The descriptive epidemiology of Streptococcus pneumoniae and Haemophilus influenzae nasopharyngeal carriage in children and adults in Kilifi district, Kenya

Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal/oropharyngeal samples

INTRODUCTION

Several important human pathogens that cause life-threatening infections are asymptomatically carried in the Nasopharynx/Oropharynx (NP/OP). DNA extraction is a prerequisite for most culture-independent techniques used to identify pathogens in the NP/OP. However, components of DNA extraction kits differ thereby giving rise to differences in performance. We compared the DNA concentration and the detection of three pathogens in the NP/OP using the discontinued DNeasy PowerSoil Kit (Kit DP) and the DNeasy PowerLyzer PowerSoil Kit (Kit DPP).

METHODS

DNA was extracted from the same set of 103 NP/OP samples using the two kits. DNA concentration was measured using the Qubit 2.0 Fluorometer. Real-time Polymerase Chain reaction (RT-PCR) was done using the QuantStudio 7-flex system to detect three pathogens: S. pneumoniae, H. influenzae, and N. meningitidis. Bland-Altman statistics and plots were used to determine the threshold cycle (Ct) value agreement for the two kits.

RESULTS

The average DNA concentration from kit DPP was higher than Kit DP; 1235.6 ng/ml (SD = 1368.3) vs 884.9 ng/ml (SD = 1095.3), p = 0.002. Using a Ct value cutoff of 40 for positivity, the concordance for the presence of S. pneumoniae was 82% (84/102); 94%(96/103) for N. meningitidis and 92%(95/103) for H. influenzae. Kit DP proportionately resulted in higher Ct values than Kit DPP for all pathogens. The Ct value bias of measurement for S. pneumoniae was +2.4 (95% CI, 1.9-3.0), +1.4 (95% CI, 0.9-1.9) for N. meningitidis and +1.4 (95% CI, 0.2-2.5) for H. influenzae.

CONCLUSION

The higher DNA concentration obtained using kit DPP could increase the chances of recovering low abundant bacteria. The PCR results were reproducible for more than 90% of the samples for the gram-negative H. influenzae and N. meningitidis. Ct value variations of the kits must be taken into consideration when comparing studies that have used the two kits.

Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci

Bacteriocins are antimicrobial peptides produced by bacteria to inhibit other bacteria in the surrounding environment. Streptococcus pneumoniae is a leading cause of disease worldwide and colonises the healthy human nasopharynx, where it competes for space and nutrients. Pneumococcal conjugate vaccines have reduced the incidence of disease, but they also restructure the bacterial population, and this restructuring likely alters the nasopharyngeal competition dynamics. Here, the distribution of bacteriocins was examined in over 5000 carriage and disease-causing pneumococci from Iceland and Kenya, recovered before and after the introduction of pneumococcal vaccination. Overall, up to eleven different bacteriocin gene clusters were identified per pneumococcus. Significant differences in the prevalence of bacteriocins were observed before and after vaccine introduction, and among carriage and disease-causing pneumococci, which were largely explained by the bacterial population structure. Genetically similar pneumococci generally harboured the same bacteriocins although sometimes different repertoires of bacteriocins were observed, which suggested that horizontal transfer of bacteriocin clusters had occurred. These findings demonstrated that vaccine-mediated changes in the pneumococcal population altered the prevalence and distribution of bacteriocins. The consequences of this for pneumococcal colonisation and disease remain to be determined.

Nasopharyngeal colonization by Streptococcus pneumoniae in children and adults before the introduction of the 10-valent conjugate vaccine, Paraguay

Streptococcus pneumoniae is a cause of invasive diseases such as pneumonia, meningitis, and other serious infections among children and adults in Paraguay. This study was conducted to establish S. pneumoniae baseline prevalence, serotype distribution, and antibiotic resistance patterns in healthy children aged 2 to 59 months and adults ≥60 years of age prior to the introduction of PCV10 in the national childhood immunization program in Paraguay. Between April and July 2012, a total of 1444 nasopharyngeal swabs were collected, 718 from children aged 2 to 59 months and 726 from adults ≥60 years of age. The pneumococcal isolation, serotyping, and antibiotic susceptibility testing were performed using standard tests. Pneumococcal colonization prevalence was 34.1% (245/718) in children and 3.3% (24/726) in adults. The most frequent pneumococcal vaccine-types (VT) detected in the children were 6B (42/245), 19F (32/245), 14 (17/245), and 23F (20/245). Carriage prevalence with PCV10 serotypes was 50.6% (124/245) and PCV13 was 59.5% (146/245). Among colonized adults, prevalence of PCV10 and PCV13 serotypes were 29.1% (7/24) and 41.6% (10/24), respectively. Colonized children were more likely to share a bedroom, have a history of respiratory infection or pneumococcal infection compared to non-colonized children. no associations were found in adults. However, no significant associations were found in children and neither in adults. Vaccine-type pneumococcal colonization was highly prevalent in children and rare in adults in Paraguay prior to vaccine introduction, supporting the introduction of PCV10 in the country in 2012. These data will be useful to evaluate the impact of PCV introduction in the country.

Feasibility, acceptability, and bacterial recovery for community-based sample collection to estimate antibiotic resistance in commensal gut and upper respiratory tract bacteria

Vietnam has high rates of antibiotic use and resistance. Measuring resistance in commensal bacteria could provide an objective indicator for evaluating the impact of interventions to reduce antibiotic use and resistance. This study aimed to evaluate the feasibility, acceptability, and bacterial recovery for different sampling strategies. We conducted a cross-sectional mixed methods study in a rural community in Ha Nam Province, northern Vietnam, and collected structured interviews, samples, and in-depth interviews from households. Out of 389 households invited, 324 participated (83%), representing 1502 individuals. Samples were collected from these individuals (1498 stool, 1002 self-administered nasal swabs, and 496 HW-administered nasopharyngeal swabs). Pneumococci were recovered from 11.1% (128/1149) of the total population and 26.2% (48/183) of those under 5-years. Recovery was higher for health-worker (HW)-administered swabs (13.7%, 48/350) than self-administered swabs (10.0%, 80/799) (OR 2.06, 95% CI 1.07-3.96). Cost per swab was cheaper for self-administered ($7.26) than HW-administered ($8.63) swabs, but the overall cost for 100 positive samples was higher ($7260 and $6300 respectively). Qualitative interviews revealed that HW-administered nasopharyngeal swabs took longer to collect, caused more discomfort, and were more difficult to take from children. Factors affecting participation included sense of contribution, perceived trade-offs between benefits and effort, and peer influence. Reluctance was related to stool sampling and negative perceptions of research. This study provides important evidence for planning community-based carriage studies, including cost, logistics, and acceptability. Self-administered swabs had lower recovery, and though cheaper and quicker, this would translate to higher costs for large population-based studies. Recovery might be improved by swab-type, transport medium, and better cold-chain to lab.

Epidemiology and surveillance implications of community-acquired pneumonia in children

Community-acquired pneumonia (CAP) is the single largest infectious cause of hospitalization and death in children worldwide. With improved immunizations, the incidence of bacterial pneumonia and the number of colonized bacteria have decreased. However, respiratory viruses are still an important cause of CAP, especially as new infectious agents such severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge. The SARS-CoV-2 virus emerged in 2019 and caused the current coronavirus disease 2019 pandemic. Therefore, it is necessary to elucidate the epidemiology and causative pathogens of CAP. Recently, the Pneumonia and Respiratory Disease Study Group, affiliated with the Korean Academy of Pediatric Allergy and Respiratory Disease, investigated the causative pathogens of respiratory infections in children hospitalized with CAP, the serotype of Streptococcus pneumoniae, and the prevalence of Mycoplasma pneumoniae with gene mutations. Antibiotic resistance and serotype test results can determine the use of empirical antibiotics. Moreover, it is possible to help develop future vaccines by comparing bacterial culture results with vaccine serotype and identifying the changes and prevalence of each serotype. Therefore, we will perform continuous national surveillance and monitor the epidemiology of respiratory pathogens in Korea and worldwide. The surveillance of these respiratory infections can play a role in monitoring the emergence of new infectious diseases such as SARS-CoV-2.

Household fuel use and its association with potential respiratory pathogens among healthy mothers and children in Ethiopia

Background

Over 90% of Ethiopians still rely on solid fuels for cooking food. The pollution from the burning process causes adverse respiratory outcomes including respiratory infections. This study aimed to assess the association of the pollution with nasopharyngeal occurrence of potential pathogens.

Methods

We conducted a comparative cross-sectional study in urban and rural settings in Ethiopia in 2016. Questionnaire-based data were collected from 168 mothers and 175 children aged below two years. Multiplex real-time PCR assays were performed on nasopharyngeal secretions for detection of bacteria and viruses and for the identification of pneumococcal serotypes/groups.

Results

High rates of bacteria and viruses in the nasopharynx were detected by PCR among both the children and the mothers. Among the detected viruses, enterovirus was more commonly detected among rural children than among children from urban areas. Streptococcus pneumoniae and Haemophilus influenzae were both more prevalent among children and mothers from rural areas compared with urban groups and among those using solid fuels compared with cleaner fuel users. Children from rural households using solid fuels and children whose mothers had educational status below high school had four times higher odds for detection of S. pneumoniae compared with those households using cleaner energy or those children having mothers with a higher educational status, respectively. One or more serotype/serogroup was identified in about 40% of the samples that were positive for pneumococci. Out of all identified serotypes/serogroups, 43% in the children and 45% in the mothers belonged to PCV13, indicating the larger majority of detected pneumococci being non-PCV13 serotypes.

