European Journal of Cardiovascular Medicine

Neonatal sepsis continues to be a significant contributor to neonatal morbidity and mortality worldwide, particularly in low- and middle-income countries where access to timely diagnostics and appropriate antimicrobial therapy remains limited (1,2). It is estimated that over one million newborns die annually due to sepsis and related complications, with the burden disproportionately higher in rural and resource-constrained healthcare settings (3).

Early-onset and late-onset neonatal sepsis differ in their microbial etiology and modes of transmission. While early-onset infections are commonly associated with maternal or perinatal sources, late-onset cases often involve nosocomial pathogens (4). The causative organisms vary geographically and temporally, emphasizing the need for region-specific data to guide empirical treatment protocols (5).

Compounding the clinical challenge is the growing threat of antimicrobial resistance (AMR), particularly among Gram-negative pathogens such as Klebsiella pneumoniae and Escherichia coli, which have shown increasing resistance to commonly used antibiotics including aminoglycosides and third-generation cephalosporins (6,7). The World Health Organization has classified AMR as one of the top global public health threats, and neonates are among the most vulnerable populations due to their immature immune systems and frequent exposure to invasive procedures (8).

Despite the critical need for local epidemiological data, there is a paucity of studies focusing on neonatal sepsis in rural tertiary care centers in India. Most available data come from urban or referral hospitals, which may not reflect the unique microbial landscape and resistance trends in rural settings (9). Therefore, this study aims to analyze the microbial profile and antibiotic resistance patterns in culture-proven neonatal sepsis cases over a five-year period in a rural tertiary hospital, with the goal of informing local treatment protocols and supporting antimicrobial stewardship efforts.

This retrospective observational study was conducted in the Neonatal Intensive Care Unit (NICU) of a rural tertiary care hospital over a five-year period, from January 2019 to December 2023.

Study Population:
Neonates aged 0 to 28 days who were admitted with clinical suspicion of sepsis and had undergone blood culture testing were included. Only cases with culture-confirmed sepsis were analyzed. Incomplete records and contaminated culture reports were excluded.

Data Collection:
Patient records were reviewed for demographic details, clinical features, and laboratory findings. Microbiological data, including the type of organisms isolated and their antibiotic susceptibility patterns, were retrieved from the microbiology department’s database.

Microbiological Analysis:
Blood samples were collected aseptically before the initiation of antibiotic therapy and inoculated into pediatric blood culture bottles. The cultures were incubated and monitored using an automated blood culture system (e.g., BACTEC or BacT/ALERT). Positive cultures were subcultured on appropriate media, and isolates were identified through standard biochemical tests.

Antibiotic Susceptibility Testing:
Antimicrobial sensitivity was assessed using the Kirby-Bauer disk diffusion method as per the Clinical and Laboratory Standards Institute (CLSI) guidelines. The antibiotics tested included ampicillin, gentamicin, cefotaxime, ceftazidime, amikacin, ciprofloxacin, piperacillin-tazobactam, meropenem, vancomycin, and linezolid, among others.

Data Analysis:
The collected data were entered into Microsoft Excel and analyzed using descriptive statistics. Results were expressed as frequencies and percentages. The yearly distribution of isolates and resistance trends were also evaluated to observe any significant shifts over time.

During the five-year study period, a total of 1240 neonates were admitted with clinical suspicion of sepsis. Of these, 368 cases (29.7%) were confirmed by positive blood cultures.

Microbial Distribution

Out of 368 culture-positive cases, Gram-negative bacteria accounted for the majority of isolates (62.5%), while Gram-positive organisms were responsible for 33.2% of infections. The remaining 4.3% were due to fungal pathogens (Table 1).

Table 1: Distribution of Microbial Isolates in Culture-Proven Neonatal Sepsis (n=368)

As shown in Table 1, Klebsiella pneumoniae was the most frequently isolated pathogen, followed by Escherichia coli and Staphylococcus aureus.

Antibiotic Resistance Patterns

Resistance patterns varied significantly between Gram-negative and Gram-positive organisms. Among Gram-negative isolates, high resistance was observed to ampicillin (82%), cefotaxime (68%), and gentamicin (55%), while meropenem retained good activity with only 14% resistance. Gram-positive organisms exhibited 72% resistance to penicillin, while vancomycin and linezolid showed the highest sensitivity (Table 2).

