Neonatal and pediatric sepsis: Microbiological insights, diagnostic innovations, and antimicrobial challenges

Abstract

Neonatal and pediatric sepsis remains a major global health concern, contributing significantly to morbidity and mortality among children under 5 years of age. The clinical and microbiological characteristics of sepsis differ markedly in neonates and children, necessitating tailored diagnostic and treatment approaches. This mini-review explores the evolving microbiological landscape, recent advancements in diagnostic methodologies, and challenges posed by antimicrobial resistance (AMR) in managing neonatal and pediatric sepsis. Emerging pathogens, including multidrug-resistant Gram-negative bacilli and fungal organisms, are reshaping the epidemiology of sepsis. Innovations in molecular diagnostics, including polymerase chain reaction-based platforms, next-generation sequencing, and artificial intelligence-integrated tools, are revolutionizing early pathogen detection and resistance profiling. However, implementation gaps persist, particularly in low- and middle-income countries. Therapeutic challenges are compounded by limited pediatric data on newer antimicrobials and rising AMR rates. Infection prevention strategies, especially in intensive care units, are crucial to outbreak containment. An integrated approach combining microbiological surveillance, rapid diagnostics, and antimicrobial stewardship is critical for improving sepsis outcomes. Future research should focus on context-specific implementation of diagnostic tools and optimizing treatment strategies for resource-limited settings.

Key Words: Sepsis biomarkers; Neonatal intensive care unit; Antimicrobial stewardship; Microbiome; AI in diagnostics; Neonatal infections

Core Tip: Neonatal and pediatric sepsis is a major contributor to global child mortality, with significant challenges in timely and accurate diagnosis. Traditional blood culture methods have limitations, necessitating advancements in molecular diagnostics and biomarker-based approaches. Emerging technologies such as metagenomic sequencing and artificial intelligence-driven diagnostic tools offer promising solutions for rapid pathogen identification. Antimicrobial resistance continues to complicate treatment, making antimicrobial stewardship programs crucial in pediatric healthcare. This review highlights microbiological insights, diagnostic advancements, antimicrobial resistance mechanisms, combination therapy strategies, and approaches to improving early detection and outcomes in pediatric sepsis.

INTRODUCTION

Sepsis remains a major global health challenge and is a leading cause of neonatal and pediatric mortality, contributing to approximately 15%-20% of neonatal deaths worldwide[1]. The burden of sepsis is particularly high in low- and middle-income countries (LMICs), where limited healthcare infrastructure, inadequate infection control measures, and the misuse of antibiotics significantly contribute to increased morbidity and mortality[2,3]. The widespread and often indiscriminate use of antibiotics has led to an alarming rise in antimicrobial resistance (AMR), further complicating sepsis management and reducing treatment efficacy[4,5].

Traditional microbiological methods, such as blood cultures, have long been considered the gold standard for diagnosing sepsis. However, these methods have significant limitations, including prolonged turnaround times, low sensitivity, and high rates of false-negative results, particularly in neonates who have received empirical antibiotic therapy prior to sample collection[6,7]. Given these constraints, there is a pressing need for rapid, accurate, and reliable diagnostic tools to facilitate early identification and targeted treatment of sepsis.

Recent advancements in molecular diagnostics, including polymerase chain reaction (PCR) and next-generation sequencing (NGS), have shown promise in enhancing the detection of bloodstream infections with higher sensitivity and specificity[8,9]. Moreover, artificial intelligence (AI)-driven algorithms are increasingly being integrated into diagnostic workflows to analyze clinical and laboratory data, enabling early risk stratification and personalized therapeutic interventions[10]. In parallel, microbiome-based approaches are emerging as potential game changers, offering insights into host–microbe interactions and facilitating the development of novel biomarkers for early sepsis diagnosis[11].

In light of these developments, this review explores the evolving landscape of sepsis diagnostics, emphasizing the role of advanced technologies in improving clinical outcomes and reducing the burden of neonatal and pediatric sepsis worldwide.

