Molecular Characterization of Antimicrobial Resistance Genes and Their Association with Clinical Outcomes Among Neonates with Sepsis: A Prospective Clinical and Molecular Study

Abstract

Background

Neonatal sepsis is a significant contributor to neonatal morbidity and mortality and AMR is a challenge to effective treatment and clinical outcomes.

Objective

To molecularly characterize antimicrobial resistance genes among neonates with sepsis and determine their association with antimicrobial susceptibility patterns and clinical outcomes

Methodology

A prospective clinical and molecular research was carried out from January 2024 to December 2025. A consecutive series of 392 neonates with sepsis were included. Culture was used to identify bacterial pathogens, antimicrobial susceptibility testing was done and selected AMR genes such as blaCTX-M, blaTEM, blaSHV, blaNDM, blaOXA-48-like and blaVIM were detected by polymerase chain reaction. Of the 231 culture-positive isolates, 117 (50.65%) were identified as AMR gene-positive and 114 (49.35%) were identified as AMR gene-negative based on the detection of at least one of the AMR genes tested. Association of AMR gene status, phenotypic resistance and clinical outcomes was evaluated.

Results

Among the 392 neonates, 211 (53.83%) were male and 181 (46.17%) female, while 231 (58.93%) had culture-positive isolates. Klebsiella pneumoniae was the most common pathogen (71, 30.74%), followed by Escherichia coli (54, 23.38%). Ampicillin showed the highest resistance (177, 76.62%). Among the 231 culture-positive isolates, blaCTX-M was most prevalent (96, 41.56%), followed by blaTEM (82, 35.50%), blaSHV (61, 26.41%), and blaNDM (39, 16.88%). Compared with the AMR gene-negative group, AMR gene-positive cases had higher treatment failure (55, 47.01% vs. 31, 27.19%; p=0.002), prolonged hospitalization (48, 41.03% vs. 32, 28.07%; p=0.039), sepsis-related complications (42, 35.90% vs. 26, 22.81%; p=0.029), septic shock (27, 23.08% vs. 13, 11.40%; p=0.019), organ dysfunction (22, 18.80% vs. 10, 8.77%; p=0.027), and mortality (31, 26.50% vs. 14, 12.28%; p=0.006).

Conclusion

Neonatal sepsis isolates were found to contain molecular AMR determinants, which were significantly linked to antimicrobial resistance and clinical outcomes, thereby justifying integrated molecular surveillance and prompt effective antimicrobial therapy.