Conclusion

This study presented a high carriage rate of S. pneumoniae and H. influenzae among both children and their mothers, especially in rural areas and among solid fuel users. Thus, interventions should target cleaner energy sources to the public and promote maternal education.

Streptococcus pneumoniae Affects Endothelial Cell Migration in Microfluidic Circulation

Bloodstream infections caused by Streptococcus pneumoniae induce strong inflammatory and procoagulant cellular responses and affect the endothelial barrier of the vascular system. Bacterial virulence determinants, such as the cytotoxic pore-forming pneumolysin, increase the endothelial barrier permeability by inducing cell apoptosis and cell damage. As life-threatening consequences, disseminated intravascular coagulation followed by consumption coagulopathy and low blood pressure is described. With the aim to decipher the role of pneumolysin in endothelial damage and leakage of the vascular barrier in more detail, we established a chamber-separation cell migration assay (CSMA) used to illustrate endothelial wound healing upon bacterial infections. We used chambered inlets for cell cultivation, which, after removal, provide a cell-free area of 500 μm in diameter as a defined gap in primary endothelial cell layers. During the process of wound healing, the size of the cell-free area is decreasing due to cell migration and proliferation, which we quantitatively determined by microscopic live cell monitoring. In addition, differential immunofluorescence staining combined with confocal microscopy was used to morphologically characterize the effect of bacterial attachment on cell migration and the velocity of gap closure. In all assays, the presence of wild-type pneumococci significantly inhibited endothelial gap closure. Remarkably, even in the presence of pneumolysin-deficient pneumococci, cell migration was significantly retarded. Moreover, the inhibitory effect of pneumococci on the proportion of cell proliferation versus cell migration within the process of endothelial gap closure was assessed by implementation of a fluorescence-conjugated nucleoside analogon. We further combined the endothelial CSMA with a microfluidic pump system, which for the first time enabled the microscopic visualization and monitoring of endothelial gap closure in the presence of circulating bacteria at defined vascular shear stress values for up to 48 h. In accordance with our CSMA results under static conditions, the gap remained cell free in the presence of circulating pneumococci in flow. Hence, our combined endothelial cultivation technique represents a complex in vitro system, which mimics the vascular physiology as close as possible by providing essential parameters of the blood flow to gain new insights into the effect of pneumococcal infection on endothelial barrier integrity in flow.

Analysis of national surveillance of respiratory pathogens for community-acquired pneumonia in children and adolescents

Background

Respiratory infections among children, particularly community-acquired pneumonia (CAP), is a major disease with a high frequency among outpatient and inpatient visits. The causes of CAP vary depending on individual susceptibility, the epidemiological characteristics of the community, and the season. We performed this study to establish a nationwide surveillance network system and identify the causative agents for CAP and antibiotic resistance in Korean children with CAP.

Methods

The monitoring network was composed of 28 secondary and tertiary medical institutions. Upper and lower respiratory samples were assayed using a culture or polymerase chain reaction (PCR) from August 2018 to May 2020.

Results

A total of 1023 cases were registered in patients with CAP, and PCR of atypical pneumonia pathogens revealed 422 cases of M. pneumoniae (41.3%). Respiratory viruses showed a positivity rate of 65.7% by multiplex PCR test, and human rhinovirus was the most common virus, with 312 cases (30.5%). Two hundred sixty four cases (25.8%) were isolated by culture, including 131 cases of S. aureus (12.8%), 92 cases of S. pneumoniae (9%), and 20 cases of H. influenzae (2%). The cultured, isolated bacteria may be colonized pathogen. The proportion of co-detection was 49.2%. The rate of antibiotic resistance showed similar results as previous reports.

Conclusions

This study will identify the pathogens that cause respiratory infections and analyze the current status of antibiotic resistance to provide scientific evidence for management policies of domestic respiratory infections. Additionally, in preparation for new epidemics, including COVID-19, monitoring respiratory infections in children and adolescents has become more important, and research on this topic should be continuously conducted in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07263-z.

Incidence of lower respiratory tract infection and associated viruses in a birth cohort in the Philippines

Background

Lower respiratory tract infection (LRTI) is an important cause of morbidity and mortality in infants and young children. However, the etiological role of viruses and the timing of developing LRTI are not well defined.

Methods

We analyzed the data of a prospective cohort study in the Philippines as a birth cohort. We detected LRTI among children who visited healthcare facilities with respiratory symptom, and collected nasopharyngeal swabs for virus detection. We analyzed the incidence rates (IRs) and cumulative proportion of LRTI and severe LRTI by age group and each virus detected.

Results

A total of 350 LRTI episodes were observed from 473 child-years yielded from 419 children. The IRs of LRTI were 70.8, 70.7, and 80.8 per 100 child-years for 0–5, 6–11, and 12–23 months of age, respectively. By 12 months of age, 45% of children developed LRTI at least once. Rhinovirus and respiratory syncytial virus were the most frequently detected viruses in all age groups. However, the IRs of influenza virus were low especially at 0–5 months of age.

Conclusions

We identified various patterns of age-specific IRs of LRTI and severe LRTI for different viruses, which should be considered to establish more effective interventions including vaccinations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07289-3.

Pneumococcal infections and homelessness

Objective

To assess the prevalence of pneumococcal nasopharyngeal carriage, the role of potential risk factors, and the pneumococcal vaccination coverage among sheltered homeless people in Marseille, France.

Methods

During the winters 2015-2018, we enrolled 571 sheltered homeless males and 54 non-homeless controls. Streptococcus pneumoniae was directly searched from nasal/pharyngeal samples using real-time polymerase chain reaction.

Results

The homeless people were mostly migrants from African countries, with a mean age of 43 years. Pneumococcal vaccination coverage was low (3.1%). The overall pneumococcal carriage rate was 13.0% and was significantly higher in homeless people (15.3% in 2018) than in controls (3.7%), with p = 0.033. Among homeless people, being aged ≥ 65 years (1.97, 95% CI; 1.01-3.87), living in a specific shelter (OR = 1.80, 95% CI: 1.06-3.05), and having respiratory signs and symptoms at the time of enrolment (OR = 2.55, 95% CI: 1.54-4.21) were independently associated with pneumococcal carriage.

Conclusion

Pneumococcal nasopharyngeal carriage, which is a precursor for pneumococcal disease in at-risk individuals, is frequent among French homeless people. Studies conducted in other countries have also reported outbreaks of pneumococcal infections in homeless people. Pneumococcal vaccination should be systematically considered for sheltered homeless people in France, as is being done in Canada since 2008.

Factors associated with pneumococcal nasopharyngeal carriage: A systematic review

Pneumococcal disease is a major contributor to global childhood morbidity and mortality and is more common in low- and middle-income countries (LMICs) than in high-income countries. Pneumococcal carriage is a prerequisite for pneumococcal disease. Pneumococcal conjugate vaccine reduces vaccine-type carriage and disease. However, pneumococcal carriage and disease persist, and it is important to identify other potentially modifiable factors associated with pneumococcal carriage and determine if risk factors differ between low, middle, and high-income countries. This information may help inform pneumococcal disease prevention programs. This systematic literature review describes factors associated with pneumococcal carriage stratified by country income status and summarises pneumococcal carriage rates for included studies. We undertook a systematic search of English-language pneumococcal nasopharyngeal carriage studies up to 30th June 2021. Peer-reviewed studies reporting factors associated with overall pneumococcal nasopharyngeal carriage in healthy, community-based study populations were eligible for inclusion. Two researchers independently reviewed studies to determine eligibility. Results are presented as narrative summaries. This review is registered with PROSPERO, CRD42020186914. Eighty-two studies were included, and 46 (56%) were conducted in LMICs. There was heterogeneity in the factors assessed in each study. Factors positively associated with pneumococcal carriage in all income classification were young age, ethnicity, symptoms of respiratory tract infection, childcare attendance, living with young children, poverty, exposure to smoke, season, and co-colonisation with other pathogens. Breastfeeding and antibiotic use were protective against carriage in all income classifications. Median (interquartile range) pneumococcal carriage rates differed by income classification, ranging from 51% (19.3-70.2%), 38.5% (19.3-51.6%), 31.5% (19.0-51.0%), 28.5% (16.8-35.4%), (P = 0.005) in low-, lower-middle, upper-middle, and high-income classifications, respectively. Our findings suggest that where measured, factors associated with pneumococcal nasopharyngeal carriage are similar across income classifications, despite the highest pneumococcal carriage rates being in low-income classifications. Reducing viral transmission through vaccination and public health interventions to address social determinants of health would play an important role.

Impact of Vaccination on Haemophilus influenzae Type b Carriage in Healthy Children Less Than 5 Years of Age in an Urban Population in Nepal

Background

Reduction in detection of asymptomatic carriage of Haemophilus influenzae type b (Hib) can be used to assess vaccine impact. In Nepal, routine vaccination against Hib in children at 6, 10, and 14 weeks of age was introduced in 2009. Before vaccine introduction, Hib carriage was estimated at 5.0% among children aged <13 years in Nepal, with higher rates among children under 5. Large-scale evaluation of Hib carriage in children has not been investigated since the introduction of the pentavalent diphtheria-tetanus-pertussis/Hib/hepatitis B (DTP-Hib-HepB) vaccine in Nepal.

Methods

A total of 666 oropharyngeal swabs were collected between August and December 2018 from healthy children between 6 months and 5 years of age attending the vaccination clinic at Patan Hospital, Kathmandu, Nepal. Of these 666 swabs, 528 (79.3%) were tested for Hib by culture. Demographic and vaccination data were collected.

