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Neonatal sepsis (NS) is responsible for over a 1 million yearly deaths worldwide. In the developing world NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents, and must be accounted for to make effective use of these data. In the present study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens, and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 hr of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings, and is enzootic in the cattle that the rural peoples of western Uganda often live in close proximity. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population., 23 pages, 2 figures

Neonatal sepsis in the developing world is incompletely characterized. We seek to characterize the microbial spectrum involved in sepsis and determine the role of maternal transmission by comparing organisms that can be cultured from septic newborn infants and their mothers. From 80 consecutive mother-infant pairs meeting clinical criteria for neonatal sepsis, we collected infant blood and spinal fluid, and maternal blood and vaginal specimens. Identifiable bacteria were recovered from the blood in 32.5% of infants, and from 2.5% of cerebrospinal fluid cultures, for a total of 35% recoverable putative causative agents. Bacteria recovered from vaginal specimens were not concordant with those recovered from infants. Similarly there was no concordance of bacteria recovered from blood and cerebrospinal fluid. We conclude that relying on traditional bacterial culture techniques does not adequately delineate the role of maternal versus environmental sources of neonatal sepsis in this setting. More sensitive molecular approaches will be needed to properly characterize the maternal and environmental microbial community involved in neonatal sepsis in such developing countries.

Background HIV and anaemia are major health challenges in Africa. Anaemia in HIV-infected individuals is associated with more rapid disease progression and a poorer prognosis if not addressed appropriately. This study aimed at determining the severity and types of anaemia among HIV infected children and its effect on short term response to antiretroviral therapy (ART). Methods At baseline, clinical and haematological parameters of 257 HIV-infected ART-naïve children aged 3 months to 18 years were assessed to determine the prevalence, severity and types of anaemia. ART eligible patients were started on therapy according to WHO criteria, enrolled (n=88) into an observational cohort and followed up for 6 months. Results Anaemia was present in 148/257 (57.6%) of children, including (93/148) 62.2% with mild anaemia, 47/148 (32.0%) moderate anaemia, and 7/148 (4.8%) with severe anaemia. The mean haemoglobin (hb) was lower among children with more advanced HIV disease (p Conclusion Anaemia is highly prevalent among HIV-infected children in a rural Ugandan clinic and is associated with poorer virological suppression. However, the anaemia did not impact clinical and immunological response to ART among these children.