial susceptibility data.
• To provide evidence for local epidemiological data such that it can become useful in the effective management of the antimicrobial molecule.

Ethical Considerations

The research was conducted using anonymous E. coli clinical isolates obtained from ordinary laboratory samples. It was not related to direct patient care, identifying patient data, or any identifiable information about patients.

Thus, ethical approval and informed consent were not required as per institutional protocol as this was an anonymous laboratory research.

Collection of Samples and Population Studied

The investigators confirmed cases of clinical Escherichia coli between 18 February and 15 April 2026. A total of seventy-five clinical isolates were collected from various hospitals and central diagnostic laboratories that provided clinical services. The specimens included urine, stool, wound swabs, and high vaginal swabs (HVS). The specimens were transported to the laboratory in sterile containers and processed in line with the requirements of the Clinical and Laboratory Standards Institute (CLSI)[23].The means of obtaining clinical isolates was the convenience sampling technique. Non-repeating Escherichia coli isolates were collected used for sampling purposes in this study.

• Inclusion criteria: The confirmed amounts of the coli isolates collected from multiple clinical samples, involved urine, stool samples, wound swabs, and high vaginal swabs (HVS) were collected from 18 February 2026 to 15 April 2026. Only those isolates were selected that were completely identified.
• Exclusion criteria: Samples with contamination, mixed bacterial culture, duplicate isolates, and isolates with incomplete identification or missing results of susceptibility tests were not taken into consideration when conducting the study.

Identification and Characterization of the Bacteria

The isolates were first cultured on standard media for identification and characterization. Identification of E. coli isolates was performed using the VITEK® 2 identification system (bioMérieux, Marcy-l’Étoile, France). Identification cards were prepared and processed according to the manufacturer’s instructions. The VITEK® 2 system identified the isolates with confidence levels ranging from 87% to 99%.

Antimicrobial Susceptibility Testing (AST)

Antimicrobial susceptibility testing was performed using the VITEK® 2 automated system to determine the minimum inhibitory concentrations (MICs). The tested antimicrobial agents included beta-lactam/beta-lactamase inhibitor combinations (Ampicillin/Sulbactam and Piperacillin/Tazobactam), cephalosporins (Cefotaxime, Ceftazidime, and Cefepime), carbapenems (Imipenem and Meropenem), aminoglycosides (Amikacin and Gentamicin), fluoroquinolones (Ciprofloxacin), Trimethoprim/Sulfamethoxazole, and Colistin.

The antimicrobial susceptibility profiles were automatically analyzed using the VITEK® 2 Advanced Expert System (AES) and interpreted according to CLSI standards. The results were categorized as Susceptible (S), Intermediate (I), Resistant (R), or Susceptible-Dose Dependent (SDD), when applicable.

Quality Control

The quality control procedures for VITEK® 2 identification and antimicrobial susceptibility testing were performed according to the manufacturer’s recommendations and Clinical and Laboratory Standards Institute (CLSI) guidelines. Reference strains were used to verify the accuracy and reliability of the identification and antimicrobial susceptibility results.

Statistical Analysis

Frequency and percentages were used to summarize categorical data. Antimicrobial susceptibility results were interpreted according to the VITEK® 2 AST outputs and reported as Susceptible (S), Intermediate (I), Resistant (R), and Susceptible-Dose Dependent (SDD) when applicable. Pearson’s chi-square test or Fisher’s exact test was used for categorical comparisons, and the odds ratio (OR) was reported when Fisher’s exact test was applied. A p-value <0.05 was considered statistically significant. Statistical analysis was performed using IBM SPSS Statistics version 32, and graphical representations were prepared using GraphPad Prism version 11.0.2. This study was conducted according to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines for observational studies.

Table 1 presents the demographic and clinical characteristics of the study population. A total of 75 Escherichia coli isolates were included in the analysis. Urine was the predominant sample source, accounting for 86.7% of isolates, while the AES confidence was reported as consistent in 90.7% of cases. Additionally, 81.3% of the reports did not include a susceptible-dose dependent (SDD) note.

Table 1: Demographic and Clinical Characteristics of the Study Population

AES: Advanced Expert System, HVS: High Vaginal Swab, SDD: Susceptible-Dose Dependent. “Not recorded” and “Not stated” indicate that the corresponding information was unavailable in the original VITEK® 2 report

Among the 75 E. coli isolates included in this study, 67 (89.3%) were classified as phenotypic ESBL producers, while 8 (10.7%) were classified as non-ESBL isolates according to the VITEK® 2 AES interpretation. The high proportion of ESBL-producing isolates indicates a high prevalence of ESBL-associated resistance phenotypes among the studied E. coli isolates (Table 2).

