Results

Clinical isolates distribution

During the 2023-2024 study period, 1072 specimens were processed. Microbial growth was observed in 352 (32.8%) specimens, whereas 720 (67.2%) showed no growth. Among the positive cultures, ESKAPEE pathogens predominated (289, 82.1%), followed by other bacteria (27, 7.7%) and Candida species (36, 10.2%).

Within the ESKAPEE group, Enterobacterales were most common (187, 64.7%). Escherichia coli was the leading pathogen (144, 49.8%), followed by Klebsiella pneumoniae (38, 13.2%), A. baumannii (28, 9.7%), P. aeruginosa (27, 9.3%), Enterococcus spp. (24, 8.3%), S. aureus (23, 8.0%), and Enterobacter spp. (5, 1.7%).

Specimen-wise distribution

Among the total specimens, midstream urine was the most frequent (680, 63.4%), followed by blood (247, 23.0%), pus (40, 3.7%), respiratory aspirates (34, 3.2%), sputum (33, 3.1%), and others (38, 3.6%).

From culture-positive samples, urine accounted for the majority (251, 71.3%), followed by blood (32, 9.1%), respiratory aspirates (25, 7.1%), pus (23, 6.5%), sputum (16, 4.6%), and others (5, 1.4%).

Most ESKAPEE pathogens were recovered from urine (201, 69.6%), followed by blood (25, 8.7%), respiratory aspirates (23, 7.6%), pus (22, 7.6%), sputum (15, 5.2%), and others (3, 1.0%).

Demographics and specimen distribution of ESKAPEE isolates

The demographic characteristics, specimen sources, and organism distribution of patients with ESKAPEE isolates are summarized in Table 1. Among these patients, 172 (59.5%) were female and 117 (40.5%) were male, with most isolates recovered from inpatients (214, 74.0%) rather than outpatients (75, 26.0%).

Category | Inpatients | Outpatients | Total
N (%) | 214 | 75 | 289
Gender |  |  | 
Male | 90 | 27 | 117 (40.5%)
Female | 124 | 48 | 172 (59.5%)
Age group |  |  | 
0-9 | 22 | 0 | 22 (7.6%)
10-19 | 6 | 9 | 15 (5.2%)
20-29 | 18 | 17 | 35 (12.11%)
30-39 | 21 | 21 | 42 (14.5%)
40-49 | 22 | 6 | 28 (9.7%)
50-59 | 29 | 8 | 37 (12.8%)
60-69 | 28 | 9 | 37 (12.8%)
70-79 | 41 | 4 | 45 (15.6%)
80-89 | 27 | 1 | 28 (9.69%)
Inpatient units |  |  | 
Medical ward | 66 (30.8%) |  | 214
ICU | 47 (22.0%) | 
Surgical ward | 32 (15.0%) | 
CCU | 27 (12.6%) | 
Pediatric ward | 23 (10.7%) | 
Obstetrics and gynecology | 19 (8.9%) | 
Specimens |  |  | 
Urine | 157 | 44 | 201 (69.6%)
Blood | 17 | 8 | 25 (8.7%)
Pus | 16 | 6 | 22 (7.6%)
Sputum | 12 | 3 | 15 (5.1%)
Tracheal aspirate | 12 | 11 | 23 (8%)
Others | 0 | 3 | 3 (1%)
Organism |  |  | 
Escherichia coli | 109 | 35 | 144 (49.8%)
Enterococcus spp. | 16 | 8 | 24 (8.3%)
Staphylococcus aureus | 18 | 5 | 23 (8.0%)
Klebsiella pneumoniae | 28 | 10 | 38 (13.1%)
Acinetobacter baumannii | 19 | 9 | 28 (9.6%)
Pseudomonas aeruginosa | 21 | 6 | 27 (9.3%)
Enterobacter spp. | 3 | 2 | 5 (1.7%)

Age-wise distribution showed the highest proportion of ESKAPEE isolates among patients aged 70-79 years, followed by other older age groups, whereas patients aged 10-19 years accounted for the comparatively lowest proportion of isolates (Table 1).

Among hospitalized patients, isolates were most frequently recovered from the medical ward, followed by the intensive care unit (Table 1).

Specimen-wise distribution showed that Escherichia coli and Enterococcus spp. were predominantly isolated from urine specimens (125/144; 86.8% and 24/24; 100%, respectively). K. pneumoniae was mainly recovered from urine (21/38; 55.3%), followed by sputum (8/38; 21.1%) and respiratory aspirates (4/38; 10.5%). S. aureus was most frequently isolated from blood (13/23; 56.5%), while nonfermenters, including A. baumannii and P. aeruginosa, were primarily recovered from urine (11/28; 39.3% and 14/27; 51.9%) and respiratory specimens (7/28; 25.0% and 3/27; 11.1%). Enterobacter spp. was infrequently isolated, mainly from urine (3/5; 60%) and respiratory aspirates (1/5; 20%).

