Invasive pneumococcal disease rates linked to meteorological factors and respiratory virus circulation (Catalonia, 2006-2012)

Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic

Background

Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic.

Methods

From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households.

Results

We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29).

Conclusion

Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults.

Association of Nonpharmaceutical Interventions During the COVID-19 Pandemic With Invasive Pneumococcal Disease, Pneumococcal Carriage, and Respiratory Viral Infections Among Children in France

IMPORTANCE

An association between pneumococcal nasopharyngeal carriage and invasive pneumococcal disease (IPD) has been previously established. However, it is unclear whether the decrease in IPD incidence observed after implementation of nonpharmaceutical interventions (NPIs) during the COVID-19 pandemic was associated with concomitant changes in pneumococcal carriage and respiratory viral infections.

OBJECTIVE

To assess changes in IPD incidence after the implementation of NPIs during the COVID-19 pandemic and examine their temporal association with changes in pneumococcal carriage rate and respiratory viral infections (specifically respiratory syncytial virus [RSV] and influenza cases) among children in France.

DESIGN, SETTING, AND PARTICIPANTS

This cohort study used interrupted time series analysis of data from ambulatory and hospital-based national continuous surveillance systems of pneumococcal carriage, RSV and influenza-related diseases, and IPD between January 1, 2007, and March 31, 2021. Participants included 11 944 children younger than 15 years in France.

EXPOSURES

Implementation of NPIs during the COVID-19 pandemic.

MAIN OUTCOMES AND MEASURES

The estimated fraction of IPD change after implementation of NPIs and the association of this change with concomitant changes in pneumococcal carriage rate and RSV and influenza cases among children younger than 15 years. The estimated fraction of change was analyzed using a quasi-Poisson regression model.

RESULTS

During the study period, 5113 children (median [IQR] age, 1.0 [0.6-4.0] years; 2959 boys [57.9%]) had IPD, and 6831 healthy children (median [IQR] age, 1.5 [0.9-3.9] years; 3534 boys [51.7%]) received a swab test. Data on race and ethnicity were not collected. After NPI implementation, IPD incidence decreased by 63% (95% CI, -82% to -43%; P < .001) and was similar for non-13-valent pneumococcal conjugate vaccine serotypes with both high disease potential (-63%; 95% CI, -77% to -48%; P < .001) and low disease potential (-53%; 95% CI, -70% to -35%; P < .001). The overall pneumococcal carriage rate did not significantly change after NPI implementation (-12%; 95% CI, -37% to 12%; P = .32), nor did the carriage rate for non-PCV13 serotypes with high disease potential (-26%; 95% CI, -100% to 52%; P = .50) or low disease potential (-7%; 95% CI, -34% to 20%; P = .61). After NPI implementation, the estimated number of influenza cases decreased by 91% (95% CI, -74% to -97%; P < .001), and the estimated number of RSV cases decreased by 74% (95% CI, -55% to -85%; P < .001). Overall, the decrease in influenza and RSV cases accounted for 53% (95% CI, -28% to -78%; P < .001) and 40% (95% CI, -15% to -65%; P = .002) of the decrease in IPD incidence during the NPI period, respectively. The decrease in IPD incidence was not associated with pneumococcal carriage, with carriage accounting for only 4% (95% CI, -7% to 15%; P = .49) of the decrease.

CONCLUSIONS AND RELEVANCE

In this cohort study of data from multiple national continuous surveillance systems, a decrease in pediatric IPD incidence occurred after the implementation of NPIs in France; this decrease was associated with a decrease in viral infection cases rather than pneumococcal carriage rate. The association between pneumococcal carriage and IPD was potentially modified by changes in the number of RSV and influenza cases, suggesting that interventions targeting respiratory viruses, such as immunoprophylaxis or vaccines for RSV and influenza, may be able to prevent a large proportion of pediatric IPD cases.

