Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa.

A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and a suspected outbreak of multi-drug-resistant Klebsiella pneumoniae was investigated using genomic characterisation. All K. pneumoniae bloodstream infections (BSIs) from patients in the neonatal ward (n=62), and a subset of K. pneumoniae BSI isolates (n=38) from other paediatric wards in the hospital, collected over a 4 year period were studied. After whole genome sequencing, the strain sequence types (STs), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of clonal complex 258 (CC258) and an ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids, was implicated as the likely cause of the outbreak. This study contributes molecular information necessary for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.

Paediatric deaths in a tertiary government hospital setting, Malawi.

Background: Malawisuccessfully achieved Millennium Development Goal (MDG) four by decreasing the under-5 mortality rate by two-thirds in 2012. Despite this progress child mortality is still high and in 2013, the leading causes of death in under-5s were malaria, acute respiratory infections and HIV/AIDS. Aims: To determine the causes of inpatient child death including microbiological aetiologies in Malawi. Methods: A prospective, descriptive study was undertaken in Queen Elizabeth Central Hospital over 12 months in 2015/2016. Data was collected for every paediatric covering HIV and nutritional status, cause of death, and microbiology. Deaths of inborn neonates were excluded. Results: Of 13,827 admissions, there were 488 deaths, giving a mortality rate of 3.5%. One-third of deaths (168) occurred in the first 24 h of admission and 255 after 48 h Sixty-eight per cent of those who died (332) were under 5 years of age. The five leading causes of death were sepsis (102), lower respiratory tract infection (67), acute gastroenteritis with severe dehydration (51), malaria (37) and meningitis (34). The leading non-communicable cause of death was solid tumour (12). Of the 362 children with a known HIV status 134 (37.0%) were HIV-infected or HIV-exposed. Of the 429 children with a known nutrional status, 93 had evidence of severe acute malnutrition (SAM). Blood cultures were obtained from 252 children 51 (20.2%) grew pathogenic bacteria with Klebsiella pneumoniae, Escherichia coli and Staphylococcus aureus being the most common. Conclusion: Despite a significant reduction in paediatric inpatient mortality in Malawi, infectious diseases remain the predominant cause. Abbreviations: ART: anti-retroviral therapy; Child PIP: Child Healthcare Problem Identification Programme; CCF: congestive cardiac failure; CNS: central nervous system; CoNS: coagulase-negative staphylococci; CSF: cerebrospinal fluid; DNA pcr: deoxyribonucleic acid polymerase chain reaction; ETAT: emergency triage assessment and treatment; LMIC: low- and middle-income countries; MDG: Millennium Development Goals; MRI: magnetic resonance imaging; MRSA: methicillin-resistant Staphylococcus aureus; NAI: non-accidental injury; NTS: non-typhi salmonella; PJP: Pneumocystis jiroveci pneumonia; PSHD: presumed severe HIV disease; QECH: Queen Elizabeth Central Hospital; RHD: rheumatic heart disease; RTA: road traffic accident; TB: tuberculosis; TBM: tuberculous meningitis; WHO: World Health Organization; SAM: severe acute malnutrition.