REVIEW METHODOLOGY AND APPROACH

The current review adopts a narrative methodology, which allows for an in-depth exploration of microbiological insights, diagnostic advancements, and antimicrobial challenges associated with neonatal and pediatric sepsis. The selection of studies was guided by their relevance to recent technological advances, emerging pathogens, and patterns of antimicrobial resistance. Priority was given to studies published within the last five years, ensuring that the review reflects the most up-to-date research. For diagnostic technologies, emerging techniques such as NGS, AI-driven tools, and PCR-based platforms were discussed based on their growing use in pediatric sepsis. Additionally, studies from both developed and developing countries were considered to highlight differences in epidemiology, diagnosis, and treatment strategies across regions.

This review provides a comprehensive understanding of the evolving landscape of neonatal and pediatric sepsis, focusing on key innovations that may have a transformative impact on clinical practice. Studies included in this review were selected based on their contribution to advancing the diagnosis, treatment, and management of these patient populations.

MICROBIOLOGICAL LANDSCAPE OF NEONATAL AND PEDIATRIC SEPSIS

Key regional variations exist in the etiology of sepsis, with Gram-negative bacteria predominating in LMICs, whereas Gram-positive organisms are more commonly encountered in high-income countries[12-14]. The pathogen distribution varies significantly between early-onset sepsis, late-onset sepsis, and pediatric sepsis, with common causative organisms summarized in Table 1. The role of fungal pathogens such as Candida spp. should also be highlighted, particularly in neonates at high risk[15,16]. These variations are further summarized in Table 2, which presents pathogen distribution by region and patient population characteristics.

Table 1 Pathogen distribution in early-onset sepsis, late-onset sepsis, and pediatric sepsis[13,14].

Sepsis type	Common pathogens
Early-onset sepsis	Group B Streptococcus, Escherichia coli, Listeria monocytogenes
Late-onset sepsis	Klebsiella pneumoniae, Staphylococcus aureus, Candida spp.
Pediatric sepsis	Pseudomonas aeruginosa, Enterobacter spp., MRSA

MRSA: Methicillin-resistant Staphylococcus aureus.

Table 2 Common pathogens in neonatal and pediatric sepsis by region and comorbidity[15,16].

Region/Condition	Neonatal sepsis - common pathogens	Pediatric sepsis - common pathogens
Developed countries	Group B Streptococcus, Escherichia coli, Listeria spp.	Streptococcus pneumoniae, Neisseria meningitidis, MRSA
Developing countries	Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli	Salmonella spp., Staphylococcus aureus, Pseudomonas aeruginosa
NICU/PICU settings	MDR Klebsiella, Candida albicans, Enterococcus spp.	Acinetobacter, Stenotrophomonas maltophilia
Immunocompromised children	Pseudomonas aeruginosa, Candida parapsilosis	Nocardia, Fusarium, Aspergillus, MDR GNB

GNB: Gram-negative bacilli; MDR: Multidrug-resistant; MRSA: Methicillin-resistant Staphylococcus aureus; NICU: Neonatal intensive care units; PICU: Pediatric intensive care unit.

To better understand the microbial etiology of sepsis across different pediatric age groups, it is useful to compare the distribution of pathogens between neonates and older children. The following figure (Figure 1) provides a visual summary of key age-related differences in sepsis-causing organisms.

Figure 1  Pathogen distribution by age group in neonatal and pediatric sepsis.

The Pathogen Distribution by Age Group in Neonatal and Pediatric Sepsis bar chart illustrates the relative prevalence of Gram-negative, Gram-positive, fungal, and viral pathogens in neonatal and pediatric sepsis. The distribution highlights age-related microbiological patterns, with Gram-negative pathogens being more common in neonates and Gram-positive organisms more frequent in pediatric patients[12,17,18].