Results

Among 528 swabs tested for Hib, 100% came from fully vaccinated children. No swabs were positive for Hib (95% confidence interval, .0–.7). The absence of Hib in 2018 suggests vaccine-induced protection against Hib carriage 9 years after vaccine introduction.

Conclusions

Following 3 doses of pentavalent DTP-Hib-HepB vaccine, Hib carriage in children under the age of 5 years in Nepal is no longer common. Ongoing high coverage with Hib vaccine in early childhood is expected to maintain protection against Hib disease in Nepal.

Oropharyngeal Carriage of hpl-Containing Haemophilus haemolyticus Predicts Lower Prevalence and Density of NTHi Colonisation in Healthy Adults

Nontypeable Haemophilus influenzae (NTHi) is a major respiratory pathogen that initiates infection by colonising the upper airways. Strategies that interfere with this interaction may therefore have a clinically significant impact on the ability of NTHi to cause disease. We have previously shown that strains of the commensal bacterium Haemophilus haemolyticus (Hh) that produce a novel haem-binding protein, haemophilin, can prevent NTHi growth and interactions with host cells in vitro. We hypothesized that natural pharyngeal carriage of Hh strains with the hpl open reading frame (Hh-hpl⁺) would be associated with a lower prevalence and/or density of NTHi colonisation in healthy individuals. Oropharyngeal swabs were collected from 257 healthy adults in Australia between 2018 and 2019. Real-time PCR was used to quantitatively compare the oropharyngeal carriage load of NTHi and Hh populations with the Hh-hpl⁺ or Hh-hpl⁻ genotype. The likelihood of acquiring/maintaining NTHi colonisation status over a two- to six-month period was assessed in individuals that carried either Hh-hpl⁻ (n = 25) or Hh-hpl⁺ (n = 25). Compared to carriage of Hh-hpl⁻ strains, adult (18–65 years) and elderly (>65 years) participants that were colonised with Hh-hpl⁺ were 2.43 or 2.67 times less likely to carry NTHi in their oropharynx, respectively. Colonisation with high densities of Hh-hpl⁺ correlated with a low NTHi carriage load and a 2.63 times lower likelihood of acquiring/maintaining NTHi colonisation status between visits. Together with supporting in vitro studies, these results encourage further investigation into the potential use of Hh-hpl⁺ as a respiratory probiotic candidate for the prevention of NTHi infection.

Prevalence and antimicrobial resistance profiles of respiratory microbial flora in African children with HIV-associated chronic lung disease

BACKGROUND

HIV-associated chronic lung disease (CLD) is common among children living with HIV (CLWH) in sub-Saharan Africa, including those on antiretroviral therapy (ART). However, the pathogenesis of CLD and its possible association with microbial determinants remain poorly understood. We investigated the prevalence, and antibiotic susceptibility of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) among CLWH (established on ART) who had CLD (CLD+), or not (CLD-) in Zimbabwe and Malawi.

METHODS

Nasopharyngeal swabs (NP) and sputa were collected from CLD+ CLWH (defined as forced-expiratory volume per second z-score < - 1 without reversibility post-bronchodilation with salbutamol), at enrolment as part of a randomised, placebo-controlled trial of azithromycin (BREATHE trial - NCT02426112 ), and from age- and sex-matched CLD- CLWH. Samples were cultured, and antibiotic susceptibility testing was conducted using disk diffusion. Risk factors for bacterial carriage were identified using questionnaires and analysed using multivariate logistic regression.

RESULTS

A total of 410 participants (336 CLD+, 74 CLD-) were enrolled (median age, 15 years [IQR = 13-18]). SP and MC carriage in NP were higher in CLD+ than in CLD- children: 46% (154/336) vs. 26% (19/74), p = 0.008; and 14% (49/336) vs. 3% (2/74), p = 0.012, respectively. SP isolates from the NP of CLD+ children were more likely to be non-susceptible to penicillin than those from CLD- children (36% [53/144] vs 11% [2/18], p = 0.036). Methicillin-resistant SA was uncommon [4% (7/195)]. In multivariate analysis, key factors associated with NP bacterial carriage included having CLD (SP: adjusted odds ratio (aOR) 2 [95% CI 1.1-3.9]), younger age (SP: aOR 3.2 [1.8-5.8]), viral load suppression (SP: aOR 0.6 [0.4-1.0], SA: 0.5 [0.3-0.9]), stunting (SP: aOR 1.6 [1.1-2.6]) and male sex (SA: aOR 1.7 [1.0-2.9]). Sputum bacterial carriage was similar in both groups (50%) and was associated with Zimbabwean site (SP: aOR 3.1 [1.4-7.3], SA: 2.1 [1.1-4.2]), being on ART for a longer period (SP: aOR 0.3 [0.1-0.8]), and hot compared to rainy season (SP: aOR 2.3 [1.2-4.4]).

CONCLUSIONS

CLD+ CLWH were more likely to be colonised by MC and SP, including penicillin-non-susceptible SP strains, than CLD- CLWH. The role of these bacteria in CLD pathogenesis, including the risk of acute exacerbations, should be further studied.

Variations in respiratory pathogen carriage among a homeless population in a shelter for men in Marseille, France, March-July 2020: cross-sectional 1-day surveys

We aimed to compare respiratory pathogen carriage by PCR during three different time periods in 2020 in sheltered homeless people in Marseille, France. The overall prevalence of respiratory pathogen carriage in late March–early April (69.9%) was significantly higher than in late April (42.3%) and mid-July (45.1%). Bacterial carriage significantly decreased between late March–early April and late April. SARS-CoV-2 was detected only in late March–early April samples (20.6%). Measures aiming at mitigating SARS-CoV-2 transmission were effective and also impacted bacterial carriage. Seasonal variations of bacterial carriage between winter and summer in this population were not marked.

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia

Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.

Does cotrimoxazole prophylaxis in HIV patients increase the drug resistance of pneumococci? A comparative cross-sectional study in southern Ethiopia

BACKGROUND

Infections caused by antibiotic-resistant bacteria results in high rates of morbidity and mortality. Although the prolonged cotrimoxazole (CTX) prophylaxis is arguably associated with the risk of increasing drug resistance in the common pathogens, information regarding its impact on Streptococci pneumoniae / pneumococcus is very limited.

OBJECTIVE

This study was conducted to investigate the effect of cotrimoxazole prophylaxis on nasopharyngeal colonization rate and antimicrobial resistance using Streptococci pneumoniae (pneumococcus) as an indicator organism among HIV patients in Arba Minch, Ethiopia.

MATERIALS AND METHODS

A comparative cross-sectional study was designed and conducted among HIV patients attending the Anti-Retroviral Treatment (ART) clinic of Arba Minch General Hospital (AMGH) from April 01 to August 31, 2018. A total of 252 participants were systematically selected and clustered into two study groups based on their CTX prophylaxis status, one taking CTX prophylaxis, and the second one, the control group (without prophylaxis). A structured questionnaire was used to collect socio-demographic and clinical data from patients. A nasopharyngeal swab was collected and cultured for pneumococcal isolation and identification in accordance with standard microbiological techniques. An antibiotics sensitivity test was performed according to the CLSI guidelines. Data were analyzed using the Statistical package for social science (SPSS) version 20. The primary outcome was determined using logistic regression analysis.

RESULTS

Of the 252 enrolled HIV patients (mean age (37.38± 9.03 years), 144 (57.14%) were males. The overall, nasopharyngeal colonization rate of S. pneumoniae was 13.5% (95% CI: 8.4-15.6). Asymptomatic pneumococcal carriage rates among patients on CTX prophylaxis and the control group were 16.3%, and 10.3% respectively (p-value = 0.03). Regarding the risk factors analyzed, CTX prophylaxis (AOR: 2.2; 95% CI: 1.05-4.9) and gender (AOR: 2.5; 95% CI: 1.09-5.93) were significantly associated with pneumococcal colonization, showing a male preponderance. Cotrimoxazole-resistant pneumococci were 85.7% vs. 47.4% in the prophylaxis group and the control group respectively and it was statistically significant (AOR: 6.7; 95% CI: 1.3-36). Percentages of multi-drug resistant isolates in these two groups were 38.09 and 15.38 respectively (p-value = 0.04). Among the CTX resistant pneumococci isolates, 85% were also found to be co-resistant towards penicillin and was statistically significant.

CONCLUSION

The percentage prevalence of nasopharyngeal pneumococci colonization was higher in patients taking CTX prophylaxis. It was noted that CTX prophylaxis eventually results in the selection of cotrimoxazole resistance and multi-drug resistance in pneumococci. There is evidence of existing cross-resistance between cotrimoxazole and penicillin antibiotics. Therefore, CTX prophylaxis must be administered judiciously. Surveillance for antimicrobial susceptibility is warranted where the prophylaxis is common.

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

•

Systematic review and meta-analysis of 18 studies and more than 6000 participants.

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Adults over the age of 60 had a pooled prevalence of pneumococcal carriage of 9%.

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Risk factors: contact with children, smoking and residing in a nursing home.

Background

Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous.

Methods

This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study.

Findings

Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70).

Interpretation

Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups.

Funding

No funding was required.

Upper respiratory tract colonization with Streptococcus pneumoniae in adults

INTRODUCTION

Most of the current evidence regarding pneumococcal upper respiratory colonization in adults suggests that despite high disease burden, carriage prevalence is low. Contemporary studies on adult pneumococcal colonization have largely followed the pediatric approach by which samples are obtained mostly from the nasopharynx and bacterial detection is evaluated by routine culture alone. Recent evidence suggests that the 'pediatric approach' may be insufficient in adults and pneumococcal detection in this population may be improved by longitudinal studies that include samples from additional respiratory sites combined with more extensive laboratory testing.

