electricsheepafrica/neonatal-sepsis-care

Neonatal Sepsis & Newborn Care Dataset

Abstract

This dataset provides 30,000 simulated neonatal records (10,000 per scenario) of neonates 0–28 days admitted with suspected sepsis to newborn care facilities in sub-Saharan Africa. Each record contains 55+ variables including birth details, gestational age, APGAR scores, risk factors, clinical signs, blood culture and microbiology, antibiotic regimen, supportive care (KMC, CPAP, phototherapy), AMR patterns, and neonatal outcomes. Three facility levels: tertiary NICU (24% mortality), district NBU (42%), and rural health centre (58%).

1. Introduction

Neonatal sepsis incidence in SSA reaches ~5000/100,000 live births, the highest globally (Fleischmann et al., Lancet 2021). Sepsis/meningitis accounts for 15% of neonatal deaths (Lawn et al., Lancet 2014). Blood culture positivity ranges 30–50% (Chaurasia et al., Lancet Glob Health 2019). Dominant pathogens include Klebsiella, E. coli, S. aureus, and GBS, with high AMR rates (Zaidi et al., Lancet 2005). KMC reduces mortality in LBW infants by 40–50% (Velaphi & Rhoda, 2012).

This dataset is entirely simulated. It must not be used for clinical decision-making.

2. Methodology

2.1 Parameterization

Parameter	Value	Source
Neonatal sepsis incidence (SSA)	~5000/100K	Fleischmann et al., Lancet 2021
Blood culture positivity	30–50%	Chaurasia et al., Lancet Glob Health 2019
Preterm birth rate (SSA)	12–18%	Blencowe et al., Lancet 2012
EOS vs LOS split	~55:45	Seale et al., Lancet Infect Dis 2009
KMC mortality reduction	40–50%	Velaphi & Rhoda, SAMJ 2012
First-line antibiotics	Ampicillin + gentamicin	WHO 2015

2.2 Scenario Design

Scenario	Facility	Blood Culture	CPAP	KMC	Mortality
NICU tertiary	Tertiary NICU	Yes (34% +ve)	Yes	60%	24%
District NBU	District hospital	No	No	40%	42%
Rural health centre	Rural HC	No	No	20%	58%

3. Schema

Column	Type	Description
id	int	Unique identifier
sex	categorical	M / F
gestational_age_weeks	int	Gestational age at birth
preterm	binary	<37 weeks
birth_weight_g	int	Birth weight in grams
low_birth_weight	binary	<2500g
very_low_birth_weight	binary	<1500g
delivery_mode	categorical	spontaneous_vaginal / assisted_vaginal / caesarean_section
place_of_birth	categorical	this_facility / other_facility / home / in_transit
maternal_age_years	int	Maternal age
apgar_1min	int	APGAR score at 1 minute
apgar_5min	int	APGAR score at 5 minutes
resuscitation_at_birth	binary	Required resuscitation
prom_over_18h	binary	Prolonged rupture of membranes
maternal_fever	binary	Maternal intrapartum fever
maternal_uti	binary	Maternal UTI
unclean_cord_care	binary	Unclean cord care
maternal_hiv	binary	Maternal HIV
multiple_birth	binary	Twin/multiple pregnancy
anc_4plus	binary	4+ ANC visits
onset_type	categorical	early_onset (<72h) / late_onset
age_at_onset_hours	int	Age at symptom onset
age_at_onset_days	int	Age at onset in days
temperature_c	float	Temperature at presentation
poor_feeding	binary	Poor feeding
lethargy	binary	Lethargy
respiratory_distress	binary	Respiratory distress
convulsions	binary	Convulsions
abdominal_distension	binary	Abdominal distension
jaundice	binary	Jaundice
umbilical_redness	binary	Umbilical redness/discharge
skin_pustules	binary	Skin pustules
bulging_fontanelle	binary	Bulging fontanelle
severity	categorical	mild / moderate / severe / critical
blood_culture_done	binary	Blood culture performed
blood_culture_result	categorical	positive / negative / not_done
organism	categorical	GBS / E. coli / Klebsiella / S. aureus / etc.
resistance_pattern	categorical	susceptible / ampicillin_resistant / MDR / ESBL / MRSA / MSSA
crp_done	binary	CRP measured
crp_mg_l	float	CRP value (-1 if not done)
wbc_done	binary	WBC count done
wbc_count	float	WBC (×10⁹/L, -1 if not done)
platelet_count	int	Platelets (-1 if not done)
lumbar_puncture_done	binary	LP performed
csf_result	categorical	normal / meningitis / not_done
antibiotic_regimen	categorical	ampicillin_gentamicin / penicillin_gentamicin / ceftriaxone / meropenem_vancomycin
antibiotic_duration_days	int	Duration of antibiotics
iv_fluids	binary	IV fluid therapy
oxygen_therapy	binary	Oxygen therapy
cpap	binary	CPAP respiratory support
phototherapy	binary	Phototherapy for jaundice
kmc	binary	Kangaroo mother care
exchange_transfusion	binary	Exchange transfusion
referred_out	binary	Referred to higher level
outcome	categorical	survived / died
length_of_stay_days	int	Hospital stay duration
discharge_weight_g	int	Weight at discharge (-1 if died)

4. Validation

Key validation checks:

• Mortality gradient: Tertiary 24% → District 42% → Rural 58% ✓
• Preterm rate: ~25% (enriched in sepsis cohort vs population 12–18%) ✓
• EOS/LOS split: 55:45, consistent with Seale et al. ✓
• Culture positivity: 34% at tertiary, consistent with Chaurasia et al. ✓
• KMC protective: Lower mortality in KMC recipients ✓
• AMR: High ESBL/MDR in Klebsiella and E. coli ✓

5. Usage

from datasets import load_dataset
dataset = load_dataset("electricsheepafrica/neonatal-sepsis-care", "district_nbu")
df = dataset["train"].to_pandas()

python generate_dataset.py --all-scenarios --n 10000 --seed 42

6. Limitations

• Simulated: Not derived from real neonatal unit records.
• No serial observations: Single admission snapshot, no hourly monitoring.
• Simplified microbiology: Single organism per culture, no polymicrobial.
• No pharmacokinetics: Antibiotic doses and levels not modelled.
• Selection bias: All records are suspected sepsis; population prevalence differs.

7. References

1. Fleischmann C, et al. (2021). Neonatal sepsis incidence. Lancet, 398(10305):1030.
2. Seale AC, et al. (2009). Neonatal sepsis in SSA. Lancet Infect Dis, 9(7):428–438.
3. WHO (2015). Managing possible serious bacterial infection in young infants.
4. Lawn JE, et al. (2014). Every Newborn. Lancet, 384(9938):189–205.
5. Zaidi AKM, et al. (2005). Neonatal sepsis pathogens. Lancet, 365(9465):1175–1188.
6. Chaurasia S, et al. (2019). Neonatal sepsis blood culture. Lancet Glob Health, 7(2):e225.
7. Blencowe H, et al. (2012). Born Too Soon. Lancet, 379(9832):2162–2172.
8. Velaphi S, Rhoda N (2012). KMC in LBW infants. SAMJ, 102(6):548–550.

Citation

@dataset{esa_neonatal_sepsis_2025,
  title={Neonatal Sepsis and Newborn Care Dataset},
  author={Electric Sheep Africa},
  year={2025},
  publisher={Hugging Face},
  url={https://huggingface.co/datasets/electricsheepafrica/neonatal-sepsis-care}
}

License

CC-BY-4.0