Gram-positive and fungal pathogens

While Gram-negative organisms are often predominant in neonatal and pediatric sepsis, particularly in LMICs, Gram-positive bacteria and fungal pathogens also contribute significantly to the disease burden, especially in high-income settings and among specific risk groups. Gram-positive organisms, such as Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus agalactiae (Group B Streptococcus), and Enterococcus spp., are common culprits in early- and late-onset neonatal sepsis, particularly in infants with indwelling catheters or those receiving intensive care[19,20]. Fungal pathogens, predominantly C. albicans and C. parapsilosis, are important causes of late-onset sepsis in preterm infants and immunocompromised children[21,22]. Their prevalence is often under-recognized due to limitations in diagnostic sensitivity and may be associated with increased morbidity, longer hospital stays, and higher mortality. The presence of these pathogens often necessitates broad-spectrum or empiric antifungal therapy, further complicating antimicrobial stewardship in neonatal intensive care units (NICUs).

ICU outbreaks and infection control

NICUs and pediatric ICUs (PICUs) are recognized as hotspots for nosocomial outbreaks. These outbreaks are frequently associated with multidrug-resistant (MDR) organisms such as Klebsiella pneumoniae, Acinetobacter baumannii, and Candida species. Studies have reported high prevalence rates of these MDR pathogens in NICU and PICU settings, underscoring the critical need for stringent infection control measures[23-25]. Contributing factors include overcrowding, suboptimal hand hygiene practices, understaffing, and prolonged use of invasive devices like central lines and ventilators[26,27]. Effective infection prevention strategies such as active surveillance, targeted environmental disinfection, and implementation of antimicrobial stewardship programs are critical for outbreak control[28,29]. Additionally, strengthening infection control teams and implementing sepsis bundles adapted to pediatric settings can significantly improve patient outcomes, particularly in low-resource environments[30,31].

ADVANCES IN SEPSIS DIAGNOSTICS

Timely and accurate diagnosis of sepsis is critical for improving patient outcomes, reducing mortality, and optimizing antimicrobial stewardship. Traditional culture-based methods, despite being the current gold standard, are often slow and have low sensitivity, particularly in patients who have received empirical antibiotic therapy prior to sample collection[4,7]. To address these limitations, recent advances in molecular diagnostics and AI-driven technologies have revolutionized sepsis detection by enabling rapid pathogen identification, risk stratification, and the development of personalized treatment approaches[6,9].

Molecular and AI-driven technologies

Multiplex PCR: Multiplex PCR has emerged as a valuable tool for the rapid detection of sepsis-causing pathogens. By simultaneously amplifying multiple bacterial and fungal DNA targets in a single reaction, this technique significantly reduces the time required for pathogen identification compared to traditional culture-based methods[32]. However, one of its primary limitations is its inability to assess antimicrobial susceptibility patterns, which necessitates supplementary testing to guide targeted antibiotic therapy[33]. Despite this drawback, commercially available platforms such as the BioFire FilmArray and Roche’s SeptiFast have demonstrated high sensitivity and specificity, making them increasingly viable options for early sepsis diagnosis[34,35].

NGS: NGS technology offers a comprehensive, culture-independent approach to diagnosing bloodstream infections by analyzing microbial DNA or RNA directly from patient samples[8]. Unlike conventional PCR-based methods, NGS provides broad-spectrum pathogen detection, including rare and fastidious organisms that are difficult to culture[36]. Additionally, metagenomic sequencing facilitates AMR gene profiling, which is crucial for antibiotic stewardship and precision medicine[37]. Despite its immense potential, challenges such as high cost, extended turnaround time, and the complexity of data interpretation currently limit its routine clinical application[38]. However, ongoing advancements in sequencing technology and bioinformatics are expected to make NGS a more accessible and practical diagnostic tool for sepsis management in the near future[39].

