Nasopharyngeal colonisation dynamics of bacterial pathogens in patients with fever in rural Burkina Faso: an observational study

Background Nasopharyngeal colonisation with clinically relevant bacterial pathogens is a risk factor for severe infections, such as pneumonia and bacteraemia. In this study, we investigated the determinants of nasopharyngeal carriage in febrile patients in rural Burkina Faso. Methods From March 2016 to June 2017, we recruited 924 paediatric and adult patients presenting with fever, hypothermia or suspicion of severe infection to the Centre Medical avec Antenne Chirurgicale Saint Camille de Nanoro, Burkina Faso. We recorded a broad range of clinical data, collected nasopharyngeal swabs and tested them for the presence of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Klebsiella pneumoniae by quantitative polymerase chain reaction. Using logistic regression, we investigated the determinants of carriage and aimed to find correlations with clinical outcome. Results Nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis was highly prevalent and strongly dependent on age and season. Females were less likely to be colonised with S. pneumoniae (OR 0.71, p = 0.022, 95% CI 0.53–0.95) and M. catarrhalis (OR 0.73, p = 0.044, 95% CI 0.54–0.99) than males. Colonisation rates were highest in the age groups < 1 year and 1–2 years of age and declined with increasing age. Colonisation also declined towards the end of the rainy season and rose again during the beginning of the dry season. K. pneumoniae prevalence was low and not significantly correlated with age or season. For S. pneumoniae and H. influenzae, we found a positive association between nasopharyngeal carriage and clinical pneumonia [OR 1.75, p = 0.008, 95% CI 1.16–2.63 (S. pneumoniae) and OR 1.90, p = 0.004, 95% CI 1.23–2.92 (H. influenzae)]. S. aureus carriage was correlated with mortality (OR 4.01, p < 0.001, 95% CI 2.06–7.83), independent of bacteraemia caused by this bacterium. Conclusions Age, sex and season are important determinants of nasopharyngeal colonisation with S. pneumoniae, H. influenzae and M. catarrhalis in patients with fever in Burkina Faso. S. pneumoniae and H. influenzae carriage is associated with clinical pneumonia and S. aureus carriage is associated with mortality in patients with fever. These findings may help to understand the dynamics of colonisation and the associated transmission of these pathogens. Furthermore, understanding the determinants of nasopharyngeal colonisation and the association with disease could potentially improve the diagnosis of febrile patients.

Differences in bacterial colonization and mucosal responses between high and low SES children in Indonesia

BACKGROUND: Nasopharyngeal carriage of pathogenic bacteria precedes invasive disease and higher rates are found in low socioeconomic-status (SES) settings. Local immune responses are important for controlling colonization, but whether SES affects these responses is currently unknown. OBJECTIVE: Examining bacterial colonization and cytokine response in nasal mucosa of children from high and low SES. METHODS: Twenty-five cytokines were measured in nasal fluid. qPCR was performed to determine carriage and density of Haemophilus influenzae (H. influenzae), Streptococcus pneumoniae (S. pneumoniae), Moraxella catarrhalis (M. catarrhalis) and Staphylococcus aureus (S. aureus). RESULTS: The densities of H. influenzae and S. pneumoniae were increased in low compared to the high SES (p=0.006, p=0.026), with respectively 6 and 67 times higher median densities. Densities of H. influenzae and S. pneumoniae were positively associated with levels of IL-1beta (p=0.002, p=0.008) and IL-6 (p<0.001, p=0.006). After correcting for bacterial density, IL-6 levels were increased in colonized children from high compared to low SES for both H. influenzae and S. pneumoniae (both p=0.039). CONCLUSION: Increased density of H. influenzae and S. pneumoniae was observed in low SES children, while IL-6 levels associated with colonization were reduced in these children, indicating that immune responses to bacterial colonization were altered by SES.

