Diagnostic and management challenges of a case of N-acetylglutamate synthase deficiency in a resource-limited healthcare setting in Tanzania: a case report

Abstract

Background

Inborn errors of metabolism represent a significant cause of childhood morbidity and mortality. These conditions are frequently missed in low-resource settings due to their anticipated rarity and similarity of symptoms to conditions such as sepsis. We present a case of a neonate with N-acetylglutamate synthase deficiency whose diagnosis and management at our facility were complicated by limited healthcare resources.

Case report

A three-day-old male of South Asian origin born to consanguineous parents presented with lethargy, hypothermia and respiratory distress. He was initially managed for suspected septic shock. However, further investigations revealed severe hyperammonemia for which he was managed with peritoneal dialysis and oral sodium benzoate. His care was coordinated by a multidisciplinary team and included teleconsultation with a metabolic specialist.

Once stabilized, he was transferred to our sister institution in Pakistan for further care where genetic analysis revealed a homozygous pathogenic variant (c.1306_1307insT; p.Thr439fs*52) in the N-acetylglutamate synthase gene, confirming the diagnosis of N-acetylglutamate synthase deficiency. However, the baby passed away at 49th day of life.

Conclusion

High index of suspicion is important in diagnosing inborn errors of metabolism. Even in resource-limited setting, a multidisciplinary team with international partnership can optimize the care for patients with rare inborn errors of metabolism. There is also a need to increase awareness, improve diagnostic capacity and establish standardized treatment protocols for rare metabolic disorders in low-resource settings like Tanzania.

Introduction

Inborn errors of metabolism (IEM) collectively contribute significantly to the global childhood morbidity and mortality. Global birth prevalence of IEM is estimated to be 50.9 per 100,000 live births [1]. Consanguinity is one of the driving factors for high IEM birth prevalence. Studies from North Africa; one in Libya revealed birth prevalence of IEM to be 68.59 per 100,000 live births and another in Tunisia to be 39.1 per 100,000 live births with consanguinity rates of 86% and 82% respectively [2, 3]. Low-income countries have high IEM case fatality rates which is attributed to diagnostic and treatment limitations [1].

N-acetylglutamate synthase (NAGS) deficiency is a rare autosomal recessive urea cycle disorder (UCD) that was first described in 1981 [4] with an estimated incidence of 1:3,500,000–7,000,000 [5]. The OMIM number for the affected gene is 608,300 and 237,310 for the phenotype.

NAGS plays a crucial role in the urea cycle by producing N-acetylglutamate (NAG), an essential cofactor for the first step of the cycle. This step catalyzed by carbamoyl phosphate synthetase 1 (CPS1) involves the conversion of ammonia and bicarbonate into carbamoyl phosphate. Without NAG, CPS1 cannot function effectively halting the urea cycle and leading to accumulation of ammonia in the body resulting in an array of manifestations of variable severity including encephalopathy, coma and death [6].

Accurate and timely diagnosis of NAGS deficiency allows successful management with carbamylglutamate, a synthetic structural analogue of NAG that activates carbamyl phosphatase 1(CPS1), the first enzyme of the urea cycle [4] so as to prevent life-threatening complications such as hyperammonemia induced brain damage.

In low-middle income countries, where infectious diseases like malaria and tuberculosis dominate the healthcare agenda [7], genetic conditions such as IEMs receive less attention, often resulting in delayed or missed diagnoses. In Tanzania, the limited availability of metabolic and genetic testing means that cases of IEM often go undiagnosed or are diagnosed too late causing critical delays in patient management.

We report a case of a neonate who presented to a private health facility in Dar-es-Salaam, Tanzania who was eventually diagnosed to have a UCD. Due to insufficient resources, there was a challenge in diagnosing and managing this neonate. To the best of our knowledge, this is the first documented case of NAGS deficiency in Tanzania.

Case report

We present a three-day-old male of South Asian origin born to consanguineous parents who was brought to the emergency department for poor feeding, excessive sleepiness and difficulty in breathing which started a day prior arrival. He was delivered via emergency caesarean section due to poor progress of labor with an Apgar Scores of 8 and 9 at one and five minutes respectively and weighed 2.9 kg. He had an uneventful post-natal stay at the hospital and discharged after 48 h. This was the mother’s first child and first pregnancy.

Upon examination, he was lethargic with signs of respiratory distress, hypothermic with body temperature of 33.9 C and had prolonged capillary refill of > 5 s. Other vital signs included; heart rate of 121 beats/min, respiratory rate of 55 breaths/min, oxygen saturation of 93% in room air and random blood glucose level of 8.2mmol/L (reference value 2.6-7mmol/L).

Arterial blood gas showed pH-7.454 (reference values 7.31–7.41), PCO2-24.0mmHg (reference values 41-51mmHg), PO2-95mmHg (reference values 80-105mmHg), HCO3-16.9mmol/L (reference values 23-28mmol/L) suggestive of primary respiratory alkalosis with coexisting metabolic acidosis possibly due to tissue hypoxia as a result of poor perfusion.