AI-based predictive models: AI-driven algorithms are transforming sepsis diagnostics by leveraging big data analytics, machine learning, and electronic health records to enhance early detection and risk prediction[40]. Models such as Sepsis Prediction and Optimization of Therapy (SPOT) and Sepsis Watch; utilize real-time clinical data including vital signs, laboratory parameters, and patient history; to generate predictive scores for sepsis risk assessment[41]. These models have demonstrated higher sensitivity and specificity than those of conventional scoring systems like the Sequential Organ Failure Assessment score[10]. Additionally, AI can assist in treatment optimization by identifying patterns of antimicrobial resistance and guiding personalized antibiotic selection, thereby reducing the overuse of broad-spectrum antibiotics[42].

Microbiome-based diagnostics: Emerging evidence suggests that gut dysbiosis in neonates and critically ill patients is strongly associated with increased susceptibility to sepsis[43]. The neonatal gut microbiota plays a crucial role in immune system development, and deviations from the normal microbial composition; often due to factors like preterm birth, prolonged hospitalization, or antibiotic overuse; can predispose infants to bloodstream infections[44]. Recent studies have identified microbiome-based biomarkers that may serve as early indicators of sepsis risk, providing a non-invasive and predictive approach to diagnosis[45]. Furthermore, advances in metabolomics and transcriptomics are enabling deeper insights into host–microbiome interactions that can inform novel therapeutic and diagnostic strategies. Transcriptomics refers to the comprehensive analysis of RNA transcripts, revealing gene expression changes in response to microbial colonization or infection. Metabolomics involves the study of small-molecule metabolites produced by both host and microbiota, offering real-time snapshots of physiological and pathological processes. These high-throughput technologies are shedding light on how specific microbial communities and their metabolic products influence immune responses during early sepsis[46].

The integration of these molecular and AI-driven diagnostic technologies into routine clinical practice holds significant promise for improving the speed and accuracy of sepsis detection, enhancing antimicrobial stewardship, and ultimately reducing the global burden of neonatal and pediatric sepsis[47].

A comparative overview of conventional and newer diagnostic modalities is provided in Table 3, highlighting their respective advantages, limitations, and clinical utility in neonatal and pediatric settings[48].

Table 3 Traditional vs emerging diagnostic techniques for neonatal and pediatric sepsis[48].

Diagnostic method	Turnaround time	Sensitivity/Specificity	Key advantages	Limitations
Blood culture	48-72 hours	Moderate	Gold standard, organism isolation	Low yield in neonates, slow
C-reactive protein	< 6 hours	Low-moderate	Widely available	Non-specific
Procalcitonin	< 6 hours	Moderate-high	Early rise in bacterial infections	Cost, variation by age
PCR-based panels	1-3 hours	High	Pathogen-specific, rapid results	Limited panels, cost
Next-generation sequencing	24-48 hours	High	Broad-range, detects rare pathogens	Expensive, needs expertise
Artificial intelligence-driven tools	Real-time	Evolving	Integration with clinical data	Limited pediatric validation

PCR: Polymerase chain reaction.

Early diagnosis and its impact on outcomes

Early diagnosis of neonatal and pediatric sepsis is critical for improving clinical outcomes. Studies have demonstrated that timely initiation of appropriate antimicrobial therapy significantly reduces mortality, particularly in neonates and young children[48,49]. Emerging diagnostic techniques such as real-time PCR, NGS, and AI-driven platforms have shown promise in reducing diagnostic turnaround times, facilitating early pathogen identification and prompt initiation of targeted therapy[50-52]. However, the adoption of these technologies remains limited in resource-constrained settings, where traditional blood cultures continue to be regarded as the gold standard, despite their long turnaround time and lower sensitivity[53]. In high-income countries, the adoption of rapid molecular diagnostics has contributed to better antimicrobial stewardship and improved survival rates. In contrast, in many LMICs, diagnostic delays continue to contribute to higher sepsis-related morbidity and mortality[54,55].