Burden of pneumococcal disease among adults in Southern Europe (Spain, Portugal, Italy, and Greece): a systematic review and meta-analysis

The aim was to summarize pneumococcal disease burden data among adults in Southern Europe and the potential impact of vaccines on epidemiology. Of 4779 identified studies, 272 were selected. Invasive pneumococcal disease (IPD) incidence was 15.08 (95% CI 11.01-20.65) in Spain versus 2.56 (95% CI 1.54-4.24) per 100,000 population in Italy. Pneumococcal pneumonia incidence was 19.59 (95% CI 10.74-35.74) in Spain versus 2.19 (95% CI 1.36-3.54) per 100,000 population in Italy. Analysis of IPD incidence in Spain comparing pre-and post- PCV7 and PCV13 periods unveiled a declining trend in vaccine-type IPD incidence (larger and statistically significant for the elderly), suggesting indirect effects of childhood vaccination programme. Data from Portugal, Greece and, to a lesser extent, Italy were sparse, thus improved surveillance is needed. Pneumococcal vaccination uptake, particularly among the elderly and adults with chronic and immunosuppressing conditions, should be improved, including shift to a higher-valency pneumococcal conjugate vaccine when available.

Association between air quality, meteorological factors and COVID-19 infection case numbers

The coronavirus disease (COVID-19) has become a global pandemic affecting many countries, including Singapore. Previous studies have investigated the relationship of air pollutant levels and meteorological factors with respiratory disease risk and hospital admission rates. However, associations between air pollutant concentrations and meteorological factors with COVID-19 infection have been equivocal. This study aimed to assess the association between core air pollutant concentrations, meteorological variables and daily confirmed COVID-19 case numbers in Singapore. Data on air pollutant levels (particulate matter [PM_2.5, PM₁₀], ozone [O₃], carbon monoxide [CO], nitrogen dioxide [NO₂], sulphur dioxide [SO₂], pollutant standards index [PSI]) and meteorological factors (rainfall, humidity, temperature) was obtained from the Singapore National Environment Agency (NEA) from January 23, 2020 to April 6, 2020. The daily reported COVID-19 case numbers were retrieved from the Singapore Ministry of Health (MOH). Generalized linear models with Poisson family distribution and log-link were used to estimate the model coefficients and 95% confidence intervals (CIs) for the association between air pollutant concentrations and meteorological factors (8-day and 15-day moving averages (MA)) with COVID-19 case numbers, adjusting for humidity, rainfall and day of week. We observed significantly positive associations between NO₂, PSI, PM_2.5 and temperature with COVID-19 case numbers. Every 1-unit increase (15-day MA) in PSI, 1 μg/m³ increase (15-day MA) in PM_2.5, NO₂ and 0.1 °C increase in temperature were significantly associated with a 35.0% (95% CI: 29.7%-40.5%), 22.6% (95% CI: 12.0%-34.3%), 34.8% (95% CI: 29.3%-40.4%) and 28.6% (95% CI: 25.0%-32.4%) increase in the average daily number of COVID-19 cases respectively. On the contrary, PM₁₀, O₃, SO₂, CO, rainfall and humidity were significantly associated with lower average daily numbers of confirmed COVID-19 cases. Similar associations were observed for the 8-day MAs. Future studies could explore the long-term consequences of the air pollutants on COVID-19 infection and recovery.

Association of nasopharyngeal viruses and pathogenic bacteria in children and their parents with and without HIV

BACKGROUND

Bacteria and respiratory viruses co-occur in the nasopharynx, and their interactions may impact pathogenesis of invasive disease. Associations of viruses and bacteria in the nasopharynx may be affected by HIV.

METHODS

We conducted a nested case-control study from a larger cohort study of banked nasopharyngeal swabs from families with and without HIV in West Bengal India, to look at the association of viruses and bacteria in the nasopharynx of parents and children when they are asymptomatic. Quantitative polymerase chain reaction for 4 bacteria and 21 respiratory viruses was run on 92 random nasopharyngeal swabs from children--49 from children living with HIV (CLH) and 43 from HIV uninfected children (HUC)-- and 77 swabs from their parents (44 parents of CLH and 33 parents of HUC).