AREAS COVERED

In this article, relevant literature published in peer review journals on adult pneumococcal colonization, epidemiology, detection methods, and recommendations were reviewed.

EXPERT OPINION

Respiratory carriage of Streptococcus pneumoniae has been underestimated in adults. Contemporary pneumococcal carriage studies in adults that collect samples from alternative respiratory sites such as the oropharynx, saliva, or nasal wash; are culture-enriched for pneumococcus; and use molecular diagnostic methods designed to target two pneumococcal DNA sequences should enhance pneumococcal detection in the adult respiratory tract. This finding may have implications for the interpretation of dynamics of pneumococcal transmission and vaccination.

Strategy using a new antigenic test for rapid diagnosis of Streptococcus pneumoniae infection in respiratory samples from children consulting at hospital

Background

Despite vaccination programs, Streptococcus pneumoniae remains among the main microorganisms involved in bacterial pneumonia, notably in terms of severity. The prognosis of pneumococcal infections is conditioned in part by the precocity of the diagnosis. The aim of this study was to evaluate the impact of a Rapid Diagnostic Test (RDT) targeting cell wall polysaccharide of Streptococcus pneumoniae and performed directly in respiratory samples, on the strategy of diagnosis of respiratory pneumococcal infections in children.

Results

Upper-respiratory tract samples from 196 children consulting at hospital for respiratory infection were tested for detecting S. pneumoniae using a newly-designed RDT (PneumoResp, Biospeedia), a semi-quantitative culture and two PCR assays. If positive on fluidized undiluted specimen, the RDT was repeated on 1:100-diluted sample. The RDT was found highly specific when tested on non-S. pneumoniae strains. By comparison to culture and PCR assays, the RDT on undiluted secretions exhibited a sensitivity (Se) and negative predictive value (NPV) of more than 98%. By comparison to criteria of S. pneumoniae pneumonia combining typical symptoms, X-ray image, and culture ≥10⁷ CFU/ml, the Se and NPV of RDT on diluted specimens were 100% in both cases.

Conclusions

In case of negative result, the excellent NPV of RDT on undiluted secretions allows excluding S. pneumoniae pneumonia. In case of positive result, the excellent sensitivity of RDT on diluted secretions for the diagnosis of S. pneumoniae pneumonia allows proposing a suitable antimicrobial treatment at day 0.

Impact of 10-Valent Pneumococcal Conjugate Vaccine Introduction on Pneumococcal Carriage and Antibiotic Susceptibility Patterns Among Children Aged <5 Years and Adults With Human Immunodeficiency Virus Infection: Kenya, 2009-2013

BACKGROUND

Kenya introduced 10-valent pneumococcal conjugate vaccine (PCV10) among children <1 year in 2011 with catch-up vaccination among children 1-4 years in some areas. We assessed changes in pneumococcal carriage and antibiotic susceptibility patterns in children <5 years and adults.

METHODS

During 2009-2013, we performed annual cross-sectional pneumococcal carriage surveys in 2 sites: Kibera (children <5 years) and Lwak (children <5 years, adults). Only Lwak had catch-up vaccination. Nasopharyngeal and oropharyngeal (adults only) swabs underwent culture for pneumococci; isolates were serotyped. Antibiotic susceptibility testing was performed on isolates from 2009 and 2013; penicillin nonsusceptible pneumococci (PNSP) was defined as penicillin-intermediate or -resistant. Changes in pneumococcal carriage by age (<1 year, 1-4 years, adults), site, and human immunodeficiency virus (HIV) status (adults only) were calculated using modified Poisson regression, with 2009-2010 as baseline.

RESULTS

We enrolled 2962 children (2073 in Kibera, 889 in Lwak) and 2590 adults (2028 HIV+, 562 HIV-). In 2013, PCV10-type carriage was 10.3% (Lwak) to 14.6% (Kibera) in children <1 year and 13.8% (Lwak) to 18.7% (Kibera) in children 1-4 years. This represents reductions of 60% and 63% among children <1 year and 52% and 60% among children 1-4 years in Kibera and Lwak, respectively. In adults, PCV10-type carriage decreased from 12.9% to 2.8% (HIV+) and from 11.8% to 0.7% (HIV-). Approximately 80% of isolates were PNSP, both in 2009 and 2013.

CONCLUSIONS

PCV10-type carriage declined in children <5 years and adults post-PCV10 introduction. However, PCV10-type and PNSP carriage persisted in children regardless of catch-up vaccination.

Factors associated with pneumococcal carriage and density in infants and young children in Laos PDR

Nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus) is a precursor to pneumococcal disease. Several host and environmental factors have been associated with pneumococcal carriage, however few studies have examined the relationship between host factors and pneumococcal carriage density. We sought to identify risk factors for pneumococcal carriage and density using data from cross-sectional pneumococcal carriage surveys conducted in the Lao People's Democratic Republic before and after the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). Nasopharyngeal swabs were collected infants from aged 5–8 weeks old (n = 999) and children aged 12–23 months (n = 1,010), pneumococci detected by quantitative PCR, and a risk factor questionnaire completed. Logistic and linear regression models were used to evaluate associations between participant characteristics and pneumococcal carriage and density. In infants aged 5–8 weeks, living in a household with two or more children under the age of five years (aOR 1.97; 95% CI 1.39–2.79) and low family income (aOR 1.64; 95% CI 0.99–2.72) were positively associated with pneumococcal carriage. For children aged 12–23 months, upper respiratory tract infection (URTI) symptoms (aOR 2.64; 95% CI 1.97–3.53), two or more children under five in the household (aOR 2.40; 95% CI 1.80–3.20), and rural residence (aOR 1.84, 95% CI 1.35–2.50) were positively associated with pneumococcal carriage. PCV13 vaccination was negatively associated with carriage of PCV13 serotypes (aOR 0.60; 95% CI 0.44–0.83). URTI symptoms (p < 0.001), current breastfeeding (p = 0.005), rural residence (p = 0.012), and delivery by Caesarean section (p = 0.035) were associated with higher mean pneumococcal density in pneumococcal carriers (both age groups combined). This study provides new data on pneumococcal carriage and density in a high disease burden setting in southeast Asia.

Nasopharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus in a Brazilian elderly cohort

We aimed to investigate the nasopharyngeal colonization (NPC) by Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus in the elderly population and to assess the demographic factors associated with NPC. This was an observational cohort study in which outpatients aged ≥60 years were enrolled from April to August 2017, with a follow-up visit from September through December 2017. Nasopharyngeal (NP) swabs were collected, bacteria were detected and isolated, and isolates were subjected to phenotypic and molecular characterization using standard microbiological techniques. At enrolment, the rates of S. aureus, methicillin-resistant S. aureus (MRSA), H. influenzae, and S. pneumoniae among 776 elderly outpatients were 15.9%, 2.3%, 2.5%, and 2.2%, respectively. Toxin production was detected in 21.1% of methicillin-susceptible S. aureus, and three SCCmec types were identified: II/IIb, IVa, and VI. At the follow-up visit, all carriage rates were similar (p > 0.05) to the rates at enrolment. Most of S. pneumoniae serotypes were not included in pneumococcal conjugate vaccines (PCVs), except for 7F, 3, and 19A. All strains of H. influenzae were non-typeable. Previous use of antibiotics and 23-valent pneumococcal polysaccharide vaccination (p < 0.05) were risk factors for S. aureus and MRSA carriage; S. aureus colonization was also associated with chronic kidney disease (p = 0.021). S. pneumoniae carriage was associated with male gender (p = 0.032) and an absence of diabetes (p = 0.034), while not receiving an influenza vaccine (p = 0.049) and chronic obstructive pulmonary disease (p = 0.031) were risk factors for H. influenzae colonization. The frailty of study participants was not associated with colonization status. We found a higher S. aureus carriage rate compared with the S. pneumoniae- and H. influenzae-carriage rates in a well-attended population in a geriatric outpatient clinic. This is one of the few studies conducted in Brazil that can support future colonization studies among elderly individuals.

Prevalence and clinical impact of Streptococcus pneumoniae nasopharyngeal carriage in solid organ transplant recipients

Background

S. pneumoniae is the leading cause of community-acquired pneumonia in the solid organ transplant recipient (SOTR); nevertheless, the prevalence of colonization and of the colonizing/infecting serotypes has not been studied in this population. In this context, the aim of the present study was to describe the rate, characteristics, and clinical impact of S. pneumoniae nasopharyngeal carriage.

Methods

A prospective observational cohort of Solid Organ Transplant recipients (SOTR) was held at the University Hospital Virgen del Rocío, Seville, Spain with the aim to evaluate the S. pneumoniae colonization and the serotype prevalence in SOTR. Two different pharyngeal swabs samples from 500 patients were included in two different seasonal periods winter and spring/summer. Optochin and bile solubility tests were performed for the isolation of thew strains. Antimicrobial susceptibility studies (MICs, mg/l) of levofloxacin, trimethoprim-sulfamethoxazole, penicillin, amoxicillin, cefotaxime, ceftriaxone, erythromycin, azithromycin and vancomycin for each isolate were determined by E-test strips. Capsular typing was done by sequential multiplex PCR reactions. A multivariate logistic regression analysis of factors potentially associated with pneumococcal nasopharyngeal carriage and disease was performed.