ANTIMICROBIAL RESISTANCE AND STEWARDSHIP STRATEGIES

AMR has emerged as a critical global health threat, particularly in neonatal and pediatric ICUs, where the overuse and misuse of antibiotics contribute to the rapid emergence of MDR pathogens. With limited treatment options available, innovative antimicrobial stewardship strategies are essential for mitigating the impact of AMR and optimizing therapeutic outcomes[56].

Global AMR trends

The increasing resistance among key pathogens such as K. pneumoniae and A. baumannii is particularly concerning. Carbapenem resistance in K. pneumoniae has been reported in more than 50% of isolates from intensive care settings in several regions, further complicating empirical treatment options[57,58]. Similarly, A. baumannii has demonstrated significant resistance to third-generation cephalosporins and aminoglycosides, rendering infections caused by these organisms difficult to treat[58]. The rapid dissemination of carbapenem-resistant Enterobacterales strains globally has heightened concerns regarding the efficacy of last-resort antibiotics such as colistin and tigecycline, both of which are now facing emerging resistance as well[58,59].

Bacteriophage therapy

Bacteriophage therapy is gaining renewed interest as a viable alternative to combat MDR infections. Phages specifically target bacterial hosts, sparing the human microbiota largely undisturbed[60]. Preclinical studies and compassionate-use cases have demonstrated efficacy in treating MDR infections, including those caused by Pseudomonas aeruginosa and Escherichia coli[61]. However, clinical trial data remain scarce, and challenges such as phage stability, bacterial resistance to phages, and regulatory hurdles must still be addressed before widespread clinical implementation[62].

Combination therapies

The use of combination therapies has shown promise in overcoming resistance mechanisms. Novel beta-lactam/beta-lactamase inhibitor combinations, such as ceftazidime-avibactam and meropenem-vaborbactam, have exhibited enhanced activity against carbapenem-resistant K. pneumoniae and P. aeruginosa[63]. Additionally, adjuvants such as efflux pump inhibitors and outer membrane permeability enhancers are being investigated for their ability to restore the effectiveness of traditional antibiotics against MDR pathogens and improve treatment outcomes[64].

Lipoglycopeptides as novel therapeutics: Among the emerging therapeutic options for resistant Gram-positive infections, lipoglycopeptides such as dalbavancin and oritavancin have garnered significant interest. These agents possess extended half-lives, allowing for infrequent dosing regimens, which is particularly advantageous in pediatric settings or resource-limited environments where long hospital stays may be challenging. Although currently approved for the treatment of acute bacterial skin and skin structure infections, off-label use of dalbavancin and oritavancin in bloodstream infections, including catheter-associated bacteremia and infective endocarditis, has shown promising outcomes in clinical studies[65]. Their broad-spectrum activity against multidrug-resistant Gram-positive pathogens, including methicillin-resistant S. aureus and vancomycin-resistant enterococci, underscores their potential role in pediatric and neonatal sepsis management, especially where conventional agents fail or are poorly tolerated.

Mandatory ASP implementation in NICUs

Antimicrobial stewardship programs (ASPs) play a crucial role in reducing inappropriate antibiotic use, thereby minimizing the selection pressure that drives AMR. Studies have shown that ASP implementation in NICUs leads to a significant reduction in the use of broad-spectrum antibiotics without compromising patient outcomes[56]. Protocols emphasizing early de-escalation, dose optimization, and duration minimization have demonstrated success in reducing the emergence of AMR while maintaining effective sepsis management[7,56]. The World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) advocate for strict ASPs in pediatric settings to curb the overuse of antibiotics and ensure sustainable infection control practices[66].

FUTURE DIRECTIONS

As neonatal and pediatric sepsis continues to pose a significant global health burden, future advancements must focus on early diagnosis, personalized treatment strategies, and robust antimicrobial stewardship to improve patient outcomes. Addressing the limitations of current diagnostic tools and treatment approaches requires a multifaceted approach, integrating cutting-edge technologies with evidence-based clinical practices.