RESULTS

Bacteria was found in 67% of children, viruses in 45%, and both in 27% of child samples. Staphylococcus aureus (53%) was the most common bacteria, followed by Streptococcus pneumoniae (pneumococcus) (37%) in children and parents (53, 20%). Regardless of HIV status, viruses were detected in higher numbers (44%) in children than their parents (30%) (p = 0.049), particularly rhinovirus (p = 0.02). Human rhinovirus was the most frequently found virus in both CLH and HUC. Children with adenovirus were at six times increased risk of also having pneumococcus (Odds ratio OR 6, 95% CI 1.12-31.9) regardless of HIV status. In addition, the presence of rhinovirus in children was associated with increased pneumococcal density (Regression coeff 4.5, 1.14-7.9). In CLH the presence of rhinovirus increased the risk of pneumococcal colonization by nearly sixteen times (OR 15.6, 1.66-146.4), and, pneumococcus and S. aureus dual colonization by nearly nine times (OR 8.7).

CONCLUSIONS

Children more frequently carried viruses regardless of HIV status. In CLH the presence of rhinovirus, the most frequently detected virus, significantly increased co-colonization with pneumococcus and S. aureus.

Meteorological rhythms of respiratory and circulatory diseases revealed by Harmonic Analysis

The intricately fluctuating onset of respiratory and circulatory diseases displays rhythms of multi-scaled meteorological conditions due to their sensitivity to weather changes. The intrinsic meteorological rhythms of these diseases are revealed in this bio-meteorological study via Fourier decomposition and harmonic analysis. Daily emergency room (ER) visit data for respiratory and circulatory diseases from three comprehensive hospitals in Haidian district of Beijing, China were used in the analysis. Meteorological data included three temperature metrics, relative humidity, sunshine duration, daily mean air pressure, and wind speed. The Fourier decomposition and harmonic analysis on ER visits and meteorological variables involve frequency, period, and power of all harmonics. The results indicated that: i) for respiratory morbidity, a strong climatic annual rhythm responding to annual temperature change was firstly revealed; its ratio of spectral density was 16-33%. Moreover, significant correlations existed between the high-frequency fluctuations (<30 d) of morbidity and short-term harmonics of humidity and solar duration. High-frequency harmonics of temperature and pressure showed no statistically significant effect. ii) With regard to all types of circulatory morbidity, their annual periodicity was weaker than that of respiratory diseases, whose harmonic energy took a ratio less than 8%. Besides, the power of all high-frequency harmonics of circulatory morbidity accounted for up to 70-90% in the original sequences, and their relationship to many short-term meteorological factors were significant, including the mean and maximum temperatures, wind speed, and solar duration. iii) The weekly rhythm appeared in respiratory ER visits with 15% of harmonic variance but not prominent in circulatory morbidity. In summary, by decomposing the sequence of respiratory and circulatory diseases as well as recognizing their meteorological rhythms, different responses to meteorological conditions on various time scales were identified.

Association of Pneumococcal Conjugate Vaccine Coverage With Pneumococcal Meningitis: An Analysis of French Administrative Areas, 2001-2016

Geographic variations of invasive pneumococcal disease incidence and serotype distributions were observed after pneumococcal conjugate vaccine introduction at regional levels and among French administrative areas. The variations could be related to regional vaccine coverage (VC) variations that might have direct consequences for vaccination-policy impact on invasive pneumococcal disease, particularly pneumococcal meningitis (PM) incidence. We assessed vaccine impact from 2001 to 2016 in France by estimating the contribution of regional VC differences to variations of annual local PM incidence. Using a mixed-effect Poisson model, we showed that, despite some variations of VC among administrative areas, vaccine impact on vaccine-serotype PM was homogeneously confirmed among administrative areas. Compared with the prevaccine era, the cumulative VC impact on vaccine serotypes led, in 2016, to PM reductions ranging among regions from 87% (25th percentile) to 91% (75th percentile) for 7-valent pneumococcal conjugate vaccine serotypes and from 58% to 63% for the 6 additional 13-valent pneumococcal conjugate vaccine serotypes. Nonvaccine-serotype PM increases from the prevaccine era ranged among areas from 98% to 127%. By taking into account the cumulative impact of growing VC and VC differences, our analyses confirmed high vaccine impact on vaccine-serotype PM case rates and suggest that VC variations cannot explain PM administrative area differences.

