Prevalence and antibiotic susceptibility of ESKAPE pathogens in skin and soft tissue infections

Introduction

Skin and soft tissue infections (SSTIs) affect the skin, subcutaneous tissues, and associated structures.¹ The most common opportunistic bacteria causing SSTIs belong to the “ESKAPE” group: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.²

In 2017, the WHO classified ESKAPE infections as a priority due to their significant role in antimicrobial resistance.³ Studies indicate that ESKAPE pathogens cause over 64% of SSTIs in India.⁴ These bacteria exhibit advanced resistance mechanisms, including drug target modifications, reduced drug absorption, biofilm formation, β-lactamase production, efflux pump overexpression, and metabolic pathway alterations. Their ability to “escape” antimicrobial treatments complicates management and increases healthcare-associated infections.⁵

The rise of ESKAPE pathogens is driven by excessive antibiotic use, prolonged hospital stay, and intensive care management based on host immunity, with septicaemia and bacteraemia being more common in immunocompromised individuals.⁶ Addressing this challenge requires strict infection control, judicious antibiotic use, and exploration of alternative treatments.^7-9

This study aims to determine the prevalence of SSTIs and analyse the resistance patterns of ESKAPE pathogens, providing critical insights for effective treatment strategies.

Methods

A prospective, observational, cross-sectional study was conducted over 1year (January–December 2024) in the Bacteriology section of the Microbiology Department at our institute, following Institutional Ethical Committee approval (IHEC/AIIMS-GKP/BMR/367/2024). A total of 2,300 specimens, including pus, pus swabs, and tissue samples, were collected under proper aseptic precaution in a sterile container by the Department of Dermatology over a period of one year from both out-patients and in-patients with SSTIs and sent to Microbiology Department for processing.

All the clinically significant specimens were included in the study.Specimens were processed using 5% sheep blood and MacConkey agar, and incubated at 37°C for 24 hours, with extended incubation as needed. Polymicrobial growth were excluded from the study. Bacterial isolates were identified using standard microbiological methods. Antibiotic susceptibility testing (AST) was performed using the modified Kirby-Bauer disc diffusion method, E-strips, and VITEK 2 COMPACT, following CLSI guidelines. Methicillin resistance was assessed via the cefoxitin disc diffusion method, while extended-spectrum beta-lactamase production in Escherichia coli and Klebsiella species was detected using the cephalosporin/clavulanate combination disc method.⁷

Demographic and clinical data were recorded in Microsoft Excel, ensuring confidentiality. Data analysis was performed using STATA 12. To ensure accuracy and reliability, quality control was maintained using Escherichia coli ATCC 25922 (non-Extended-Spectrum β-Lactamase (ESBL) producer) and Klebsiella pneumoniae ATCC 700603 (ESBL producer).⁷

Results

Of the 2,300 clinical samples processed, 1,311 (57%) yielded bacterial growth, while 989 (43%) showed no growth. Among culture-positive samples, ESKAPE pathogens were identified in 808 (61.6%) samples, predominantly from pus (460, 57%), pus swabs (193, 23.9%), and infected tissue samples (155, 19.1%). The males (61.8%) outnumbered the females (38.2%), with the most affected age group being 41–60 years (22%).Out of the total patients, 1174 (51%) were on prior antibiotic therapy before the sampling.

Staphylococcus aureus (481, 59.5%) was the most frequently isolated ESKAPE pathogen, followed by Pseudomonas aeruginosa (144, 17.8%), Klebsiella pneumoniae (92, 11.4%), Acinetobacter baumannii (65, 8%), Enterococcus faecium (19, 2.4%), and Enterobacter spp. (7, 0.9%) [Table 1]. In our study, the majority of ESKAPE pathogen-associated cases were uncomplicated SSTIs (uSSTIs) (52%), including folliculitis, impetigo, simple abscesses, and erysipelas [Table 1]. Complicated SSTIs (cSSTIs) accounted for 34.8% and included infected burn wounds, ulcers, diabetic foot infections, and deep-seated ulcers. Severe infections, such as scarlet skin syndrome (SSS), toxic shock syndrome (TSS), non-healing ulcers, and cellulitis, made up 11% of cases. Additionally, 2.2% of patients remained undiagnosed [Table 1].

S. aureus showed high susceptibility to vancomycin and teicoplanin (98%), followed by amikacin (96%) and chloramphenicol (93.6%). Methicillin-resistant S. aureus (MRSA) was detected in 251 isolates. Additionally, 26.3% of Enterococcus spp. were vancomycin resistant. Among Gram-negative isolates, P. aeruginosa showed high sensitivity to imipenem (94.8%), K. pneumoniae to imipenem (76%), and A. baumannii to tobramycin (85%). ESBL production was observed in 57% of K. pneumoniae isolates [Table 2]. Of 308 Gram-negative isolates, 47 (15.3%) were multidrug-resistant (MDR), all susceptible to colistin, while 261 (84.7%) were non-MDR [Table 3] [Figure 1].

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Figure 1:

Antibiotic susceptibility heatmap – A heatmap illustrating antibiotic resistance/susceptibility patterns.

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Discussion

SSTIs are a major public health concern, particularly due to the involvement of MDR pathogens. In the present study, the clinical samples showed bacterial growth, with a significant proportion comprising ESKAPE pathogens. These pathogens play a crucial role in antimicrobial resistance.