Integration of rapid molecular diagnostics into routine clinical workflows

The adoption of rapid molecular diagnostic tools, such as multiplex PCR and NGS, is essential for overcoming the delays associated with conventional blood cultures. These technologies enable the early and precise identification of pathogens, allowing for targeted therapy that minimizes the unnecessary use of broad-spectrum antibiotics[6,33]. However, their integration into clinical workflows requires cost-effective implementation, accessibility in low-resource settings, and standardized protocols for data interpretation[10,40-42].

AI-powered sepsis risk prediction models for early intervention

Machine learning and AI models, such as SPOT and Sepsis Watch, are revolutionizing sepsis prediction and management. These AI-driven tools analyze patient biomarkers, electronic health records, and hemodynamic parameters to identify high-risk patients at an early stage, allowing for timely interventions and improved clinical decision-making[67]. Future research should focus on refining these models for pediatric populations, ensuring accuracy, reliability, and real-time clinical applicability[40-42].

Expanded clinical trials on phage therapy and monoclonal antibodies

The resurgence of bacteriophage therapy offers a promising alternative for combating MDR infections in neonates and children. Despite successful compassionate-use cases, large-scale randomized clinical trials are necessary to establish dosing, safety, and efficacy guidelines[60-62]. Similarly, monoclonal antibodies targeting bacterial virulence factors are emerging as a potential adjunct therapy for severe sepsis, though their clinical utility remains under investigation[68]. Future research should focus on optimizing the phage-antibiotic synergy and exploring host-directed immunotherapies as alternative treatment strategies[69].

Strengthened global collaboration for AMR surveillance

The fight against AMR requires global cooperation through initiatives led by the WHO and the CDC. Standardized AMR surveillance programs, such as the Global Antimicrobial Resistance and Use Surveillance System, help track resistance patterns, inform empirical antibiotic guidelines, and promote sustainable infection control practices[70]. Enhancing collaborative networks between low- and high-resource settings is vital in ensuring equitable access to diagnostic technologies, antimicrobial stewardship programs, and emerging therapeutic interventions[71-73].

CONCLUSION

Neonatal and pediatric sepsis continues to be a major contributor to morbidity and mortality globally, particularly in low- and middle-income countries. Despite significant progress in understanding the microbial etiology and in developing rapid diagnostic tools, sepsis remains difficult to detect early and treat effectively in these populations. Traditional culture-based techniques, although standard, are slow and often yield false negatives due to prior antibiotic use or low bacteremia levels. Emerging diagnostic technologies such as PCR, next-generation sequencing, proteomics, and metabolomics offer promising alternatives with higher sensitivity and reduced turnaround times.

This review highlights the evolution of diagnostic strategies, emphasizing the growing role of molecular and AI-driven technologies in identifying causative agents swiftly and accurately. The implementation of these tools in clinical practice can significantly reduce diagnostic delays, optimize antimicrobial therapy, and improve clinical outcomes. However, their high cost, infrastructural demands, and limited accessibility in resource-poor settings continue to be major barriers.

There is a pressing need for cost-effective, scalable diagnostic platforms tailored to the healthcare systems in developing nations. Moreover, integrating these platforms with antimicrobial stewardship programs and continuous surveillance can facilitate better management of resistant pathogens. Multi-center studies involving standardized diagnostic algorithms, outcome tracking, and economic feasibility analyses are warranted to validate and implement these novel technologies on a broader scale.

Translating recent advances into clinical practice requires collaborative efforts between researchers, clinicians, and public health policymakers. Investing in diagnostic innovation, clinician education, and point-of-care systems will pave the way toward achieving Sustainable Development Goals related to child health, especially in under-resourced settings.

ACKNOWLEDGEMENTS

The authors wish to thank Mr. Vinod Jogdand, Asst. Librarian, MIMSR Latur for his technical support.