Table 2: Frequency and Prevalence of ESBL-Producing Escherichia coli among Clinical Isolates

Among all isolates and ESBL-positive isolates, urine was the most frequent sample source. The distribution of ESBL-positive isolates did not show a significant difference according to sample source (urine vs. non-urine) (p = 0.587). However, this comparison should be interpreted with caution due to the limited number of non-urine isolates (Table 3).

Table 3: Distribution of Escherichia coli Isolates by Sample Source and ESBL Status

The susceptibility profile revealed high levels of resistance to several beta-lactam and cephalosporin agents, particularly ampicillin, cefuroxime, ceftriaxone, cefotaxime, ceftazidime, and cefepime. A clinically significant resistance rate was also observed for ciprofloxacin. In contrast, imipenem, meropenem, amikacin, ceftazidime/avibactam, and ceftolozane/tazobactam remained highly active in vitro against the majority of isolates (Table 4).

Table 4: Antimicrobial Susceptibility Profile of Escherichia coli Isolates Detected by VITEK 2 System

Not assessed indicates that susceptibility testing for the corresponding antimicrobial agent was not performed or the result was unavailable in the VITEK® 2 report. Abbreviations: S, susceptible; I, intermediate; R, resistant; SDD, susceptible-dose dependent

A total of 75 Escherichia coli isolates identified by the VITEK® 2 system were included in this study. Urine  was the most common sample source (86.7%, 65 isolates), followed by wound swabs, stool, and high vaginal swabs (HVS). AES confidence was reported as consistent in the majority of isolates, supporting the reliability of the automated identification and susceptibility results (Table 3).

ESBL-positive isolates showed significantly higher resistance rates to piperacillin/tazobactam, cefotaxime, ceftazidime, cefepime, and ciprofloxacin compared with ESBL-negative isolates. These findings indicate that the ESBL-positive phenotype was not limited to resistance against third-generation cephalosporins but was also associated with resistance to other antimicrobial classes. Most non-significant differences were observed among agents that retained good activity or had a limited number of resistant isolates (Table 5).

Table 5: Comparison of Antimicrobial Resistance Rates between ESBL-Positive and ESBL-Negative Escherichia coli Isolates

Not assessed indicates that susceptibility testing for the corresponding antimicrobial agent was not performed or the result was unavailable in the VITEK® 2 report. OR, odds ratio

Multidrug resistance was prevalent, with 50 isolates (66.7%) classified as multidrug-resistant (MDR). Resistance to third-generation cephalosporins and fluoroquinolones represented the most common resistance phenotypes, followed by trimethoprim/sulfamethoxazole resistance. Carbapenem resistance remained rare, indicating that carbapenems retained high in vitro activity against the studied isolates (Table 6).

Table 6: Distribution of Multidrug Resistance Phenotypes among Escherichia coli Isolates

The categorical susceptibility results were supported by the MIC distribution analysis. Several cephalosporins and ciprofloxacin showed higher MIC50 and MIC90 values, reflecting reduced susceptibility among the studied isolates. In contrast, the lower MIC values observed for imipenem, meropenem, amikacin, and some beta-lactam/beta-lactamase inhibitor combinations provided further evidence of their higher in vitro activity against the tested E. coli isolates (Table 7).

Table 7: Minimum Inhibitory Concentration Distribution of Selected Antimicrobials among Escherichia coli Isolates   

MIC50 = minimum inhibitory concentration required to inhibit 50% of isolates; MIC90 = minimum inhibitory concentration required to inhibit 90% of isolates

The existence of ESBL-producing E. coli strains on a global scale poses a significant challenge to clinicians and substantially reduces the availability of empirical treatment methods. The results of the analysis of E. coli strains showed that the majority of the strains in question were ESBL producers (89.3%, or 67/75). This knowledge corresponds well with the recent data published discussing ESBL production rates and the growing problem with the emergence of resistant strains in hospitals across the world [19,4]. The high levels of ESBL production can result from massive and wrongful use of third-generation cephalosporins in the community and health care facilities, which creates selection pressure for resistant strains [5,6]. Moreover, antibiotic misuse and unregulated access to antibiotics, as well as the lack of control over the availability of antibiotics contribute to the ongoing exposure of bacteria to antibiotics thus speeding up ESBL-producing E. coli spread [18,12].

