Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child’s life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

Characterising the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition, and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within individual infants and their mothers by deep sequencing whole pneumococcal populations from longitudinal nasopharyngeal samples. We demonstrate deep sequencing has unsurpassed sensitivity for detecting multiple colonisation, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared to gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated infants were at an elevated risk of both the acquisition, and persistent colonisation, of a multidrug resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonisation imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

Background: Preterm and low birth weight (LBW) (<2500g) infants are at greater risk of mortality and morbidity. Interventions to support parents to care for their newborn infant in the home may help to improve outcomes. Objective: To determine what interventions, approaches, or strategies to support mothers/fathers/caregivers and families in caring for preterm or LBW infants in the home have been effective in improving outcomes. Methods: A comprehensive search of relevant electronic databases, including MEDLINE, Embase, CINAHL and Cochrane Central Register of Controlled Trials was completed in September 22. Two reviewers screened papers in Covidence and extracted data from 41 included papers. Quality of papers and certainty of evidence were assessed using CASP and GRADE, respectively. Results: There is some evidence that support interventions may improve outcomes related to infant mortality, improvements in infant growth, exclusive breastfeeding, infant cognitive development, immunisation uptake, and reduction in maternal stress and depression. However, the overall certainty of evidence is low or very low in the majority of studies. Conclusions: Interventions providing support for parents to care for infants in the home may improve outcomes for this population. There is a need for well-considered large scale support interventions, prioritised and developed with women and families.