ESKAPEE pathogens AMR profile

The antimicrobial resistance patterns of ESKAPEE pathogens are illustrated in Figure 1. Among Gram-positive isolates, S. aureus showed high resistance to erythromycin and penicillin (91.30% each), while Enterococcus spp. showed high resistance to gentamicin (79.17%, high-level aminoglycoside resistance) and tetracycline (79.17%). Vancomycin and linezolid retained the greatest activity against both organisms.

Figure 1: Heatmap of antimicrobial resistance (% resistant) among ESKAPEE pathogens isolated in this study. Color intensity reflects the percentage of isolates resistant to each antibiotic, from pale orange (low resistance) to dark red (high resistance), as indicated by the color scale. Values within each cell denote the percentage of resistant isolates. Gray cells indicate antibiotic–organism combinations that were not tested or were not clinically applicable.a Gentamicin resistance for Enterococcus spp. reflects high-level aminoglycoside resistance (HLAR) screening performed to assess potential synergy with a cell wall–active agent, rather than standalone susceptibility testing.b Fosfomycin susceptibility for K pneumoniae is reported for informational purposes only; its clinical efficacy against this organism is not well established, and it is not recommended as a primary treatment option.Full susceptible/intermediate/resistant counts and percentages for all antibiotic–organism combinations are provided in Supplementary Table S1.

Among Gram-negative isolates, resistance to third-generation cephalosporins and ciprofloxacin/ofloxacin exceeded 60% in most organisms, with slightly lower resistance to levofloxacin. Carbapenem resistance was lowest in E. coli (11.11-25.69%) but remained substantial in K. pneumoniae and P. aeruginosa, with the highest levels among adequately sampled organisms observed in A. baumannii (60.71-64.29%). Enterobacter spp. showed an even higher carbapenem resistance rate (80% for meropenem and imipenem); however, this finding should be interpreted with caution because only five isolates were recovered. Full susceptibility data for all organism–antibiotic combinations are provided in Supplementary Table S1.

AMR categories

ESKAPEE pathogens were classified according to international resistance criteria [8,9], with detailed distributions shown in Table 2 and illustrated in Figure 2, Figure 3.

Microorganism | Drug Resistance Classification [8] No. (%) | CDC & IDSA Phenotypes [9] No. (%)
 | Total (n) | WT | Non-MDR | MDR | XDR | Possible PDR | CR | ESCR | FQR | DTR
E coli | 144 | 5 (3.5) | 27 (18.8) | 82 (56.9) | 20 (13.9) | 10 (6.9) | 37 (25.7) | 78 (54.2) | 80 (55.6) | 16 (11.1)
K pneumoniae | 38 | 0 | 7 (18.4) | 3 (7.9) | 11 (28.9) | 17 (44.7) | 19 (50) | 31 (81.6) | 27 (71.1) | 7 (18.4)
Enterobacter spp. | 5 | 0 | 0 | 1 (20) | 3 (60) | 1 (20) | 2 (40) | 3 (60) | 2 (40) | 0
A baumannii | 28 | 6 (21.4) | 4 (14.3) | 4 (14.3) | 5 (17.9) | 9 (32.1) | 19 (67.9) | 19 (67.9) | 16 (57.1) | 9 (32.1)
P aeruginosa | 27 | 7 (25.9) | 0 | 5 (18.5) | 6 (22.2) | 9 (33.3) | 16 (59.3) | 15 (55.6) | 15 (55.6) | 6 (22.2)
S aureus | 23 | 0 | 4 (17.4) | 17 (73.9) | 1 (4.3) | 1 (4.3) | NA | NA | NA | NA
Enterococcus spp. | 24 | 0 | 5 (20.8) | 16 (66.7) | 3 (12.5) | 0 | NA | NA | NA | NA

Figure 2: ESKAPEE isolates resistance categories, Magiorakos et al. [8] classification.Abbreviations: MDR, multidrug-resistant; PDR, pandrug-resistant; WT, wild type; XDR, extensively drug-resistant.

Figure 3: Distribution of CDC and IDSA resistance phenotypes [9] among Gram-negative ESKAPEE pathogens.Abbreviations: CDC, Centers for Disease Control and Prevention; CR, carbapenem-resistant; DTR, difficult-to-treat resistance; ESCR, extended-spectrum cephalosporin-resistant; FQR, fluoroquinolone-resistant; IDSA, Infectious Diseases Society of America.

Among Gram-negative isolates, MDR was the predominant phenotype in E. coli (56.9%), whereas XDR and possible PDR phenotypes were more frequent among K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp. (Figure 2). Carbapenem resistance was lowest in E. coli (25.7%) and highest in A. baumannii (67.9%), with intermediate rates observed in K pneumoniae, Enterobacter spp., and P. aeruginosa. ESCR exceeded 50% across all Gram-negative organisms, whereas FQR exceeded 50% in all except Enterobacter spp. (40%) (Figure 3).

Among Gram-positive isolates, MDR predominated in both S. aureus (73.9%) and Enterococcus spp. (66.7%), with XDR and possible PDR phenotypes comparatively rare (Figure 2); CDC/Infectious Diseases Society of America (IDSA) phenotyping criteria [9] were not applicable to these organisms. No isolate could be classified as true PDR [8], as the complete CLSI/EUCAST-recommended antibiotic panels were not tested [12,13].