The most common clinical specimen in our study was pus, followed by pus swabs and tissue samples. Among the identified pathogens, ESKAPE organisms were responsible for 61.6% of all clinical isolates, underscoring their significant role in healthcare-associated infections. These findings align with other studies. Additionally, we observed a predominance of Gram-positive bacteria, with Staphylococcus aureus emerging as the most frequently isolated pathogen from pus samples. Among Gram-negative bacteria, Pseudomonas aeruginosa was the most prevalent isolate. Similar studies have also demonstrated a high isolation rate of Staphylococcus aureus, corroborating our observations.⁹ Moreover, another study has highlighted Enterococcus faecium as a significant clinical isolate, consistent with our results.^10-13 Conversely, a survey conducted in German emergency departments reported that the enterobacterales group was the most frequently isolated pathogen, differing from our study, which found a higher prevalence of gram-positive organisms.¹⁴ Furthermore, a study from a U.S. Emergency department presented contrasting results, as it focused on all clinical samples and reported a dominance of gram-negative bacteria, particularly Escherichia coli.¹⁵ Similar findings were observed in a study from Hungary, further emphasising regional variations in microbial distribution.¹⁶

These discrepancies may be attributed to differences in patient demographics, healthcare settings, antibiotic prescribing patterns, and infection control practices. Further multicentric studies with larger sample sizes are warranted to better understand the epidemiological trends of bacterial infections.

A study reported a male predominance among SSTI patients (51% males, 49% females),¹⁷ consistent with our findings. Our data also showed that patients in the age group of <40 years were more affected by SSTIs, similar to the findings of a study by Benko R., et al.¹⁷ These findings suggest that middle-aged adults are more susceptible to SSTIs, possibly due to occupational exposures, comorbidities, or compromised immune responses. The infections were predominantly uncomplicated SSTIs, while complicated cases included ulcers and deep-seated infections, consistent with other studies.¹⁸

In our study, Staphylococcus aureus was the most frequently identified gram-positive pathogen, constituting 59.52% (481) of all ESKAPE isolates. Among these, MRSA was detected in 251 cases (52.18%), a prevalence rate that differs from findings reported in similar studies. Notably, S. aureus exhibited a high susceptibility to glycopeptides such as vancomycin (98%) and teicoplanin (98%), followed by amikacin (96%) and chloramphenicol (93.6%), consistent with prior studies.¹⁶ These findings underscore the continued effectiveness of glycopeptides and aminoglycosides. The recently published World Society of Emergency Surgery (WSES) guidelines recommend empiric coverage with an anti-MRSA agent (vancomycin or linezolid) in combination with broad-spectrum Gram-negative coverage (piperacillin–tazobactam or carbapenem) along with clindamycin due to its antitoxin effect.¹⁰

Among Enterococcus faecium isolates, five (26.3%) demonstrated vancomycin resistant enterococcus (VRE), reflecting the increasing challenge of antimicrobial resistance in this pathogen. This trend aligns with observations from previous studies. ^{11,12,15,18,19} Furthermore, high-level aminoglycoside resistance (HLAR) was detected in three (15%) Enterococcus isolates. The emergence of VRE and HLAR highlights the urgent need for alternative therapeutic strategies, including the use of linezolid or daptomycin, to effectively manage resistant enterococcal infections.

Among Pseudomonas aeruginosa isolates, the highest susceptibility was observed to imipenem (94.8%) and meropenem (91.5%), findings that align with previous reports.¹⁶ Conversely, aztreonam exhibited the lowest sensitivity (15%), raising concerns regarding the diminishing efficacy of certain beta-lactam antibiotics against P. aeruginosa. These results reaffirm the role of carbapenems as key therapeutic agents for P. aeruginosa-associated infections, though the limited effectiveness of aztreonam underscores the need for cautious antibiotic selection.

For Klebsiella pneumoniae, the highest sensitivity was observed to imipenem (76%) and chloramphenicol (74.7%), findings divergent from those reported in other studies.^20-22 Notably, ESBL production was detected in 57% (156) of K. pneumoniae isolates, a trend consistent with previous literature.^23,24 The significant prevalence of ESBL-producing strains highlights the challenge posed by β-lactamase-mediated resistance and underscores the necessity for judicious carbapenem use alongside stringent infection control measures to curb the spread of resistant strains.

In Acinetobacter baumannii, the highest susceptibility rates were observed for tobramycin (85%) and piperacillin-tazobactam (83.1%), findings contrasting with those of previous studies.¹⁶ Given the MDR nature of A. baumannii, the retained efficacy of tobramycin and β-lactam/β-lactamase inhibitor combinations is promising. Among the 308 gram-negative isolates analysed, 47 (15.25%) were identified as MDR, a prevalence consistent with findings reported in previous studies,while the remaining 261 (84.74%) were classified as non-MDR. All MDR isolates exhibited susceptibility to colistin, reinforcing its critical role as a last-resort antibiotic.

Limitations

The study was carried out at a single institution, so the results may not reflect variations in patient demographics, healthcare practices, or regional microbial resistance patterns. The study did not include long-term patient outcomes, preventing an assessment of the sustained efficacy of interventions or potential relapses.

Conclusion

Our study provides insights into the prevalence, distribution, and antimicrobial resistance patterns of ESKAPE pathogens in SSTIs, highlighting the burden posed by resistant pathogens and underscoring the need for comprehensive strategies to address this growing threat.