Table 2: Antibiotic Resistance Profile of Major Isolates (%)

As demonstrated in Table 2, resistance to first-line antibiotics remains high, particularly among Gram-negative pathogens. Staphylococcus aureus showed a relatively low resistance to vancomycin and linezolid, suggesting their continued efficacy in serious infections.

Year-wise Trend in Multidrug-Resistant (MDR) Isolates

An increasing trend in multidrug-resistant isolates was observed from 2019 to 2023. The proportion of MDR organisms rose from 41.2% in 2019 to 57.8% in 2023, indicating a growing concern in antimicrobial stewardship (Table 3).

Table 3: Year-wise Prevalence of Multidrug-Resistant Isolates

(Table 3) illustrates a progressive rise in MDR strains, underlining the need for continuous monitoring and strict infection control policies in NICUs.

Neonatal sepsis remains a formidable challenge in both developing and developed countries, with higher incidence and mortality rates reported in rural and resource-limited settings (1,2). The present study evaluated the microbial landscape and resistance trends over a five-year period, revealing significant insights relevant to empirical therapy and infection control in rural neonatal intensive care units.

Our findings indicate a predominance of Gram-negative organisms, particularly Klebsiella pneumoniae and Escherichia coli, accounting for nearly two-thirds of culture-positive cases. This trend is consistent with previous studies conducted in India and other parts of Asia, where Gram-negative bacilli continue to dominate the neonatal sepsis burden (3–5). Pseudomonas aeruginosa also emerged as a significant pathogen, although less frequent, which aligns with studies from similar rural settings (6).

Among Gram-positive isolates, Staphylococcus aureus and coagulase-negative staphylococci (CONS) were commonly identified. This is comparable to previous reports that highlight CONS as a frequent cause of late-onset sepsis in neonates, often associated with invasive devices (7,8). The identification of Enterococcus faecalis also supports the emerging role of enterococci in neonatal infections (9).

Alarmingly, our data showed high levels of resistance to first-line antibiotics, including ampicillin, cefotaxime, and gentamicin. Similar resistance profiles have been reported in other Indian studies, reflecting widespread misuse and over-the-counter availability of antibiotics (10,11). Resistance to third-generation cephalosporins, especially among Klebsiella spp., raises concerns about extended-spectrum beta-lactamase (ESBL) production, a phenomenon increasingly reported in neonatal units (12).

Encouragingly, carbapenems like meropenem retained better activity against Gram-negative isolates, while vancomycin and linezolid remained effective against Gram-positive cocci. However, the rising use of these last-resort antibiotics may further drive resistance if antimicrobial stewardship practices are not strengthened (13). The rise in multidrug-resistant (MDR) isolates over the study period, from 41.2% in 2019 to 57.8% in 2023, underscores this evolving threat and mirrors trends observed globally (14,15).

The yearly increase in MDR prevalence could be attributed to prolonged hospitalization, inadequate infection control, and empirical antibiotic use without sensitivity data. These findings support the need for routine surveillance of pathogens and their susceptibility profiles, especially in rural healthcare systems where microbiological infrastructure may be limited.

One limitation of this study was its retrospective design and dependence on the accuracy of recorded data. Additionally, molecular characterization of resistance genes and ESBL production was not performed, which could have provided deeper insights into resistance mechanisms.

In conclusion, this study highlights the evolving microbial spectrum and increasing antibiotic resistance in neonatal sepsis cases from a rural tertiary care center. These results emphasize the necessity for local antibiograms, strict infection control, and rational antibiotic policies to guide clinical decision-making and preserve the efficacy of existing antimicrobials.

