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СпутникиРНSpaceXРоскосмосNASABackground Neonatal mortality remains a major public health challenge in low- and middle-income countries. Although the clinical causes of neonatal deaths are well documented, less is known about the health system and clinician-related challenges associated with neonatal deaths in rural South African hospitals. Aim To describe the documented health system and clinician- related challenges among neonatal deaths at a rural district hospital in the Eastern Cape between 2019 and 2025. Methods A retrospective descriptive study was conducted using routinely documented data from neonatal and maternal records, as well as Perinatal Problem Identification Programme (PPIP) audits for neonatal deaths between 2019 and 2025. All in-hospital neonatal deaths of patients who died in the labour ward and those admitted to the nursery were included. Data were extracted and analysed using IBM SPSS version 30. Denominators varied due to missing or incomplete records; only valid cases were analysed for each variable. Results Among 28,107 live births, 252 neonatal deaths were recorded. The identified documentation challenges form a backdrop against which these patterns should be interpreted. Incorrect maternal management (29.7%), incorrect emergency management (22.3%), delayed clinician response (17.9%), and failure to act on clinical findings (16.4%) were the most frequently documented clinician-related issues. Health system weaknesses included insufficient doctors (18.5%), insufficient nurses (13.3%), limited theatre capacity, equipment shortages, and documentation failures. Hypothermia was significantly more common among neonates born outside the facility (p
Research Article
[version 1; peer review: awaiting peer review]
https://orcid.org/0009-0009-4934-7543
1,2, Guillermo Alfredo Pulido Estradahttps://orcid.org/0000-0001-6485-2059
1,3, Ntiyiso Vinny Khosahttps://orcid.org/0000-0002-3857-8225
1-4, Laston Gonahhttps://orcid.org/0000-0001-6070-2176
1, Mirabel Nanjohhttps://orcid.org/0009-0002-4749-4258
1, Siyonela Mlonyenihttps://orcid.org/0009-0006-7704-6834
1,2https://orcid.org/0009-0009-4934-7543
1,2, Guillermo Alfredo Pulido Estradahttps://orcid.org/0000-0001-6485-2059
1,3, [...] Ntiyiso Vinny Khosahttps://orcid.org/0000-0002-3857-8225
1-4, Laston Gonahhttps://orcid.org/0000-0001-6070-2176
1, Mirabel Nanjohhttps://orcid.org/0009-0002-4749-4258
1, Siyonela Mlonyenihttps://orcid.org/0009-0006-7704-6834
1,21 School of Public Health, Walter Sisulu University Faculty of Health Sciences, Mthatha, Eastern Cape, 5117, South Africa
2 WSU Institute for Clinical Governance and Healthcare Administration, Walter Sisulu University Faculty of Health Sciences, East London, Eastern Cape, 5200, South Africa
3 Biostatistics and Analytics Training Services Unit, Walter Sisulu University Faculty of Health Sciences, East London, Eastern Cape, 5200, South Africa
4 Division of Epidemiology and Biostatistics, Walter Sisulu University Faculty of Health Sciences, East London, Eastern Cape, 5200, South Africa
Babalwa Ntshalintshali
Roles: Conceptualization, Data Curation, Investigation, Methodology, Project Administration, Resources, Software, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing
Guillermo Alfredo Pulido Estrada
Roles: Formal Analysis, Validation
Ntiyiso Vinny Khosa
Roles: Data Curation, Methodology, Supervision, Validation, Visualization, Writing – Review & Editing
Laston Gonah
Roles: Visualization, Writing – Review & Editing
Mirabel Nanjoh
Roles: Conceptualization, Methodology, Supervision, Writing – Review & Editing
Siyonela Mlonyeni
Roles: Conceptualization, Methodology, Supervision, Validation, Visualization, Writing – Review & Editing
OPEN PEER REVIEW
REVIEWER STATUS AWAITING PEER REVIEW
Corresponding author: Babalwa Ntshalintshali Competing interests: No competing interests were disclosed.
Grant information: The author(s) declared that no grants were involved in supporting this work.