Invasive Pneumococcal Disease and Influenza Activity in a Pediatric Population: Impact of PCV13 Vaccination in Pandemic and Nonpandemic Influenza Periods

The objective of this study was to analyze the incidence, clinical presentation, and severity of invasive pneumococcal disease (IPD)-causing serotypes and the impact of the 13-valent pneumococcal conjugate vaccination during epidemic and nonepidemic influenza periods in Catalonia, Spain. This was a prospective study in persons aged <18 years diagnosed with IPD between 2012 and 2015 in three Catalan pediatric hospitals. IPD was defined as clinical infection together with isolation of Streptococcus pneumoniae by culture and/or detection by reverse transcription-PCR in a normally sterile sample. Incidence rate ratios (IRRs) and the fraction of IPD prevented associated with 13-valent pneumococcal conjugate vaccine (PCV13) were calculated. The bivariate analysis used the χ² test and the multivariate analysis nonconditional logistic regression. A total of 229 cases of IPD were recorded. The incidence was higher during influenza epidemic periods (IRR, 2.7; 95% confidence interval [CI], 2.05 to 3.55; P < 0.001), especially for pneumonia (IRR, 3.25; 95% CI, 2.36 to 4.47; P < 0.001), with no differences in the distribution of pneumococcal serotypes. Complications during admission and sequel at discharge were greater during epidemic periods (adjusted odds ratio [aOR], 2.00; 95% CI, 1.06 to 3.77; P = 0.03) than at nonepidemic periods (aOR, 3.38; 95% CI, 1.37 to 8.29; P = 0.01). The prevented fraction for the population (PFp) of IPD in children aged 7 to 59 months was 48% to 49.4%. The PFp was higher in influenza epidemic than nonepidemic periods and increased when ≥2 doses of PCV13 or ≥1 after 24 months were administered. Influenza virus circulation increases the incidence of IPD in persons aged <18 years. In influenza epidemic periods, IPD cases were more severe. Increased PCV13 coverage might increase the fraction of IPD prevented in epidemic and nonepidemic periods.

Complicated pneumococcal pneumonia with pleural effusion or empyema in the 13-valent pneumococcal conjugate vaccine era

AIM

The aim was to analyze the epidemiological, microbiological and clinical characteristics of patients with complicated pneumococcal pneumonia with pleural effusion (PE) or empyema.

METHOD

Prospective study in three Catalan hospitals in persons aged <18 years diagnosed with complicated pneumonia with PE or empyema with isolation of Streptococcus pneumoniae in blood or pleural fluid by culture or real-time PCR between January 2012 and June 2016. Patients were divided into <2 years and 2-17 years age groups. Epidemiological, microbiological, and clinical data of patients were compared annually in both groups. PCV13 vaccination coverage increased from 48.2% in 2012 to 74.5% in 2015.

RESULTS

We included 143 patients. The incidence of pneumococcal pneumonia was 6.83 cases × 10^-5 persons/year in cases with PE or empyema and 2.09 cases × 10^-5 person-years in cases without (rate ratio [RR]: 3.27; 2.25-4.86; P < 0.001). Empyema was more frequent than PE (79.7% vs 20.3%, P < 0.005). Of 143 cases studied, 93 (65.0%, P < 0.001) were diagnosed by real-time-PCR, 43 (30.1%) by culture and RT-PCR and 7 (4.9%) by culture only. PCV13 serotypes were more frequent in complicated than in uncomplicated pneumonia (116/142, 81.7% vs 27/45, 60.0%; P = 0.003), especially serotype 1 (41/142, 28.9% vs 6/45, 13.3%, P : 0.036). From 2012 to 2015 there was a significant reduction in serotype 1 (16/43, 37.2% vs 3/27, 11.1%, P = 0.026), and a trend to an increase in non-PCV13 serotypes (6/43, 14% vs 9/27, 33.3%, P = 0.054).

CONCLUSIONS

A directly proportional relationship was observed between the reduction in pneumonia complicated with PE or empyema and a significant reduction in PCV13 serotypes, especially serotype 1, coinciding with increased PCV13 coverage.