He was placed under a radiant warmer, resuscitated with intravenous fluids, given antibiotics and kept on continuous positive airway pressure (CPAP). An initial clinical impression of probable sepsis with septic shock was made based on the patient’s presentation. Duct-dependent congenital heart disease was also considered as a differential diagnosis.

However, following further evaluationincluding septic markers, electrocardiogram and echocardiography—all results were found to be normal, effectively ruling out both sepsis and congenital heart disease as the underlying cause.

The neonate’s condition deteriorated after 12 hours of hospital stay. He became unresponsive, had a fisting posture, unequal pupils, seizures, bradycardia and high blood pressure. He was intubated, mechanically ventilated and anticonvulsants initiated.

An urgent Magnetic Resonance Imaging (MRI) of the Brain was ordered that showed bilateral and symmetrical involvement of the basal ganglia, brainstem corona radiata and centrum semiovale characteristic of metabolic or hypoxic encephalopathies with high T2W signal intensities as shown in Fig. 1 that represent oedema or myelin damage due to possible metabolic insult which is suggestive of IEM. Also, an electroencephalogram was done that showed slow background with right cerebral hemisphere epileptiform discharges corroborating MRI findings.

Fig. 1.

Images of brain MRI on the left-Diffusion Weighted Imaging (DWI) and on the right-Apparent Diffusion Coefficient (ADC) showing symmetrical high fluid restriction at bilateral basal ganglia (blue arrows) and corona radiata (white arrows) on DWI with corresponding low signal intensity on ADC

In view of the above MRI findings that suggested a possibility of inborn errors of metabolism, we were prompted to perform metabolic workup that showed elevated serum ammonia level 293.6umol/L (reference value < 100umol/L), elevated serum lactate level 3.44mmol/L (reference values 0.5-2.2mmol/L) but normal serum blood glucose levels and ketones in urine were insignificant.

Arterial blood gas showed pH-7.567 (reference values 7.31–7.41), PCO2-16.4 (reference values 41-51mmHg), PO2-198 (reference values 80-105mmHg), HCO3-14.9 (reference values 23-28mmol/L) suggestive of respiratory alkalosis reflecting hyperventilation secondary to hyperammonemia.

Based on MRI findings suggestive of metabolic encephalopathy along with elevated ammonia levels resulting into signs of acute encephalopathy and arterial blood gas showing respiratory alkalosis, a probable diagnosis of UCD was made. The elevated lactate levels could be a result of either Krebs cycle inhibition or mitochondrial dysfunction triggering anaerobic glycolysis as a result of very high ammonia levels.

A proximal UCD was considered. However, Ornithine transcarbamylase deficiency was thought to be less likely as urine sample for organic acids that was outsourced did not reveal elevated levels of orotic acid.

Peritoneal dialysis was commenced as soon as possible using an improvised central line catheter however, it was not successful hence, ammonia levels further increased to 986.5umol/L (reference value < 100umol/L). Nasogastric tube was then used for peritoneal dialysis.

The neonate also required ammonia-lowering agents but neither intravenous sodium benzoate nor carbamylglutamate were available in Tanzania, hence oral sodium benzoate was initiated. Other supplements such as Biotin, Cobalamine and L-carnitine had to be imported from overseas. Gradually, his neurological status improved and on the 9th day of life, serum ammonia levels reduced to 159.72umol/L (reference value < 100umol/L) whereby frequency of peritoneal dialysis was reduced.

On the 10th day of life, the neonate was successfully extubated and total parenteral nutrition was gradually transitioned to enteral feeding using breast milk. However, as the volume of breast milk was increased, the infant began to show worsening levels of consciousness and respiratory distress. Unfortunately, by this time no laboratory in the country could run ammonia test hence, we resorted to reduce feeds and increase dialysis cycles.

We continued with this pattern and on the 16th day of life, the neonate was kept on special nutrition for UCDs which the parents managed to import from overseas. Once he was fit to fly, on the 39th day of life, the family flew to our sister institution in Pakistan for continued care and genetic diagnostics.

Whole genome sequencing confirmed a homozygous likely pathogenic variant in the NAGS gene (c.1306_1307insT; p.Thr439fs*52), consistent with the diagnosis of N-acetylglutamate synthase deficiency. Consanguinity between the parents is a significant factor in the inheritance of this disorder (Fig. 2). Further analysis revealed that the proband is also a carrier of five genetic conditions, although none were directly related to the current diagnosis. The baby passed away on the 49th day of life.

Fig. 2.

The pedigree chart represents a family with a confirmed case of N-acetylglutamate synthase (NAGS) deficiency, an autosomal recessive disorder. The consanguineous relationship increases the likelihood that both parents pass on the same recessive allele, resulting in the affected status of the proband

Discussion

Diagnostic limitations

Advanced metabolic and genetic testing were limited in our setting. Although outsourcing the neonate’s sample for genetic testing was initially considered, it was not feasible due to cost constraints.