Copyright: © 2026 Ntshalintshali B et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Ntshalintshali B, Pulido Estrada GA, Khosa NV et al. Documented Health System and Clinician-related Challenges among Neonatal Deaths at a Rural District Hospital, Eastern Cape, South Africa: A Retrospective Descriptive Study (2019–2025) [version 1; peer review: awaiting peer review]. F1000Research 2026, 15:1266 (https://doi.org/10.12688/f1000research.187210.1) First published: 31 Jul 2026, 15:1266 (https://doi.org/10.12688/f1000research.187210.1) Latest published: 31 Jul 2026, 15:1266 (https://doi.org/10.12688/f1000research.187210.1)
Neonatal mortality rates (NMRs) serve as a valuable indicator of a country’s healthcare quality and socioeconomic status (Nabila et al., 2024). Neonatal mortality (NM), defined as the death of a newborn within the first four weeks of life, poses a significant public health challenge worldwide, particularly in low- and middle-income countries (LMICs) (Kresnawati et al., 2025; Soni et al., 2025).
In South Africa, rural hospitals face ongoing disparities in staffing, infrastructure, equipment availability, and access to timely care (Chitha et al., 2024; Ngene et al., 2023). To achieve Sustainable Development Goal (SDG) 3.2, which aims to reduce preventable newborn deaths to fewer than 12 per 1,000 live births, South Africa has aligned its policies to support this endeavour (Mahuntsi, 2024).
The existing literature has extensively documented the clinical causes of neonatal deaths, including prematurity, neonatal infections, and intrapartum-related complications, but has paid less attention to health system and clinician-related issues that influence the quality of care in resource-constrained settings (Gabriells and Le Roux, 2023; Kresnawati et al., 2025; Musa et al., 2023). Disparities in health services amplify risks for vulnerable populations (Nguse, 2022; Ngene et al., 2023). Addressing neonatal mortality requires acknowledging both clinical and structural determinants. Population differences and limited data, especially in the Eastern Cape, further hinder the translation of findings from better-resourced settings into targeted interventions in rural areas (Housseine et al., 2020; Musa et al., 2023; Soni et al., 2025).
While a companion paper describes maternal and neonatal characteristics among neonatal deaths at this hospital, the present study focuses specifically on health system challenges and clinician-related issues recorded during the study period. Understanding these patterns is essential for informing quality improvement efforts and strengthening care processes in similar resource-limited settings.
This study aims to describe clinician-related and health system challenges documented in cases of neonatal death at a rural hospital in the Eastern Cape, South Africa, between 2019 and 2025.
This study employed a quantitative, retrospective, descriptive design, using routinely collected neonatal and corresponding maternal medical records and Perinatal Problem Identification Programme (PPIP) documentation from 1 April 2019 to 30 November 2025.
This is a rural district hospital in the Alfred Ndzo District of the Eastern Cape Province. It serves approximately 350,000 people, many (95%) of whom live in resource-limited surrounding villages (Madikizela et al., 2021; Maphumulo & Qwaka, 2026). Youth unemployment figures range from 59,2% to 77,2% in this region (Zikhali & Matsiliza, 2024).
The hospital provides maternity, neonatal, paediatric, surgical, medical, and emergency services. It is part of a referral network with primary health care (21 clinics and one community health centre), as well as regional and tertiary hospitals with neonatal intensive care units.
During the seven-year study period, approximately 4,000 live births occurred annually at this facility. The maternity ward is staffed by four doctors who provide care across various areas, including the antenatal care ward (16 beds), the postnatal care ward (27 beds), the labour ward, the operating theatre, and the high-risk antenatal clinic. Additionally, a visiting specialist gynaecologist-obstetrician from the health district office supports the team.
The nursery ward consists of 24 beds, including 19 standard care beds and 5 high-care beds. Two medical officers and two community service doctors are assigned to oversee both the pediatric and nursery wards.
Pregnant women who are less than 28 weeks of gestation typically give birth in the Acute and Emergency department, as the babies are not yet viable. If these babies are born alive, they are subsequently admitted to the nursery ward for further care.
The study population included all in-hospital neonatal deaths (0–28 days) recorded at this hospital during the study period. Neonates referred to other facilities, those who died at home or in transit to the hospital, and those who died after discharge or readmission were excluded. Cases with no retrievable clinical data were also excluded. These exclusions reflect the limitations of routine hospital, paper-based data and may have introduced selection bias, as the study captures only deaths occurring within the facility. The findings, therefore, represent patterns among in-hospital neonatal deaths.