Results

Twenty-six (5.6%) and fifteen (3.2%) patients were colonized in winter and spring/summer periods, respectively. Colonized SOT recipients compared to non-colonized patients were more frequently men (79.5% vs. 63.1%, P < 0.05) and cohabitated regularly with children (59% vs. 32.2%, P < 0.001). The most prevalent serotype in both studied periods was 35B. Forty-five percent of total isolates were included in the pneumococcal vaccine PPV23. Trimethoprim-sulfamethoxazole and macrolides were the less active antibiotics. Three patients had non-bacteremic pneumococcal pneumonia, and two of them died.

Conclusions

Pneumococcal colonization in SOTR is low with the most colonizing serotypes not included in the pneumococcal vaccines.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4321-8) contains supplementary material, which is available to authorized users.

Sputum Quality Assessment Regarding Sputum Culture for Diagnosing Lower Respiratory Tract Infections in Children

BACKGROUND

The clinical relevance of specimens from the lower airways is often debatable. However, they are most commonly examined for diagnosing lower respiratory tract infections (LRTIs).

AIM

This study aimed to determine the diagnostic value of sputum quality assessment about sputum culture for diagnosing LRTIs in children.

METHODS

In six months, a total of 1485 sputum samples were quality assessed by using Bartlett's grading system. All samples, regardless of their quality, were cultured, identified, and antimicrobial susceptibility testing was performed by Kirby-Bauer disc-diffusion method.

RESULTS

Among the acceptable category, defined by Bartlett's grading system, 132 (63.2%) samples showed culture positivity of which Streptococcus pneumoniae 48 (36.4%) was most commonly isolated, followed by Moraxella catarrhalis 22 (16.7%) and Haemophilus influenza 21 (15.9%). Among the non-acceptable category, 185 (14.5%) samples were culture positive of which most commonly isolated were Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa with 64 (34.6%), 54 (29.2%) and 28 (15.1%), respectively.

CONCLUSION

Sputum quality assessment is a useful tool for distinguishing the true respiratory pathogens from possible colonising flora for which antibiotic treatment should not be highly considered.

Relationship between nasopharyngeal microbiota and patient's susceptibility to viral infection

Introduction: The burden of respiratory viral infections is a global public health concern with significant mortality, morbidity, and economic impact. While Koch's postulate led to considering only the etiological agent, numerous works have demonstrated that commensal microbes could contribute to both the susceptibility and the severity of these infections, in particular those of the nasopharynx. Areas covered: Herein, we first propose to briefly recall the historical background that led to considering microbes inhabiting the nasopharyngeal microbiota as a potential contributor to human viral infections. We describe the evolution of the normal nasopharyngeal microbiota composition over time, especially during the first year of life. We aimed to resume the changes of the nasopharyngeal microbiota during viral respiratory infections. We also develop how nasopharyngeal microbiota could contribute to the acquisition of respiratory viral infections. We finally provide the potential therapeutic perspectives deriving from these findings. Expert opinion: Prospective studies focusing on children have identified that nasopharyngeal microbiota composition is associated with predisposition to acute respiratory illness and bronchiolitis, while data are scarce regarding adults. For the latter, further works are needed, in particular as a part of the multi-OMICS approach that should probably be performed in conjunction with gut microbiota studies.

Nasopharyngeal carriage of Streptococcus pneumoniae and antimicrobial susceptibility pattern among school children in South Ethiopia: post-vaccination era

Objective

The aim of this study was to investigate nasopharyngeal carriage rate and antibiotic susceptibility patterns of Streptococcus pneumoniae among school children.

Results

Three hundred eleven (43.8%) became culture positive for S. pneumoniae. The carriage rate among children, 3–5 years old was 62.5%, which was higher than the carriage rate of 38.6% among 6–13 years old children. Age ≤ 5 years and co-sleeping with siblings remained significantly associated with S. pneumoniae carriage. 155 (49.8%) of the isolates were resistant to co-trimoxazole, 152 (48.9%) of the isolates were resistant to tetracycline, and 88 (28.3%) of isolates were resistant to oxacillin. Multi drug resistant S. pneumoniae was observed in 90 (28.9%) of isolates. There is high prevalence of S. pneumoniae in primary school children in our study area. Relatively high carriage rate of resistance to oxacillin, tetracycline and co-trimoxazole were observed. These findings provide baseline data for future studies to further compare pneumococcal carriage rates and antibiotic resistance patterns.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4330-0) contains supplementary material, which is available to authorized users.

Pneumococcal pneumonia prevalence among adults with severe acute respiratory illness in Thailand - comparison of Bayesian latent class modeling and conventional analysis

BACKGROUND

Determining the etiology of pneumonia is essential to guide public health interventions. Diagnostic test results, including from polymerase chain reaction (PCR) assays of upper respiratory tract specimens, have been used to estimate prevalence of pneumococcal pneumonia. However limitations in test sensitivity and specificity and the specimen types available make establishing a definitive diagnosis challenging. Prevalence estimates for pneumococcal pneumonia could be biased in the absence of a true gold standard reference test for detecting Streptococcus pneumoniae.

METHODS

We conducted a case control study to identify etiologies of community acquired pneumonia (CAP) from April 2014 through August 2015 in Thailand. We estimated the prevalence of pneumococcal pneumonia among adults hospitalized for CAP using Bayesian latent class models (BLCMs) incorporating results of real-time polymerase chain reaction (qPCR) testing of upper respiratory tract specimens and a urine antigen test (UAT) from cases and controls. We compared the prevalence estimate to conventional analyses using only UAT as a reference test.

RESULTS

The estimated prevalence of pneumococcal pneumonia was 8% (95% CI: 5-11%) by conventional analyses. By BLCM, we estimated the prevalence to be 10% (95% CrI: 7-16%) using binary qPCR and UAT results, and 11% (95% CrI: 7-17%) using binary UAT results and qPCR cycle threshold (Ct) values.

CONCLUSIONS

BLCM suggests a > 25% higher prevalence of pneumococcal pneumonia than estimated by a conventional approach assuming UAT as a gold standard reference test. Higher quantities of pneumococcal DNA in the upper respiratory tract were associated with pneumococcal pneumonia in adults but the addition of a second specific pneumococcal test was required to accurately estimate disease status and prevalence. By incorporating the inherent uncertainty of diagnostic tests, BLCM can obtain more reliable estimates of disease status and improve understanding of underlying etiology.

Serotype and molecular diversity of nasopharyngeal Streptococcus pneumoniae isolates from children before and after vaccination with the ten-valent pneumococcal conjugate vaccine (PCV10) in Ethiopia

Background

Streptococcus pneumoniae is a major human pathogen, and nasopharyngeal colonization is the first step for transmission and pathogenesis of pneumococcal diseases. Ethiopia introduced the 10-valent pneumococcal conjugate vaccine (PCV10) in October 2011. Here we studied nasopharyngeal carriage rates of pneumococci in children and analyzed the serotype and genetic diversity of pneumococcal isolates before first dose and after completion of the vaccine.

Method

A longitudinal study was conducted from February 2013 to November 2016. Totally 789 infants were enrolled at the age of 6 weeks before first dose of PCV10 vaccination, 206 were re-sampled at the age of 9 months, and 201 at 2 years of age after the final dose of PCV10 at the age of 14 weeks. One hundred sixteen children were followed during all the three sampling periods. A total of 422 nasopharyngeal isolates were serotyped using gel diffusion and the Quellung reaction, 325 were typed with pulsed field gel electrophoresis (PFGE), and 12 were selected for multi locus sequence typing (MLST).

Results

Pneumococcal carriage rates at the age of 6 weeks, 9 months and 2 years of age were 26.6% (210/789), 56.8% (117/206) and 48.3% (97/201), respectively. Out of 116 children none of them carried the same strain during the three period and the carriage rate at the age of 6 weeks, 9 months and 2 years were 32.7% (38/116), 59.% (69/116) and 49.1% (57/116) respectively. Totally 59 pneumococcal serotypes were identified among 422 isolates. Serotype 6A (5.0%) dominated followed by 34 (4.5%), 10A (4.0%), 11A (4.0%), 19F (3.8%), 15B (3.8%), 23F (3.6%), and 15A (3.6%). The proportion of non-PCV10 serotypes among the isolates recovered at 6 weeks, 9 months and 2 years was 79.4, 88.9 and 89.7% respectively. Molecular typing of 325 isolates collected at 6 weeks and 9 months of age showed a high genetic diversity.

Conclusion

This study highlights the presence of very diverse serotypes in Ethiopia where non-vaccine serotypes were predominant. Completion of the PCV10 schedule was associated with an approximately 50% reduction of vaccine-type carriage and increase of non-vaccine types. PCV13 would potentially reduce vaccine-type carriage by further 10%.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4024-1) contains supplementary material, which is available to authorized users.

Isolation and Antibiotic Susceptibility Testing of Haemophilus influenzae from Nasopharynx of Children under Five Years Attending Maternal and Child Health Clinic in Mbarara Regional Referral Hospital

Background. H. influenzae remains an organism of a major public health challenge worldwide despite the availability of the Hib vaccine, particularly among children under 5 years. Information on the current carriage status and antibiotic susceptibility is key on proper health-care provision. Therefore, we conducted a study to determine H. influenzae carriage rate and antibiotic susceptibility testing of the isolates among the children. Methods. This was a cross-sectional study conducted between January and May 2018, among clinically healthy children under five years attending Maternal and Child Health (MCH) Clinic in Mbarara Regional Referral Hospital (MRRH). We carried out standard microbiology methods to culture, isolate, and identify H. influenzae, and then, we tested for their susceptibility to commonly used antibiotics following the CLSI standards. Results. Of the 248 participants included in the study, 116 (46.77%) were females and 132 (53.23%) males and 78 (31.45%) were below the age of 3 months. Fifty one of the study participants had H. influenzae in their nasopharynx, which represents 20.56% carriage (95% CI 15.49 to 25.63). There was a general high susceptibility of the isolates to the antimicrobial agents commonly used. There was 100% susceptibility to ciprofloxacin and imipenem antibiotic agents, though 6 (11.76%) and 4 (7.84%) of the isolates showed resistance to chloramphenicol and ampicillin, respectively. Conclusion. The high burden presented by H. influenzae and the resultant impact on child health require much attention to prevention of infections associated with the organism. A well-funded molecular study focusing on typing the isolates would determine the impact of the vaccine, given the carriage rates are still high.