Association of seasonal viral acute respiratory infection with pneumococcal disease: a systematic review of population-based studies

OBJECTIVE

Animal and in vitro studies suggest that viral acute respiratory infection (VARI) can predispose to pneumococcal infection. These findings suggest that the prevention of VARI can yield additional benefits for the control of pneumococcal disease (PD). In population-based studies, however, the evidence is not in accordance, possibly due to a variety of methodological challenges and problems in these studies. We aimed to summarise and critically review the methods and results from these studies in order to inform future studies.

METHODS

We conducted a systematic review of population-based studies that analysed the association between preceding seasonal VARI and subsequent PD. We searched MEDLINE, Embase and Global Health databases using tailored search strategies.

RESULTS

A total of 28 studies were included. After critically reviewing the methodologies and findings, 11 studies did not control for seasonal factors shared by VARI and PD. This, in turn, could lead to an overestimation of the association between the two illnesses. One case-control study was limited by its small sample size (n case=13). The remaining 16 studies that controlled for seasonal factors suggested that influenza and/or respiratory syncytial virus (RSV) infections were likely to be associated with the subsequent occurrence of PD (influenza: 12/14 studies; RSV: 4/5 studies). However, these 16 studies were unable to conduct individual patient data-based analyses. Nevertheless, these studies suggested the association between VARI and subsequent PD was related to additional factors such as virus type and subtype, age group, comorbidity status, presentation of PD and pneumococcal serotype.

CONCLUSIONS

Population-based studies do not give consistent support for an association between preceding seasonal VARI and subsequent PD incidence. The main methodological challenges of existing studies include the failure to use individual patient data, control for seasonal factors of VARI and PD, or include other factors related to the association (eg, virus, age, comorbidity and pneumococcal serotype).

Influence of environmental conditions and pollution on the incidence of Streptococcus pneumoniae infections

Streptococcus pneumoniae colonizes a large percentage of the population and while it can cause mild respiratory infections it is also responsible for more severe illnesses, such as invasive pneumococcal disease. Patient co-morbidities, concomitant viral infection, low temperature and environmental pollutants all have a synergistic effect that predisposes to pneumococcal infection, exerting deleterious effects on respiratory epithelium and local immune system, diminishing bacterial clearance and favouring infection [1].

Fossil fuel derived pollutants (SO₂, NO), dry air and cold increase the incidence of S. pneumoniae infectionshttp://ow.ly/RnLW30gogb1

Nasopharyngeal bacterial load as a marker for rapid and easy diagnosis of invasive pneumococcal disease in children from Mozambique

BACKGROUND

Current diagnostic methods for detection of Streptococcus pneumoniae in children with suspected invasive pneumococcal disease have limitations of accuracy, timeliness, and patient convenience. This study aimed to determine the performance of pneumococcal load quantified with a real-time polymerase-chain reaction in nasopharyngeal samples to diagnose invasive pneumococcal disease in children.

METHODS

Matched case-control study of patients <5 years of age with invasive pneumococcal disease admitted to the Manhiça District Hospital (Mozambique) and asymptomatic controls recruited in different periods between 2006 and 2014. Cases were confirmed by a positive bacterial culture for S. pneumoniae in blood or cerebrospinal fluid. Nasopharyngeal aspirates were collected from cases and controls and pneumococcal density was quantified by lytA real-time polymerase-chain reaction.

RESULTS

Thirty cases (median age 12.8 months) and sixty controls (median age 11.7 months) were enrolled and 70% of them were male. Nasopharyngeal pneumococcal carriage was high in both groups: 28/30 (93.3%) for cases vs. 53/60 (88.3%) for controls (p = 0.71). Mean nasopharyngeal pneumococcal load was identified as a marker for invasive pneumococcal disease (7.0 log10 copies/mL in cases vs. 5.8 log10 copies/mL in controls, p<0.001) and showed good discriminatory power (AUC-ROC: 82.1%, 95% CI 72.5%-91.8%). A colonization density of 6.5 log10 copies/mL was determined as the optimal cut-off value to distinguish cases from controls (sensitivity 75.0%, specificity 73.6%).

CONCLUSION

Use of non-invasive nasopharyngeal aspirates coupled with rapid and accurate quantification of pneumococcal load by real-time polymerase chain reaction has the potential to become a useful surrogate marker for early diagnosis of invasive pneumococcal disease in children.