A census sampling approach was used. All in-hospital neonatal deaths recorded at this hospital between 1 April 2019, and 30 November 2025 were considered for inclusion. A total of 252 neonatal deaths were recorded in the official hospital records. During file retrieval, 37 additional neonatal deaths not reflected in the official records were identified; however, these were not included in the denominator of reported hospital deaths. Clinical records were retrieved for 205 neonatal deaths, of which 200 met the inclusion criteria and contained sufficient information for analysis. No formal sample size calculation was performed because all eligible cases during the study period were included.
Data were extracted from routinely collected maternal and neonatal medical records using a structured data extraction tool developed for the study. The extraction tool was informed by variables from the Perinatal Problem Identification Programme (PPIP), the national perinatal audit system, and published literature on neonatal mortality. Extracted variables included maternal and neonatal demographic and clinical characteristics; health system and administrative factors (staffing, equipment, theatre availability, and documentation); clinician-related factors (management, response times, referrals, and clinical documentation); and neonatal outcomes, including hypothermia and place of birth, where applicable.
Clinical files were retrieved from three locations across the hospital, as there was no designated filing room for maternal or neonatal medical records. This fragmented storage arrangement likely contributed to the large number of missing or untraceable files. The absence of a formal filing system has implications for the completeness and reliability of routine hospital data and may have influenced the number of cases available for review in this study, consistent with reports of documentation weaknesses in paper-based systems in low-resource settings (Tsai et al., 2020).
During retrieval, 37 additional neonatal files were identified that were not reflected in the official hospital records. Additionally, 104 clinical files corresponding to recorded neonatal deaths could not be located, despite extensive searching across all storage areas. Because routine hospital records were incomplete, denominators varied across variables, and only cases with valid data for each variable were included in the analysis.
A total of 252 neonatal deaths were recorded. Of these, 205 clinical records were retrieved, and 200 met the inclusion criteria for analysis.
Data were entered into Microsoft Excel and analysed using IBM SPSS Statistics version 30. Descriptive statistics were used to summarise maternal, neonatal, health system, administrative, and clinician-related variables. Categorical variables were summarised using frequencies and percentages, while continuous variables were summarised using means and standard deviations or medians and interquartile ranges, as appropriate. Owing to missing or incomplete records, analyses were conducted using only valid responses, and denominators varied across variables. Pearson’s chi-square test was used to examine the association between place of birth and hypothermia among neonatal deaths. Statistical significance was set at p < 0.05. Tables and figures were used to present the findings.
Ethical approval was obtained from Walter Sisulu University Human Research Ethics Committee (WSU HREC 110/2025). The Eastern Cape Health Research Committee (EC_202507_061) and the hospital Chief Executive Officer (CEO) granted access to the facility data.
Data from 01 April 2024 to 30 November 2025 was collected after the extension was granted on 18 November 2025.
As this was a retrospective review of routinely collected hospital records, informed consent from individual patients was waived. Confidentiality was maintained throughout the study by anonymising all extracted data and restricting access to study records to the research team only. The study was conducted in accordance with the principles of the Declaration of Helsinki.
Between 2019 and 2025, the study hospital recorded 28,107 live births and 252 in-hospital neonatal deaths, corresponding to a neonatal mortality rate of 9.0 per 1,000 live births. During file retrieval, an additional 37 neonatal deaths not included in the official hospital records were identified, primarily because of misclassification as stillbirths or omission from routine reporting, increasing the number of potentially eligible neonatal deaths to 289 ( Table 1).
Clinical records were retrieved for 205 neonatal deaths. Of these, 5 records contained insufficient or illegible information for data extraction and were excluded, leaving a final analytic sample of 200 neonatal deaths. Clinical files for 104 recorded neonatal deaths could not be retrieved despite repeated searches of hospital records.
Additional unreported neonatal deaths (n = 37) and missing clinical files (n = 104) were identified throughout the study period, with the greatest number of missing files occurring in 2019 and 2023. Because some variables were missing or incompletely documented, the number of observations available for analysis differed across variables. Accordingly, denominators presented in subsequent tables reflect valid responses only.