Acute Respiratory Illness in Rural Haiti

•

Top viruses detected in Haitian children are Rhinovirus, Influenza A and Adenovirus.

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Top bacteria detected in Haitian children are S. pneumoniae and S. aureus.

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Younger children are more likely to have Influenza A and S. pneumoniae detected.

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Younger children are more likely to present with fever and diagnosed with pneumonia.

•

These data support early use of Influenza A and S. pneumoniae vaccines in Haiti.

Objectives

Acute Respiratory Infection (ARI) is the most common cause of childhood morbidity and mortality in developing countries, including Haiti. Our objective was to detect pathogens found in children with ARI in rural Haiti to help develop evidence-based guidelines for treatment and prevention.

Methods

Retrospective study of students with ARI at four schools in rural Haiti. Viral and/or bacterial pathogens were identified by qPCR in 177 nasal swabs collected from April 2013 through November 2015.

Results

Most common viruses detected were Rhinovirus (36%), Influenza A (16%) and Adenovirus (7%), and bacteria were Streptococcus pneumoniae (58%) and Staphylococcus aureus (28%). Compared to older children, children aged 3–5 years had more Influenza A (28% vs. 9%, p = 0.002) and Adenovirus detected (14% vs. 3%, p = 0.01). Similarly, S. pneumoniae was greatest in children 3–5 years old (71% 3–5yrs; 58% 6–15 years; 25% 16–20 years; p = 0.008). Children 3–10 years old presented with fever more than children 11–20 years old (22% vs 7%; p = 0.02) and were more often diagnosed with pneumonia (28% vs 4%, p < 0.001).

Conclusions

Younger children had increased fever, pneumonia, and detection of Influenza A and S. pneumoniae. These data support the need for influenza and pneumococcus vaccination in early childhood in Haiti.

Streptococcus pneumoniae colonization after introduction of 13-valent pneumococcal conjugate vaccine for US adults 65 years of age and older, 2015-2016

BACKGROUND

Vaccination of children with 13-valent pneumococcal conjugate vaccine (PCV13) led to declines in vaccine-type pneumococcal nasopharyngeal carriage among adults through indirect effects. In August 2014, PCV13 immunization of all U.S. adults ≥65 years of age was recommended. This study sought to define prevalence and serotype distribution of pneumococcal carriage among adults ≥65 years of age and to describe risk factors for colonization soon after introduction of PCV13 in adults.

METHODS

A cross-sectional survey of non-institutionalized U.S. adults ≥65 years of age was conducted in four states in 2015-2016. Demographic information, risk factors for disease, PCV13 vaccination history, and nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected. NP and OP swabs were processed separately and pneumococcal isolates were serotyped by Quellung reaction. Antimicrobial susceptibility of pneumococcal isolates was performed. NP swabs also underwent real-time PCR for pneumococcal detection and serotyping.

RESULTS

Of 2989 participants, 45.3% (1354/2989) had been vaccinated with PCV13. Fifty-five (1.8%) carried pneumococcus (45 identified by culture and 10 by real-time PCR only) and PCV13 serotypes were found in eight (0.3%) participants. Almost half (22/45) of pneumococcal isolates were not susceptible to at least one of the antibiotics tested. Vaccine-type carriage among vaccinated and unvaccinated individuals was similar (0.2% vs. 0.1%, respectively). Respiratory symptoms were associated with higher odds of pneumococcal colonization (adjusted OR: 2.1; 95% CI = 1.1-3.8).

CONCLUSIONS

Pneumococcal carriage among non-institutionalized adults ≥65 years of age was very low. Less than 0.5% of both vaccinated and unvaccinated individuals in our study carried vaccine-type serotypes. Over a decade of PCV vaccination of children likely led to indirect effects in adults. However, given the low vaccine-type carriage rates we observed in an already high PCV13 adult coverage setting, it is difficult to attribute our findings to the direct versus indirect effects of PCV13 on adult carriage.

Risk factors associated with nasopharyngeal carriage and density of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in young children living in Indonesia

Background

Potentially pathogenic bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus are commonly carried in the nasopharynx of young children. Host and environmental factors have been linked with pathogen carriage, and in many studies rural children have higher carriage rates than their urban counterparts. There are few published data on what factors contribute to increased pathogen density. The objectives of this study were to identify risk factors for nasopharyngeal carriage and density of S. pneumoniae, H. influenzae, M. catarrhalis, and S. aureus in young children in Indonesia.

Methods

Risk factor analysis was done using data on bacterial carriage and participant characteristics from a cross-sectional study that enrolled 302 children aged 12–24 months living in urban or semi-rural areas of Indonesia. Associations between host factors and odds of pathogen carriage were explored using logistic regression. Characteristics identified to be independent predictors of carriage by univariable analysis, as well as those that differed between urban and semi-rural participants, were included in multivariable models. Risk factors for increased pathogen density were identified using linear regression analysis.

Results

No differences in carriage prevalence between urban and semi-rural children were observed. Multiple children under the age of 5 years in the household (< 5y) and upper respiratory tract infection (URTI) symptoms were associated with S. pneumoniae carriage, with adjusted odds ratios (aOR) of 2.17 (95% CI 1.13, 4.12) and 2.28 (95% CI 1.15, 4.50), respectively. There was some evidence that URTI symptoms (aOR 1.94 [95% CI 1.00, 3.75]) were associated with carriage of M. catarrhalis. Children with URTI symptoms (p = 0.002), and low parental income (p = 0.011) had higher S. pneumoniae density, whereas older age was associated with lower S. pneumoniae density (p = 0.009). URTI symptoms were also associated with higher M. catarrahlis density (p = 0.035). Low maternal education (p = 0.039) and multiple children < 5y (p = 0.021) were positively associated with H. influenzae density, and semi-rural residence was associated with higher S. aureus density (p < 0.001).

Conclusions

This study provides a detailed assessment of risk factors associated with carriage of clinically-relevant bacteria in Indonesian children, and new data on host factors associated with pathogen density.

Electronic supplementary material

The online version of this article (10.1186/s41479-018-0058-1) contains supplementary material, which is available to authorized users.

Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections

Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, it remains unclear how the frequency and nature of human interactions shape an individual's risk of infection. We analysed data on daily social encounters individually matched to data on S. pneumoniae carriage and acute respiratory symptoms (ARS), from 566 individuals who took part in a survey in South-West Uganda. We found that the frequency of physical (i.e. skin-to-skin), long (≥1 h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact - was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 7% (2-13%) respectively. In contrast, the number of casual contacts (<5 min long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people suffering from ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models, and more studies should be undertaken to further validate our results.

Donkor E. Pneumococcal carriage among sickle cell disease patients in Accra, Ghana: Risk factors, serotypes and antibiotic resistance

BACKGROUND

Pneumococcal carriage is the precursor for development of pneumococcal disease, and is also responsible for transmission of the organism from person-to-person. Individuals with Sickle Cell Disease (SCD) are more likely to develop invasive disease with S. pneumoniae compared to their healthy counterparts and the presentation of disease in the former is usually abrupt and severe. In Africa, little is known about the pneumococcus in relation to people with SCD Sickle Cell Disease (SCD). The aim of the study was to investigate the epidemiology of pneumococcal carriage among SCD patients including the carriage prevalence, risk factors, serotypes and antibiotic resistance.

METHOD

This was a cross sectional study involving 402 SCD patients recruited from Korle Bu Teaching Hospital and Princess Marie Louis Hospital in Accra from October 2016 to March 2017. The study subjects included 202 children of the age groups: ≤5 years (94), >5-9 years (75), ≥10-13 years (33) and 200 adults of the age groups: 14-20 years (46), 21-40 years (112), 41-60 years (25), ≤ 61 years (17). Nasopharyngeal (NP) swabs were collected from the study participants as well as epidemiological data on demographic, household and clinical features. The NP specimens were cultured for S. pneumoniae and the isolates were serotyped by latex agglutination. Antimicrobial susceptibility tests of the isolates were done by the disc diffusion test and E-test.

RESULTS

Prevalence of S. pneumoniae carriage among children and adult SCD patients enrolled in the study were 79/202 (39.1%; 95% CI: 32.3 to 46.2) and 20/200 (10.0%; 95% CI: 6.2 to 15.0) respectively. Risk factors associated with pneumococcal carriage were age (OR = 1.137; 95% CI: 1.036-1.248; p = 0.007) and runny nose (OR = 5.371; 95% CI: 1.760-16.390; p = 0.003). Overall, twenty-six pneumococcal serotypes were isolated from the study participants and the predominant serotype was 6B (10.6%), followed by 23B (8.2%). Among the children, serotype coverage of the 13-valent Pneumococcal Conjugate Vaccine, which is currently used in Ghana was 32.4%. Prevalence of penicillin resistance among the pneumococcal isolates was 37.4% (37/99) and all the penicillin-resistant isolates exhibited intermediate penicillin resistance with the exception of one isolate that showed full resistance and was susceptible to ceftriaxone. Prevalence of resistance to the other antibiotics ranged from 2.5% (levofloxacin) to 85% (cotrimoxazole). Multidrug resistance occurred among 34.3% (34/99) of the pneumococcal isolates.

