Rapid Identification of Neonatal Sepsis Pathogens Using MALDI-TOF MS: Bacteriological Profile and Antimicrobial Susceptibility Patterns in a North Indian Tertiary Care Hospital

Background Neonatal sepsis is a major cause of mortality in low- and middle-income countries (LMICs) such as India, where delayed diagnosis and antimicrobial resistance (AMR) challenge effective management. Conventional blood cultures, taking 2-5 days for pathogen identification, delay targeted therapy, worsening outcomes, and fueling AMR. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (bioMérieux, USA) offers rapid diagnostics, potentially transforming neonatal sepsis care. This study assesses the diagnostic speed of MALDI-TOF MS versus conventional methods in neonates with suspected sepsis at a North Indian tertiary hospital, alongside bacteriological and AMR profiling. Methodology From November 2022 to November 2023, we prospectively enrolled 100 consecutive outborn neonates (<28 days) with suspected sepsis (positive sepsis screen: ≥2 parameters, e.g., C-reactive protein, leukocyte count) at a tertiary care hospital. Neonates with prior antibiotics, severe asphyxia, or malformations were excluded. Blood samples underwent BacT/Alert culture, with pathogens identified by conventional methods (2-5 days) and MALDI-TOF MS (VITEK MS, bioMérieux, USA). Time-to-identification was compared (paired t-test, p < 0.05). Antimicrobial susceptibility testing used VITEK-2 (bioMérieux, USA) per Clinical and Laboratory Standards Institute guidelines, with chi-square tests analyzing microbiological and AMR data. Results Among 100 neonates (50 early-onset sepsis (EOS), mean age = 1.34 ± 0.692 days; 50 late-onset sepsis (LOS), mean age = 14.418 ± 9.395 days), MALDI-TOF MS identified pathogens in 1.47 ± 0.979 days (median = 2 days) versus 2.83 ± 0.817 days (median = 3 days) for conventional culture (p = 0.0052), a 48% reduction. <i>Klebsiella pneumoniae</i> (35%) and <i>Acinetobacter baumannii</i> (28%) predominated EOS, while LOS included <i>K. pneumoniae</i> (30%), <i>A. baumannii</i> (30%), and <i>Pseudomonas aeruginosa</i> (10%, LOS-only). Gram-negative isolates showed >85% susceptibility to meropenem and ertapenem; amikacin and colistin were effective, though <i>P. aeruginosa</i> had reduced amikacin sensitivity (60%). Beta-lactams were poorly effective (<40%). Gram-positive isolates were sensitive to linezolid and vancomycin (>90%), except <i>Enterococcus</i> spp. (0% vancomycin susceptibility). Conclusions MALDI-TOF MS accelerates neonatal sepsis diagnosis by 1.36 days, enabling earlier targeted therapy. Coupled with dominant pathogens (<i>K. pneumoniae</i>, <i>A. baumannii</i>) and rising AMR (e.g., vancomycin-resistant <i>Enterococcus</i>), it highlights the need for rapid diagnostics in LMICs. Carbapenems remain viable empirical options, but resistance trends demand stewardship. This study supports integrating MALDI-TOF MS into neonatal care, enhancing outcomes and informing antibiotic policies.