Documented health system and administrative factors identified during neonatal death reviews are presented in Table 2. Staffing-related challenges were the most frequently documented, with insufficient doctors (18.5%) and insufficient nurses (13.3%) most often reported. Human resource capacity was further reflected by documentation indicating that personnel were considered too junior to manage the patient in 10.8% of cases.
Infrastructure and service delivery constraints were also documented. These included congenital anomalies not diagnosed antenatally (10.1%), insufficient theatre facilities (8.2%), unavailable equipment (7.1%), and theatre occupancy at the time of need (5.1%). Less commonly reported factors included lack of available beds (3.8%), investigations not performed (1.9%), and laboratory results that could not be traced (1.3%). Overall, staffing-related challenges were documented more frequently than infrastructure, equipment, or diagnostic service-related challenges.
Documented clinician-related factors identified during neonatal death reviews are presented in Table 3. The most frequently documented factors related to clinical management were incorrect management of the mother (29.7%) and incorrect emergency management (22.3%). Delayed clinician response was also documented, including delayed response to calls (17.9%) and failure to respond appropriately to the clinical history and examination findings (16.4%).
Other documented factors included incorrect management of the baby (13.4%), insufficient clinical documentation (9.6%), failure to detect foetal distress (8.4%), delayed referral to a higher level of care (7.7%), and delayed calling of the doctor (7.1%). Less frequently recorded factors included twins not diagnosed antenatally (5.7%), incomplete physical examination (3.8%), over- or under-estimation of foetal size (2.5%), and inadequate advice provided to the mother (1.9%). Overall, factors related to clinical management and delayed clinical response were documented more frequently than those related to antenatal assessment, physical examination, or patient counselling.
The distribution of documented hypothermia according to place of birth is presented in Table 4. Documented hypothermia was most frequent among neonates born outside the health facility (75.8%) and those born in other hospital wards (66.7%).
Pearson’s chi-square test demonstrated a statistically significant association between place of birth and documented hypothermia among neonatal deaths (p < 0.001).
This study described documented health system and clinician-related challenges identified during neonatal death reviews at a rural district hospital in the Eastern Cape. Four principal findings emerged: (1) discrepancies between routine hospital records and retrieved clinical files highlighted important weaknesses in neonatal mortality surveillance and records management; (2) staffing shortages and resource constraints were the predominant identified health system challenges; (3) clinician-related issues, particularly those relating to clinical management and delayed clinical response, were frequently identified during neonatal death reviews; and (4) documented hypothermia was more common among neonates born outside designated maternity areas, suggesting that the circumstances surrounding birth and early stabilisation may influence neonatal condition on admission. Although the retrospective descriptive design limits causal inference, these findings provide insight into documented care processes and health system constraints that may inform quality improvement in similar rural settings.
One of the key findings pointed to deficiencies in neonatal mortality surveillance and clinical record management. The identification of additional neonatal deaths not captured in routine hospital records, together with the inability to retrieve a substantial number of clinical files, suggests limitations in mortality reporting, classification, and record management. Similar challenges have been reported in other low- and middle-income countries, where underreporting, misclassification of stillbirths and neonatal deaths, and incomplete clinical documentation compromise the accuracy of routine health information systems and perinatal audits (Bhattacharya et al., 2019; Dadzie et al., 2021; Lundin et al., 2022). Reliable mortality surveillance is fundamental to identifying preventable factors, monitoring trends, and evaluating quality improvement initiatives. In resource-constrained settings, paper-based record systems, fragmented documentation processes, and limited administrative capacity have been identified as important contributors to poor data quality (Tsai et al., 2020; Tuti et al., 2022). Consequently, strengthening data governance and clinical record management should be considered an essential component of improving neonatal care, while recognising that missing records in this study may have influenced the completeness of the observed patterns.
The documented health system and clinician-related challenges may reflect the broader context in which neonatal care is delivered in rural South African hospitals. Staffing shortages, limited theatre capacity, equipment constraints, and junior personnel managing complex cases are consistent with longstanding evidence describing human resource shortages and resource limitations within South Africa’s public health sector, particularly in underserved rural districts (Chitha et al., 2024; Ngene et al., 2023). These structural constraints are likely to interact with clinician-related challenges, including delayed responses, deviations from recommended management, and incomplete documentation, by increasing workload, reducing supervision, and limiting opportunities for timely intervention. Similar observations have been reported from other resource-limited settings, where health system pressures influence adherence to clinical guidelines and the quality of intrapartum and neonatal care (Housseine et al., 2020). However, because the present study relied on routinely documented records, it is not possible to determine whether these documented issues accurately reflect the care provided or whether some resulted from incomplete documentation, a recognised limitation of retrospective record reviews.