CONCLUSION

Pneumococcal carriage was four-fold higher in SCD children than adults and was characterized by predominance of non-vaccine serotypes and considerable level of multidrug resistance, though penicillin, cefotaxime and levofloxacin resistance appeared to be very low.

Outpacing the pneumococcus: Antibody dynamics in the first few days following pneumococcal capsular antigen stimulation

Children in developing countries are frequently exposed to the pneumococcus, but few develop invasive pneumococcal disease (IPD). We test the hypothesis that natural variation exists in the rapidity of IgG responses following exposure to pneumococcal polysaccharides, and that these differences are sufficiently great to affect susceptibility to and outcome of IPD. We recruited children aged 24–36 months, who had recovered from IPD, and age-matched healthy controls and vaccinated them with 1 dose of the 23-valent PPV to mimic natural exposure. We collected serum samples after vaccination and analysed the dynamics of anti-polysaccharide antibody responses to several capsular antigens. Mean IgG response times to different serotypes were 6.4–7.3 days, with standard deviations of 0.9–1.85 days, suggesting a natural range in response times of up to 7 days. Serotype 1 elicited the largest fold-rise, serotype 23F the smallest. The proportion of responses achieved by day 7 was similar in children with a history of IPD and healthy children. There was considerable natural variation in the rapidity of anti-capsular IgG responses extending over 4–7 days. There was no evidence to suggest that children who have experienced IPD respond more slowly to heterologous pneumococcal capsular antigens than do healthy children.

Role of Inflammatory Risk Factors in the Pathogenesis of Streptococcus pneumoniae

Streptococcus pneumoniae (Spn) is a colonizer of the human nasopharynx (NP), causing a variety of infections in humans including otitis media, pneumonia, sepsis, and meningitis. The NP is an immune permissive site which allows for the persistence of commensal bacteria. Acute or chronic respiratory airway inflammation constitutes a significant risk factor for the manifestation of Spn infections. The inflammatory conditions caused by an upper respiratory viral infection or respiratory conditions such as allergic asthma and chronic obstructive pulmonary disorders (COPDs) are implicated in the dysregulation of airway inflammation and tissue damage, which compromise the respiratory barrier integrity. These immune events promote bacterial outgrowth leading to Spn dissemination and invasion into the bloodstream. Therefore, suppression of inflammation and restoration of respiratory barrier integrity could contain Spn infections manifesting in the backdrop of an inflammatory disease condition. The gained knowledge could be harnessed in the design of novel therapeutic interventions to circumvent Spn bacterial infections.

Early Declines in Vaccine Type Pneumococcal Carriage in Children Less Than 5 Years Old After Introduction of 10-valent Pneumococcal Conjugate Vaccine in Mozambique

BACKGROUND

Pneumococcal carriage is a precursor of invasive pneumococcal disease. Mozambique introduced 10-valent pneumococcal conjugate vaccine (PCV10) in April 2013, using a 3-dose schedule without a booster. We evaluated PCV10 impact on pneumococcal carriage and colonization density by HIV status.

METHODS

We conducted 2 cross-sectional surveys (pre and post PCV10 introduction) among children 6 weeks to 59 months old. Participants included HIV-infected children presenting for routine care at outpatient clinics and a random sample of HIV-uninfected children from the community. We collected demographic data, vaccination history and nasopharyngeal swabs. Swabs were cultured and isolates serotyped by Quellung. We selected serotypes 11A, 19A and 19F for bacterial density analyses. We compared vaccine-type (VT) carriage prevalence from the pre-PCV10 with the post-PCV10 period by HIV status.

FINDINGS

Prevalence of VT carriage declined from 35.9% (110/306) pre already defined in the background. It should be pre-PCV (PCV) to 20.7% (36/174 fully vaccinated) post PCV (P < 0.001) in HIV-uninfected and from 34.8% (144/414) to 19.7% (27/137 fully vaccinated) (P = 0.002) in HIV-infected children. Colonization prevalence for the 3 serotypes (3, 6A, 19A) included in the 13-valent PCV but not in PCV10 increased from 12.4% (38/306) to 20.7% (36/174 fully vaccinated) (P = 0.009) among HIV- uninfected children, mainly driven by 19A; no significant increase was observed in HIV-infected children. VT carriage among unvaccinated children decreased by 30% (P = 0.005) in HIV-infected children, with no significant declines observed in HIV-uninfected children.

CONCLUSION

Declines in VT carriage were observed in both HIV-uninfected and HIV-infected children after PCV10 introduction with an early signal of herd effect especially in HIV-infected children. Ongoing monitoring of increases in 19A carriage and disease is necessary.

Epidemiology of respiratory pathogen carriage in the homeless population within two shelters in Marseille, France, 2015-2017: cross sectional 1-day surveys

Objectives

To assess risk factors for respiratory tract infection symptoms and signs in sheltered homeless people in Marseille during the winter season, including pathogen carriage.

Methods

Data on 479 male participants within two shelters who completed questionnaires and a total of 950 nasal and pharyngeal samples were collected during the winters of 2015–2017. Respiratory pathogen carriage including seven viruses and four bacteria was assessed by quantitative PCR.

Results

The homeless population was characterized by a majority of individuals of North African origin (300/479, 62.6%) with a relatively high prevalence of chronic homelessness (175/465, 37.6%). We found a high prevalence of respiratory symptoms and signs (168/476, 35.3%), a very high prevalence of bacterial carriage (313/477, 65.6%), especially Haemophilus influenzae (280/477, 58.7%), and a lower prevalence of virus carriage (51/473, 10.8%) with human rhinovirus being the most frequent (25/473, 5.3%). Differences were observed between the microbial communities of the nose and throat. Duration of homelessness (odds ratio (OR) 1.77, p 0.017), chronic respiratory diseases (OR 5.27, p <0.0001) and visiting countries of origin for migrants (OR 1.68, p 0.035) were identified as independent risk factors for respiratory symptoms and signs. A strong association between virus (OR 2.40, p 0.012) or Streptococcus pneumoniae (OR 2.32, p 0.014) carriage and respiratory symptoms and signs was also found.

Conclusions

These findings allowed identification of the individuals at higher risk for contracting respiratory tract infections to better target preventive measures aimed at limiting the transmission of these diseases in this setting.

Colonization Density of the Upper Respiratory Tract as a Predictor of Pneumonia-Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii

Background.

There is limited information on the association between colonization density of upper respiratory tract colonizers and pathogen-specific pneumonia. We assessed this association for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii.

Methods.

In 7 low- and middle-income countries, nasopharyngeal/oropharyngeal swabs from children with severe pneumonia and age-frequency matched community controls were tested using quantitative polymerase chain reaction (PCR). Differences in median colonization density were evaluated using the Wilcoxon rank-sum test. Density cutoffs were determined using receiver operating characteristic curves. Cases with a pathogen identified from lung aspirate culture or PCR, pleural fluid culture or PCR, blood culture, and immunofluorescence for P. jirovecii defined microbiologically confirmed cases for the given pathogens.

Results.

Higher densities of H. influenzae were observed in both microbiologically confirmed cases and chest radiograph (CXR)–positive cases compared to controls. Staphylococcus aureus and P. jirovecii had higher densities in CXR-positive cases vs controls. A 5.9 log₁₀ copies/mL density cutoff for H. influenzae yielded 86% sensitivity and 77% specificity for detecting microbiologically confirmed cases; however, densities overlapped between cases and controls and positive predictive values were poor (<3%). Informative density cutoffs were not found for S. aureus and M. catarrhalis, and a lack of confirmed case data limited the cutoff identification for P. jirovecii.

Conclusions.

There is evidence for an association between H. influenzae colonization density and H. influenzae–confirmed pneumonia in children; the association may be particularly informative in epidemiologic studies. Colonization densities of M. catarrhalis, S. aureus, and P. jirovecii are unlikely to be of diagnostic value in clinical settings.

Nasopharyngeal Pneumococcal Carriage in Nigeria: a two-site, population-based survey

Changes in nasopharyngeal (NP) carriage of vaccine-type (VT) Streptococcus pneumoniae can be used to assess the effectiveness of a pneumococcal conjugate vaccine (PCV10). We conducted a baseline carriage survey in rural (Kumbotso, Kano) and urban (Pakoto, Ogun) Nigeria. In this cross-sectional study, we obtained data on demography, clinical history, risk factors, and took NP swabs for pneumococcal culture. We calculated crude and age-standardised carriage prevalence and used log-binomial regression to assess risk factors for carriage. Among children aged <5 years, 92% (95% CI: 88–95%) and 78% (73–82%), respectively, carried any pneumococcus and 48% and 50%, respectively, carried PCV10 serotypes. In Kumbotso, carriage prevalence was >40% across all ages. The age-standardized prevalence of pneumococcal carriage was 66% in Kumbotso and 40% in Pakoto. The most commonly identified serotypes were 19 F, 6 A and 23 F. Risk factors for carriage were young age, recent rhinorrhoea, cohabitation with ≥2 children aged <5 years, and sharing a bed with ≥2 persons. Pneumococcal carriage prevalence is high in this Nigerian population. Persisting prevalence of VT-carriage in older children and adults suggests that PCV10 introduction in children will not eliminate transmission of vaccine serotypes rapidly. High vaccine coverage will therefore be required to ensure full protection of children.

