Azithromycin is becoming an effective alternative medicine against antibiotic resistant Escherichia coli (E. coli), and in parallel, is frequently detecting in wastewater and fresh water media. The current study aimed to evaluate the presence of azithromycin resistance genes (AzRGs) in E. coli isolated from urban wastewater for which there is a serious lack of information. For this, the samples were collected from four vital points of an urban wastewater treatment plant (WWTP), analyzed for physicochemicfial parameters, and identified for the azithromycin resistant isolates. The isolates were then subjected to 13 other extensively used antibiotics (from seven different classes), including amikacin, aztreonam, ceftazidime, ciprofloxacin, cefepime, ceftriaxone, cefotaxime, doxycycline, gentamicin, imipenem, norfloxacin, tetracycline, and trimethoprim/sulfamethoxazole; detected for AzRGs, phylogenic group, and molecular typing. The results clearly showed that: a) except for amikacin in all samples and gentamicin in effluent samples, E. coli isolates were resistant to all other the antibiotics studied in the mean respective values of 53.8%, 90.4%, 50%, 40.4%, 86.5%, 86.5%, 63.5%, 13.5%, 73.1%, 46.2%, 65.4%, 69.2%; b) for 75% of them (i.e. except for amikacin, gentamicin, and trimethoprim/sulfamethoxazole), the antibiotic resistance prevalence in effluent samples were significantly higher than that of sludge (p-value = 0.011), aeration (p-value = 0.023), and even influent (p-value = 0.038) samples, suggesting that WWTP facilities acquiring the resistance gene; c) The high values of multiple antibiotic resistance (MAR) index in almost all of the isolates (0.21–0.91) were categorized them in high-risk group, though the values were not found to be influenced by WWTP. Surprisingly, from 10 AzRGs, only two genes of mph(A) and erm(B) were detected in 100% and 67.3% of the isolates, respectively. The prevalence of erm(B) was significantly influenced by MAR index (p-value = 0.004), which MAR in turn, influenced by physicochemical parameters of wastewater in the relative effectiveness of COD (36%) > EC (29%) > TS (16%) > TDS (9%) > temperature (6%) > pH (4%), as modeled using artificial neural network (ANN) approach (R2 = 0.85 and MSE = 0.006302). The phylogenetic group A (59.6%) and clusters of III and V with 23 and 18 isolates, respectively, were dominant among the isolates which both showed a high correlation with MAR indices and therefore erm(B) prevalence. These results were interesting as highlight the effect of WWTP on acquiring antibiotic resistance and AzRGs prevalence in E. coli. Therefore, defining new strategies for relieving the challenge is of great importance.