The observed association between place of birth and documented hypothermia further illustrates how health systems and clinical processes may interact during the immediate neonatal period. Neonates born outside designated maternity areas may experience delays in thermal protection, resuscitation, and stabilisation before admission to neonatal services, increasing their vulnerability to hypothermia. Similar findings have been reported internationally, where out-of-facility or outborn neonates are more likely to experience inadequate thermal care and early physiological instability (Brambilla Pisoni et al., 2022; Goodwin et al., 2024). Although contrasting findings have been reported in some tertiary settings (Tshehla et al., 2023), differences in referral pathways, levels of care, and timing of neonatal transfer may explain these inconsistencies.
The findings collectively suggest that improvements in neonatal outcomes will require integrated approaches that strengthen routine data systems, address health system constraints, support clinicians working in resource-limited environments, and ensure consistent thermal care and early stabilisation wherever births occur.
This study has several limitations that warrant consideration. Only in-hospital neonatal deaths were included, excluding deaths occurring after referral, at home, or during transport, which may limit the generalisability of the findings. In addition, missing clinical files and incomplete documentation reduced the number of observations available for some analyses and may have introduced information bias. The study also relied on routinely collected clinical records and perinatal audit documentation, the completeness and accuracy of which depended on contemporaneous recording by healthcare providers. Furthermore, the retrospective descriptive design precluded causal inference, and the documented health system and clinician-related challenges should not be interpreted as determinants of neonatal mortality. Finally, because the study was conducted at a single rural district hospital, the findings may not be generalisable to other healthcare settings. Despite these limitations, the study provides valuable insight into documented care processes and health system challenges within a resource-constrained rural context. The findings provide a foundation for local quality improvement initiatives and future research aimed at strengthening neonatal care and health system performance in similar settings.
This study highlights the value of routinely documented neonatal death reviews for identifying opportunities to strengthen neonatal care in rural district hospitals. The findings suggest that improvements in neonatal outcomes require not only high-quality clinical care but also robust mortality surveillance systems, reliable clinical documentation, adequate staffing, functional infrastructure, and timely neonatal stabilisation. Although the study does not establish causal relationships, it identifies modifiable health system and clinician-related issues that may inform quality improvement initiatives, strengthen perinatal audit processes, and guide future research aimed at improving neonatal care in similar resource-constrained settings.
The following abbreviations are used in this manuscript |
ANC Antenatal care |
NM Neonatal mortality |
NMR Neonatal mortality rate |
PPIP Perinatal Problem Identification Programme |
WSU Walter Sisulu University |
The study was conducted in accordance with the Declaration of Helsinki and approved by the Institutional Review Board of Walter Sisulu University (WSU HREC 110/2025) on 27 July 2025, and an extension of the study period was granted on 18 November 2025.
Patient consent was waived by the Walter Sisulu University Human Research Ethics Committee (WSU HREC 110/2025) due to the study’s retrospective design and the use of medical records.
The underlying data for this study consist of individual-level neonatal and maternal clinical records and PPIP audit forms. These data contain sensitive patient information and cannot be made publicly available due to ethical and legal restrictions related to patient confidentiality and South African health data regulations.
The Walter Sisulu University Human Research Ethics Committee (WSU HREC 110/2025) and the Eastern Cape Health Research Committee (EC_202507_061) approved the study on the condition that individual-level data remain restricted and are not shared publicly.
The authors would like to express their gratitude to Walter Sisulu University and the Health Sciences Research Ethics Committee for their review and approval of this study. We greatly appreciate the support of the Eastern Cape Department of Health, as well as the CEO, management, and administrative clerk at the maternity department, for their essential roles in this research. The authors have reviewed and edited the output and take full responsibility for the content of this publication.”
The author(s) declared that no grants were involved in supporting this work.
© 2026 Ntshalintshali B et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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