Hence, our management relied on clinical suspicion, basic metabolic workup such as serum ammonia levels, multidisciplinary team guidance and international teleconsultation with metabolic specialist for expert opinion. It was only later that the diagnosis of NAGS deficiency was confirmed.

Therapeutic challenges

Initial management for suspected UCDs in an undiagnosed patient with serum ammonia levels more than or equal to 500umol/L involves: Intravenous Sodium Benzoate, Carbamylglutamate and Dialysis [8]. Intravenous sodium benzoate was not available but upon literature review we noted oral sodium benzoate to be effective [9] and had been used previously in patients with reduction in serum ammonia levels and clinical improvement [10]. Hence, discussed with family and they consented for the use of oral sodium benzoate and pharmacist assisted with its preparation.

In addition, carbamylglutamate was also unavailable in our country and it was expensive to purchase from overseas costing USD 2000 per pill. Carbamylglutamate is the most efficacious therapy and early treatment without any other interventions can predict a good prognosis [11]. 

Three infants from Afghan descent [5] revealed NAGS deficiency similar to our patient. However, early diagnosis and treatment with carbamylglutamate had a favourable neurological outcome. This was in contrast to an Iranian infant [12] and Turkish infant [13] who showed delayed milestones due to unavailability of carbamylglutamate and delay in initiation of carbamylglutamate respectively. 

Furthermore, dialysis was initiated to our patient as soon as results of serum ammonia levels were obtained. Due to unavailability of a standard peritoneal dialysis catheter, we managed to improvise with locally available resources. 

Dietary management for suspected urea cycle defects involves restarting enteral feeds as soon as possible with gradual increments. Essential amino acid supplements for urea cycle defects can be used alongside natural protein if serum ammonia levels rise [8].

Our patient was kept on breast milk and special feeds for UCD, given serum ammonia testing was no longer available in the country and the special feeds were exhausted, a careful balance between breast milk volume, intravenous fluids, and dialysis was maintained to keep the neonate stable.

Genetic counselling was offered to parents. Beyond the initial counselling, it is equally important to provide post mortem family support. This includes discussion of recurrence risk in future pregnancies and the availability of prenatal testing options where feasible. Such counselling can help families make informed reproductive decisions and mitigate the psychological burden following the loss of a child with a rare metabolic disorder. Summary of events is provided in Fig. 3.

Fig. 3.

Showing timeline of events

Conclusion

Importance of maintaining a high index of suspicion for IEM in critically ill neonates cannot be over-emphasized. Early diagnosis and appropriate management are crucial to prevent severe complications. There is a need to increase awareness, improve diagnostic capacity and establish standardized treatment protocols for rare metabolic disorders in low-resource settings like Tanzania.

Nevertheless, while awaiting diagnostic services and protocols to be put in place, a multidisciplinary team, international teleconsultation/partnership and improvised use of locally available resources are crucial in optimization of care for patients with IEM in low resource settings like Tanzania.

Public health implications

Rare metabolic disorders such as NAGS deficiency highlight the urgent need to strengthen local and regional laboratory capacity for metabolic and genetic testing. Establishing functional referral networks and integrating these services within national and regional health systems would facilitate early diagnosis and improved management.

Policy level advocacy is essential to prioritize rare diseases within health care agendas, particularly in low-middle income countries where they are often overlooked. Moreover, partnerships with international rare disease networks can provide opportunities for training, collaborative research and access to diagnostic platforms, ensuring more equitable care for affected families worldwide.

Abbreviations

IEM

Inborn Errors of Metabolism

NAGS

N-Acetyl Glutamate Synthase

UCD

Urea Cycle Disorder

CPS1

Carbamyl Phosphatase 1

MRI

Magnetic Resonance Imaging

DWI

Diffusion Weighted Imaging

ADC

Apparent Diffusion Coefficient

Authors’ contributions

Dr ST wrote the main manuscript text, prepared Fig. 3, did literature review and was involved in the management of the patient. Dr YA, Dr MN and Dr ME edited the main manuscript text, did literature review and were involved in the management of the patient. Dr MZ edited the main manuscript text, prepared Fig. 2 and was involved in the management of the patient. Dr FF edited the main manuscript text and was involved in the management of the patient. Dr EK interpreted the brain MRI and EEG findings and was involved in the management of the patient. Dr JK edited the main manuscript text and was involved in the management of the patient. Dr ZF prepared Fig. 1 and was involved in the interpretation of the brain MRI findings. All authors read and approved the final manuscript.

Funding

There is no source of funding for the publication of the case report.

Data availability

The sequence data that supports the findings of this manuscript are deposited in ClinVar with accession number SCV006082424.

Declarations

Ethics approval and consent to participate

This case report has been granted exemption from requiring ethical approval by The Ethical Review Committee of The Aga Khan University, Dar-es-Salaam.

Consent for publication

Written consent was obtained from the patient’s parents for publication of the case report. A copy of the written consent is available for review by the corresponding author.

Competing interests

The authors declare no competing interests.