1. Minotti C, Di Caprio A, Facchini L, Bedetti L, Miselli F, Rossi C, et al. Antimicrobial resistance pattern and empirical antibiotic treatments in neonatal sepsis: A retrospective, single-center, 12-year study. Antibiotics (Basel). 2023;12(10):1488. doi:10.3390/antibiotics12101488. PMID: 37887188.
2. Acheampong EN, Tsiase JA, Afriyie DK, Amponsah SK. Neonatal sepsis in a resource-limited setting: Causative microorganisms and antimicrobial susceptibility profile. Interdiscip Perspect Infect Dis. 2022;2022:7905727. doi:10.1155/2022/7905727. PMID: 35669534.
3. Jihwaprani MC, Sula I, Coha D, Alhebshi A, Alsamal M, Hassaneen AM, et al. Bacterial profile and antimicrobial susceptibility patterns of common neonatal sepsis pathogens in Gulf Cooperation Council countries: A systematic review and meta-analysis. Qatar Med J. 2024;2024(4):62. doi:10.5339/qmj.2024.62. PMID: 39552951.
4. Yadav NS, Sharma S, Chaudhary DK, Panthi P, Pokhrel P, Shrestha A, et al. Bacteriological profile of neonatal sepsis and antibiotic susceptibility pattern of isolates admitted at Kanti Children's Hospital, Kathmandu, Nepal. BMC Res Notes. 2018;11(1):301. doi:10.1186/s13104-018-3394-6. PMID: 29764503.
5. Pokhrel B, Koirala T, Shah G, Joshi S, Baral P. Bacteriological profile and antibiotic susceptibility of neonatal sepsis in neonatal intensive care unit of a tertiary hospital in Nepal. BMC Pediatr. 2018;18(1):208. doi:10.1186/s12887-018-1176-x. PMID: 29950162.
6. Nguyen TQN, Do THG, Nguyen TV, Pham TN, Hoang TBN. Neonatal sepsis in Vietnam: Bacterial profiles and antibiotic susceptibility in a tertiary care setting. Am J Infect Control. 2025;53(4):453–7. doi:10.1016/j.ajic.2024.12.016. PMID: 39742918.
7. Mutlu M, Aslan Y, Aktürk Acar F, Kader Ş, Bayramoğlu G, Yılmaz G. Changing trend of microbiologic profile and antibiotic susceptibility of the microorganisms isolated in the neonatal nosocomial sepsis: a 14 years analysis. J Matern Fetal Neonatal Med. 2020;33(21):3658–65. doi:10.1080/14767058.2019.1582633. PMID: 30760078.
8. Lu Q, Zhou M, Tu Y, Yao Y, Yu J, Cheng S. Pathogen and antimicrobial resistance profiles of culture-proven neonatal sepsis in Southwest China, 1990–2014. J Paediatr Child Health. 2016;52(10):939–43. doi:10.1111/jpc.13278. PMID: 27500793.
9. Vijayakumar S, Kumar H, Basu S, Chandy S, Anbarasu A, Manoharan A, et al. Changing landscape of antimicrobial resistance in neonatal sepsis: An in silico analyses of multidrug resistance in Klebsiella pneumoniae. Pediatr Infect Dis J. 2024;43(8):777–84. doi:10.1097/INF.0000000000004358. PMID: 38621154.
10. Alharbi AS. Common bacterial isolates associated with neonatal sepsis and their antimicrobial profile: A retrospective study at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. Cureus. 2022;14(1):e21107. doi:10.7759/cureus.21107. PMID: 35165566.
11. Lamba M, Sharma D, Sharma R, Vyas A, Mamoria V. To study the profile of Candida isolates and antifungal susceptibility pattern of neonatal sepsis in a tertiary care hospital of North India. J Matern Fetal Neonatal Med. 2021;34(16):2655–9. doi:10.1080/14767058.2019.1670799. PMID: 31581861.
12. Roy MP, Bhatt M, Maurya V, Arya S, Gaind R, Chellani HK. Changing trend in bacterial etiology and antibiotic resistance in sepsis of intramural neonates at a tertiary care hospital. J Postgrad Med. 2017;63(3):162–8. doi:10.4103/0022-3859.201425. PMID: 28272077.
13. Sorsa A, Früh J, Stötter L, Abdissa S. Blood culture result profile and antimicrobial resistance pattern: a report from neonatal intensive care unit (NICU), Asella teaching and referral hospital, Asella, south East Ethiopia. Antimicrob Resist Infect Control. 2019;8:42. doi:10.1186/s13756-019-0486-6. PMID: 30828446.
14. Geleta D, Abebe G, Tilahun T, Gezahegn D, Workneh N, Beyene G. Phenotypic bacterial epidemiology and antimicrobial resistance profiles in neonatal sepsis at Jimma medical center, Ethiopia: Insights from prospective study. PLoS One. 2024;19(9):e0310376. doi:10.1371/journal.pone.0310376. PMID: 39283882.

15. Pillay D, Naidoo L, Swe Swe-Han K, Mahabeer Y. Neonatal sepsis in a tertiary unit in South Africa. BMC Infect Dis. 2021;21(1):225. doi:10.1186/s12879-021-05869-3. PMID: 33639864.