Effect of childhood vaccination and antibiotic use on pneumococcal populations and genome-wide associations with disease among children in Nepal: an observational study.

BACKGROUND: Pneumococcal disease is a leading cause of bacterial pneumonia and invasive bacterial disease among children globally. The reason some strains of pneumococci are more likely to cause disease, and how interventions such as vaccines and antibiotics affect pneumococcal strains is poorly understood. We aimed to identify genetic regions under selective pressure and those associated with disease through the analysis of pneumococcal whole-genome sequences. METHODS: Whole-genome sequencing was performed on pneumococcal isolates collected between January, 2005, and May, 2018, in Kathmandu, Nepal, which included programmatic ten-valent pneumococcal conjugate vaccine (PCV10) introduction in 2015. Isolates were from three distinct cohorts: nasopharyngeal swabs of healthy community-based children, nasopharyngeal swabs of children admitted to hospital with pneumonia, and sterile-site cultures from children admitted to hospital. Across these cohorts we examined serotype distribution, antibiotic resistance, strain distribution, and regions of recombination to determine genes that were undergoing diversifying selection. Genome-wide association studies comparing pneumonia and sterile-site isolates with healthy carriage were used to determine novel variants associated with disease. FINDINGS: After programmatic introduction of PCV10, there was a decline in vaccine covered serotypes; however, strains that had expressed these serotypes continued to exist in the post-PCV population. We identified GPSC9 to be a strain of concern due to its high prevalence in disease, multidrug resistance, and ability to switch to an unencapsulated phenotype via insertion of virulence factor pspC into the cps locus. Antibiotic resistance loci to co-trimoxazole were found to be prevalent (pre-PCV10 78% vs post-PCV10 81%; p=0·27) and increasingly prevalent to penicillin (pre-PCV10 15% vs post-PCV10 32%; p<0·0001). Regions with multiple recombinations were identified spanning the surface protein virulence factors pspA and pspC and antibiotic targets pbpX, folA, folC, folE, and folP. Furthermore, we identified variants in lacE2 to be strongly associated with isolates from children with pneumonia and PRIP to be strongly associated with isolates from sterile sites. INTERPRETATION: Our work highlights the effect of pneumococcal conjugate vaccines, antibiotics, and host-pathogen interaction in pneumococcal variation, and the pathogen's capability of adapting to these factors at both population-wide and strain-specific levels. Ongoing surveillance of disease-associated strains and further investigation of lacE2 and PRIP as serotype-independent targets for therapeutic interventions is required. FUNDING: Gavi, The Vaccine Alliance; WHO; Bill & Melinda Gates Foundation; Wellcome Sanger Institute; and US Centers for Disease Control and Prevention.

Association between longitudinal tooth fractures and visual detection methods in diagnosis.

OBJECTIVES: This study investigated the distribution of longitudinal tooth fractures (LTFs) according to the patient's age and analyzed the association between visual detection methods and the types of LTFs. METHODS: Patients with symptomatic teeth with LTFs were examined at the department of conservative dentistry in a dental hospital from September 1, 2009 to March 31, 2014. Naked eye examination, staining with a dye, operating microscopy, transillunimation, and periapical radiography were used to identify the fracture lines. Diagnostic surgery was performed to visualize the fracture line in some cases with vertical root fractures. The final diagnosis was based on the American Association of Endodontists (AAE) classification: cracked tooth, fractured cusp, split tooth, and vertical root facture. The probability density function for each type of LTF was calculated to assess the risks of LTF development according to age. The association between the detection methods and types of LTFs was identified using the association plot. RESULTS: A total of 245 teeth with LTFs were enrolled. Overall, 71.8% of LTFs was observed in patients aged 40-69 years, and 65.7% of LTFs were diagnosed as cracked teeth. The mean age in patients with cracked teeth was 49.3 years, while the mean age in patients with fractured cusps was 59.1 years. A significant association was observed between the detection method and type of LTF (p < 0.001). CONCLUSIONS: Cracked tooth was the most common type of LTF. The probability of occurrence of cracked teeth peaked in patients aged approximately 50 years, while the probability of occurrence of fractured cusps peaked in patients aged approximately 60 years. Cracked teeth were detected most often using transillumination. CLINICAL SIGNIFICANCE: LTFs occurred mostly in patients aged 40 years and older. Transillumination is useful for the diagnosis of cracked teeth.