Prevalence of Pneumococcal Carriage among Jordanian Infants in the First 6 Months of Age, 2008–2016

Background: Streptococcus pneumoniae is an opportunistic human-adapted pathogen driven by nasopharyngeal carriage. Aims: To find the pneumococcal carriage rate, resistance, serotypes, and coverage of pneumococcal conjugate vaccines (PCVs) among infants in the first six months of age in the period from March 2008 to April 2016. Methods: Nasopharyngeal swabs (NP) were taken from healthy infants from the northern part of Jordan. Swabs were processed for cultivation, identification, resistance testing and serotyping according to standard methods. Results: During the surveillance period, 484 infants of this age group were tested, with a total carriage rate of 56.2%. 96.2% of infants one to two months of age got one PCV7 injection and were 58% carriers at the time of the first injection. At age three to four months, 84.9% had received two injections, with a carriage rate of 54.9% at the time of the second injection. At ages five to six months, 12.5% had received one to three injections, with a carriage rate of 43.8%. Predominant serotypes in all age groups were 19F (12.5%), 6A (11.4%), 11A (8.4%), 19A (7.0%), 6B (6.6%), 23F (5.9%), 15B (5.1%), 15A and 23A (4.0% each). Coverage of PCV7, PCV13 and the future PCV20 among all cases were 30.5%, 50.7% and 70.6%, respectively. The highest coverage rate of 78.6% was noticed in the age group at five to six months with the future PCV20. Antibiotic resistance was the highest in the first age group. Conclusions: Pneumococcal carriage starts from the first month of the infant’s life. The highest coverage was noticed for PCV20, which implies the necessity for inoculation with future vaccines.

PCR and Culture Analysis of Streptococcus pneumoniae Nasopharyngeal Carriage in Healthy Children

Invasive Streptococcus pneumoniae disease is preceded by asymptomatic nasopharyngeal carriage. Measuring carriage in healthy populations provides data on what serotypes are present in communities, which is of interest in the era of polyvalent pneumococcal conjugate vaccines. Nasopharyngeal swabs from a survey of 682 and 800 healthy children in 2016 and 2018, respectively, were analyzed by culture and Quellung reaction to determine rates of carriage and serotypes. All swabs from 2016 and 300 randomly selected swabs from 2018 were then analyzed using real-time semi-quantitative PCR (qPCR) to detect S. pneumoniae gene targets lytA, piaA, and SP2020 and determine serotype. There were 71 (10.4%) and 68 (8.5%) culture positive samples in 2016 and 2018, respectively. All of these were also positive by qPCR except one that was equivocal. In total, 46.0% of 2016 swabs were positive by qPCR. In 2018, results from the selected sample extrapolated to the complete sample showed 49.0% positive by qPCR. PCV13 serotypes were detected in 29.3% and 21.7% of S. pneumoniae qPCR positive samples from 2016 and 2018, respectively; compared with only 8.4% and 6.0% PCV13 serotypes detected by Quellung reaction in culture positive samples. Compared with culture, qPCR detected S. pneumoniae more frequently. Further, qPCR serotyping detected PCV13 serotypes in a larger proportion of samples than culture and Quellung reaction did, showing that, despite established universal childhood PCV13 immunization, vaccine serotypes can still be detected in a large proportion of young children.

89Factors associated with pneumococcal nasopharyngeal carriage: a systematic review

Background Pneumococcal disease is a major contributor to global childhood morbidity and mortality. Pneumococcal carriage is a prerequisite for pneumococcal disease. Identifying factors associated with pneumococcal carriage can aid public health intervention programs. It is unknown if risk factors for pneumococcal carriage differ between low, middle, and high-income countries. We present preliminary findings of our systematic review of factors associated with pneumococcal carriage in community settings, in all ages. Methods A systematic search for pneumococcal nasopharyngeal carriage studies, published in English before July 2019. Two researchers independently reviewed studies that described factors associated with pneumococcal nasopharyngeal carriage. Study quality was assessed using the NIH Study Quality Assessment Tools. Results are presented as narrative summaries due to heterogeneity amongst factor definitions. Results Preliminary results are shown. Sixty-seven studies were included. 49% were conducted in high-income countries. Pneumococcal prevalence ranged from 0.3%-97%, 2.6%-89.6%, 14%-73%, 1.6%-82.4% in low-, lower-middle, upper-middle, and high-income classifications. Age, respiratory tract infection symptoms, living with young children, poverty, exposure to smoke, and season were positively associated with pneumococcal carriage in all income classifications. Conclusions Pneumococcal carriage prevalence was highest in low-income classifications. Pneumococcal carriage is associated with similar factors across income classifications. Differences in prevalence of risk factors associated with pneumococcal carriage by income classification may contribute to differences in carriage prevalence by income classifications. Key messages Pneumococcal carriage is considered a prerequisite for pneumococcal disease. Pneumococcal carriage prevalence is highest in low-income countries, however preliminary results suggest risk factors for carriage may be similar across income classifications.