Nasopharyngeal carriage of Streptococcus pneumoniae among HIV-infected and -uninfected children <5 years of age before introduction of pneumococcal conjugate vaccine in Mozambique

Nasopharyngeal carriage is a precursor for pneumococcal disease and can be useful for evaluating pneumococcal conjugate vaccine (PCV) impact. We studied pre-PCV pneumococcal carriage among HIV-infected and -uninfected children in Mozambique. Between October 2012 and March 2013, we enrolled HIV-infected children age <5 years presenting for routine care at seven HIV clinics in 3 sites, including Maputo (urban-south), Nampula (urban-north), and Manhiça (rural-south). We also enrolled a random sample of HIV-uninfected children <5 years old from a demographic surveillance site in Manhiça. A single nasopharyngeal swab was obtained and cultured following enrichment in Todd Hewitt broth with yeast extract and rabbit serum. Pneumococcal isolates were serotyped by Quellung reaction and multiplex polymerase chain reaction. Factors associated with pneumococcal carriage were examined using logistic regression. Overall pneumococcal carriage prevalence was 80.5% (585/727), with similar prevalences among HIV-infected (81.5%, 339/416) and HIV-uninfected (79.1%, 246/311) children, and across age strata. Among HIV-infected, after adjusting for recent antibiotic use and hospitalization, there was no significant association between study site and colonization: Maputo (74.8%, 92/123), Nampula (83.7%, 82/98), Manhiça (84.6%, 165/195). Among HIV-uninfected, report of having been born to an HIV-infected mother was not associated with colonization. Among 601 pneumococcal isolates from 585 children, serotypes 19F (13.5%), 23F (13.1%), 6A (9.2%), 6B (6.2%) and 19A (5.2%) were most common. The proportion of serotypes included in the 10- and 13-valent vaccines was 44.9% and 61.7%, respectively, with no significant differences by HIV status or age group. Overall 36.9% (n = 268) of children were colonized with a PCV10 serotype and 49.7% (n = 361) with a PCV13 serotype. Pneumococcal carriage was common, with little variation by geographic region, age, or HIV status. PCV10 was introduced in April 2013; ongoing carriage studies will examine the benefits of PCV10 among HIV-infected and–uninfected children.

Pediatric Community-Acquired Pneumonia in the United States: Changing Epidemiology, Diagnostic and Therapeutic Challenges, and Areas for Future Research

Community-acquired pneumonia (CAP) is one of the most common serious infections in childhood. This review focuses on pediatric CAP in the United States and other industrialized nations, specifically highlighting the changing epidemiology of CAP, diagnostic and therapeutic challenges, and areas for further research.

Prevalence and serotype distribution of nasopharyngeal carriage of Streptococcus pneumoniae in China: a meta-analysis

BACKGROUND

To explore the overall prevalence and serotype distribution of nasopharyngeal carriage of Streptococcus pneumoniae(S. pneumoniae) among healthy children.

METHODS

A search for pneumococcal nasopharyngeal carriage studies including children published up to July 31th, 2016 was conducted to describe carriage in China. The review also describes antibiotic resistance in and serotypes of S. pneumoniae and assesses the impact of vaccination on carriage in this region. Summary measures for overall prevalence, antibiotic resistance, and serotype distributions extracted from the analyzed data were determined with 95% confidence intervals (CIs) using random-effects models. Heterogeneity was assessed using I 2 test statistics.

RESULTS

Thirty-seven studies were included in this review, and the majority of studies (64.9%) were located in the pre-introduction period of 7-valent pneumococcal conjugate vaccine (PCV7) in China. The pooled prevalence of S. pneumoniae nasopharyngeal carriage was 21.4% (95% CI: 18.3-24.4%). Carriage was highest in children attending kindergartens [24.5%, (19.7-29.3%)] and decreased with increasing age. Before the introduction of PCV7 into China, the prevalence of S. pneumoniae nasopharyngeal carriage was 25.8% (20.7-30.9%), the pooled carriage of S. pneumoniae sharply dropped into the 14.1% (11.3-16.9%) by PCV7 vaccination period (P < 0.001). Before the pneumococcal conjugate vaccine (PCV) was introduced in China, the penicillin resistance rate in S. pneumoniae isolated from healthy children was 31.9% (21.2-42.6%); however, this rate sharply decreased after the introduction of PCV7 in China [21.6%, (7.4-35.9%)], and the difference between the rates during these two time periods was statistically significant (P value <0.05). Serotypes 19F, 6A and 23F were the most commonly isolated. Meta-analysis of data from young children showed a pooled rate estimate of 46.6% (38.8-54.4%) for PCV7 vaccine coverage and 66.2% (58.6-73.8%) for PCV13 vaccine coverage.

CONCLUSIONS

The prevalence of nasopharyngeal carriage among children was high in China. PCV7 immunization was found to be associated with reduction of nasopharyngeal colonization of S. pneumoniae. Conjugate vaccination coverage was slightly affected by the introduction of PCV7 into China because of low vaccination rate. The government should implement timely adjusted conjugate vaccination strategies based on our findings.

Epidemiology of Nasopharyngeal Carriage by Haemophilus influenzae in Healthy Children: A Study in the Mediterranean Coast Region

BACKGROUND

Haemophilus influenzae, a colonizer of the nasopharynx, in children causes mainly otitis and sinusitis. The primary objective of this study was to determine the prevalence of pharyngeal colonization by H. influenzae, and the secondary objectives were to identify risk factors associated with H. influenzae colonization and its antibiotic susceptibility.

METHODS

A prospective, multicenter study of nasopharyngeal carriers of H. influenzae was conducted in the pediatric consulting rooms of 10 primary healthcare centers in Murcia (Spain). The study consisted of 404 healthy children less than 5 years of age and was carried out during winter (January-March) and summer (July-September) of 2015. A nasopharyngeal sample was collected from each child, and an epidemiologic survey was completed by a pediatrician.

RESULTS

In total, 112 (27.7%) children had colonization by H. influenzae, with 73.2% of cases in winter and 26.8% of cases in summer (P < 0.001). The median (interquartile range) age in months of the colonized children (13 months, 12-47.5) was lower than that of the noncolonized children (46 months, 12-49) (P < 0.001). All H. influenzae found were nontypeable H. influenzae (NTHi). Among 112 isolates, 20% were ampicillin resistant, of which 10% produced β-lactamase, and 9% were ampicillin resistant and did not produce β-lactamase. A logistic regression analysis showed that young age (odds ratio: 0.98) and the winter period (odds ratio: 3.41; P < 0.001) were risk factors for colonization by NTHi.

CONCLUSIONS

Colonization by NTHi is high in this Mediterranean coast region with remarkable ampicillin resistant. Younger age and the winter period were facilitating factors.

Carriage prevalence and serotype distribution of Streptococcus pneumoniae prior to 10-valent pneumococcal vaccine introduction: A population-based cross-sectional study in South Western Uganda, 2014

Background

Information on Streptococcus pneumoniae nasopharyngeal (NP) carriage before the pneumococcal conjugate vaccine (PCV) introduction is essential to monitor impact. The 10-valent PCV (PCV10) was officially introduced throughout Ugandan national childhood immunization programs in 2013 and rolled-out countrywide during 2014. We aimed to measure the age-specific Streptococcus pneumoniae carriage and serotype distribution across all population age groups in the pre-PCV10 era in South Western Uganda.

Methods

We conducted a two-stage cluster, age-stratified, cross-sectional community-based study in Sheema North sub-district between January and March 2014. One NP swab was collected and analyzed for each participant in accordance with World Health Organization guidelines.

Results

NP carriage of any pneumococcal serotype was higher among children <2 years old (77%; n = 387) than among participants aged ≥15 years (8.5%; n = 325) (chi² p < 0.001).

Results

Of the 623 positive cultures, we identified 49 serotypes among 610 (97.9%) isolates; thirteen (2.1%) isolates were non-typeable. Among <2 years old, serotypes 6A, 6B, 14, 15B, 19F and 23F accounted for half of all carriers. Carriage prevalence with PCV10 serotypes was 29.4% among individuals aged <2 years (n = 387), 23.4% in children aged 2–4 years (n = 217), 11.4% in 5–14 years (n = 417), and 0.4% among individuals ≥15 years of age (n = 325). The proportion of carried pneumococci serotypes contained in PCV10 was 38.1% (n = 291), 32.8% (n = 154), 29.4% (n = 156), and 4.4% (n = 22) among carriers aged <2 years, 2–4 years, 5–14 years and ≥15 years, respectively.

Discussion

In Sheema district, the proportion of PCV10 serotypes was low (<40%), across all age groups, especially among individuals aged 15 years or older (<5%). PCV10 introduction is likely to impact transmission among children and to older individuals, but less likely to substantially modify pneumococcal NP ecology among individuals aged 15 years or older.

Secondary Bacterial Infections Associated with Influenza Pandemics

Lower and upper respiratory infections are the fourth highest cause of global mortality (Lozano et al., 2012). Epidemic and pandemic outbreaks of respiratory infection are a major medical concern, often causing considerable disease and a high death toll, typically over a relatively short period of time. Influenza is a major cause of epidemic and pandemic infection. Bacterial co/secondary infection further increases morbidity and mortality of influenza infection, with Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus reported as the most common causes. With increased antibiotic resistance and vaccine evasion it is important to monitor the epidemiology of pathogens in circulation to inform clinical treatment and development, particularly in the setting of an influenza epidemic/pandemic.