Most E. coli isolates in this study were obtained from different urine sample types (86.7%), with nearly all wounds having a total of 5.3%, feces having 5.3%, and vaginal swabs having 2.7%. This finding is consistent with results that indicated high prevalence of E. coli as a causative agent of both community-acquired and hospital-acquired urinary tract infections [3,25]. Uropathogenic E. coli (UPEC) have different virulence traits such as fimbrial adhesins and other factors through which the strains gain access to the urinary tract [26]. The combination of virulence factor characteristics and ESBL resistance traits causes difficulties in treating the infections as well as facilitating recurrent infections and long hospitalization [27,29]. Moreover, the identification of E. coli strains from wound swabs and high vaginal swabs proves this organism has potential to cause opportunistic infections at various body locations [28].

Analysis of susceptibility to antimicrobials revealed the presence of a highly resistant multidrug-resistant (MDR) phenotype in the isolates of the studied pathogen. High levels of resistance were noted against a number of beta-lactam agents, e.g., Ampicillin/Sulbactam, Cefotaxime, Ceftazidime, and Cefepime. The associated process leading to such phenomenon is the enzymatic hydrolysis of beta-lactam antibiotics by ESBL enzymes, namely CTX-M, TEM, and SHV [7,9]. The observed resistance to Cefepime, one of the fourth-generation cephalosporins, is concerning because it indicates evidence for an occurrence of strong beta-lactamase activity, which may lead to failure of treatment [30].

The use of the VITEK® 2 system revealed also co-resistance towards other classes of antimicrobials excluding beta-lactams, in particular, aminoglycosides (gentamicin) and fluoroquinolones (ciprofloxacin). The phenomenon can be explained by co-existence of various determinants of resistance, such as aminoglycoside-modifying enzymes and plasmid-mediated quinolone-resistance genes located on transferable plasmids containing ESBL genes [29,31]. Genetic association in this case provides an opportunity for horizontal transfer of many resistance mechanisms and limits therapeutic options available for outpatient therapies [31].

In the present investigation, the isolates of E. coli producing ESBLs were shown to be very susceptible to carbapenems (imipenem and meropenem) and amikacin. The above-mentioned results confirm the importance of carbapenems as treatment options for serious infections caused by ESBL-producing Enterobacterales [33].

Nevertheless, this overuse can lead to the emergence of carbapenem-resistant Enterobacteriaceae (CRE) by way of certain mechanisms such as carbapenemase and porin [34].

In this study, the VITEK® 2 Advanced Expert System (AES) provided reliable interpretation of susceptibility patterns of antimicrobials, attaining 93.3% confidence level. The automated phenotypic systems give quick interpretations of MIC patterns, and minimize manual interpretation mistakes while helping in timely interventions in the antimicrobial stewardship [22].

The results of this study indicating a high occurrence of ESBL-producing E. coli are consistent with the reports from the countries around the area where the prevalence of ESBL-producing E. coli has been increasing. The case in the Middle East and the neighboring countries, such as Iraq, reflected that there was an increase of ESBL-mediated resistance consistently. This may be attributed to the excessive use of antibiotics, lack of measures to fight resistance, and dissemination of resistance plasmids in Enterobacterales. The conclusions stress the importance of conducting constant regional surveillance [35,11].The high percentage of urine isolates detected in this study (86.7%) can present as a limiting factor in the study as urine samples are the commonly used clinical samples for the detection of E. coli. This may also lead to selection bias and can affect the application of the findings to other E. coli infection types such as bacteremia, pneumonia, etc. [3].

Although carbapenems were shown to be effective against ESBL-producing E. coli isolates in the study, their usage needs to be monitored carefully. It is crucial to use them properly in antimicrobial stewardship programs to minimize the selection pressure and to prevent the occurrences of carbapenem-resistant Enterobacterales [11,34].

Limitations

This study has several limitations. First, it was conducted in a single geographical region with a relatively small sample size, which may limit the generalizability of the findings. In addition, most isolates were obtained from urine specimens, potentially introducing selection bias. Molecular confirmation of ESBL genes (such as blaCTX-M, blaTEM, and blaSHV) was not performed, and patient clinical characteristics were unavailable because only anonymized laboratory isolates were used. Finally, the relatively short study period may not fully reflect long-term antimicrobial resistance patterns.

In conclusion, this research showed that there is a high rate of ESBL-generating Escherichia coli in the clinical samples analyzed in this research. The VITEK® 2 system was efficient in identifying the samples and determining their susceptibility to antibiotics, hence enabling the identification of the presence of important patterns of drug resistance in the tested samples. The drugs carbapenems and amikacin were effective in treating the studied isolates, but careful treatment choices should be made when using these drugs in order to maintain their efficacy. There is local knowledge available about ESBL-producing E. coli and the importance of constant monitoring and antibiotic stewardship has also been identified. Further multicenter studies with larger sample sizes and molecular characterization are recommended to validate and expand upon these findings.

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