Reducing exacerbations in children and adults with primary ciliary dyskinesia using erdosteine and/or azithromycin therapy (REPEAT trial): study protocol for a multicentre, double-blind, double-dummy, 2×2 partial factorial, randomised controlled trial

Introduction

Primary ciliary dyskinesia (PCD) is a rare, progressive, inherited ciliopathic disorder, which is incurable and frequently complicated by the development of bronchiectasis. There are few randomised controlled trials (RCTs) involving children and adults with PCD and thus evidence of efficacy for interventions are usually extrapolated from people with cystic fibrosis. Our planned RCT seeks to address some of these unmet needs by employing a currently prescribed (but unapproved for long-term use in PCD) macrolide antibiotic (azithromycin) and a novel mucolytic agent (erdosteine). The primary aim of our RCT is to determine whether regular oral azithromycin and erdosteine over a 12-month period reduces acute respiratory exacerbations among children and adults with PCD. Our primary hypothesis is that: people with PCD who regularly use oral azithromycin and/or erdosteine will have fewer exacerbations than those receiving the corresponding placebo medications. Our secondary aims are to determine the effect of the trial medications on PCD-specific quality-of-life (QoL) and other clinical outcomes (lung function, time-to-next exacerbation, hospitalisations) and nasopharyngeal bacterial carriage and antimicrobial resistance.

Methods and analysis

We are currently undertaking a multicentre, double-blind, double-dummy RCT to evaluate whether 12 months of azithromycin and/or erdosteine is beneficial for children and adults with PCD. We plan to recruit 104 children and adults with PCD to a parallel, 2×2 partial factorial superiority RCT at five sites across Australia. Our primary endpoint is the rate of exacerbations over 12 months. Our main secondary outcomes are QoL, lung function and nasopharyngeal carriage by respiratory bacterial pathogens and their associated azithromycin resistance.

Ethics and dissemination

Our RCT is conducted in accordance with Good Clinical Practice and the Australian legislation and National Health and Medical Research Council guidelines for ethical conduct of Research, including that for First Nations Australians.

Trial registration number

ACTRN12619000564156.

BIGDATA: A Protocol to Create and Extend a 25-Year Clinical Trial and Observational Data Asset to Address Key Knowledge Gaps in Otitis Media and Hearing Loss in Australian Aboriginal and Non-Aboriginal Children

INTRODUCTION

Otitis media (OM) is a common childhood illness, often resolving without intervention and acute and long-term complications are rare. However, Australian Aboriginal and Torres Strait Islander infants and children experience a high burden of OM and are at high risk of complications (tympanic membrane perforation and chronic infections). Bacterial OM is commonly associated with Streptococcus pneumoniae, non-typeable Haemophilus influenzae, and Moraxella catarrhalis. BIGDATA is a data asset combining over 25 years of microbiology and OM surveillance research from the Ear Health Research Program at Menzies School of Health Research (Northern Territory, Australia), including 11 randomized controlled trials, four cohort studies, eight surveys in over 30 remote communities (including data from Western Australia), and five surveys of urban childcare centers including Aboriginal and Torres Strait Islander and non-Indigenous children. Outcome measures include clinical examinations (focusing on OM), antibiotic prescriptions, pneumococcal vaccination, modifiable risk factors such as smoking and household crowding, and nasopharyngeal and ear discharge microbiology including antimicrobial resistance testing.

METHODS AND ANALYSIS

The initial series of projects are planned to address the following key knowledge gaps: (i) otitis media prevalence and severity over pre pneumococcal conjugate vaccines (PCVs) and three eras of increasing PCV valency; (ii) impact of increasing valency PCVs on nasopharyngeal carriage dynamics of pneumococcal serotypes, and antimicrobial resistance; (iii) impact of increasing valency PCVs on nasopharyngeal carriage dynamics and antimicrobial resistance of other otopathogens; and (iv) serotype specific differences between children with acute OM and OM with effusion or without OM. These data will be utilized to identify research gaps, providing evidence-based prioritization for ongoing research.

ETHICS AND DISSEMINATION

Data asset creation and priority analyses were approved by the Human Research Ethics Committee of Northern Territory Department of Health and Menzies School of Health Research (EC00153, 18-3281), the Child and Adolescent Health Service Human Research Ethics Committee and Western Australian Aboriginal Health Ethics Committee. Dissemination will be through peer review publication and conference presentations.

Nasopharyngeal carriage of otitis media pathogens in infants receiving 10-valent non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV10), 13-valent pneumococcal conjugate vaccine (PCV13) or a mixed primary schedule of both vaccines: A randomised controlled trial

BACKGROUND

Aboriginal children in Northern Australia have a high burden of otitis media, driven by early and persistent nasopharyngeal carriage of otopathogens, including non-typeable Haemophilus influenzae (NTHi) and Streptococcus pneumoniae (Spn). In this context, does a combined mixed primary series of Synflorix and Prevenar13 provide better protection against nasopharyngeal carriage of NTHi and Spn serotypes 3, 6A and 19A than either vaccine alone?

METHODS

Aboriginal infants (n = 425) were randomised to receive Synflorix™ (S, PHiD-CV10) or Prevenar13™ (P, PCV13) at 2, 4 and 6 months (_SSS or _PPP, respectively), or a 4-dose early mixed primary series of PHiD-CV10 at 1, 2 and 4 months and PCV13 at 6 months of age (SSSP). Nasopharyngeal swabs were collected at 1, 2, 4, 6 and 7 months of age. Swabs of ear discharge were collected from tympanic membrane perforations.

FINDINGS

At the primary endpoint at 7 months of age, the proportion of nasopharyngeal (Np) swabs positive for PCV13-only serotypes 3, 6A, or 19A was 0%, 0.8%, and 1.5% in the _PPP, _SSS, and SSSP groups respectively, and NTHi 55%, 52%, and 52% respectively, and no statistically significant vaccine group differences in other otopathogens at any age. The most common serotypes (in order) were 16F, 11A, 10A, 7B, 15A, 6C, 35B, 23B, 13, and 15B, accounting for 65% of carriage. Ear discharge swabs (n = 108) were culture positive for NTHi (52%), S. aureus (32%), and pneumococcus (20%).

CONCLUSIONS

Aboriginal infants experience nasopharyngeal colonisation and tympanic membrane perforations associated with NTHi, non-PCV13 pneumococcal serotypes and S. aureus in the first months of life. Nasopharyngeal carriage of pneumococcus or NTHi was not significantly reduced in the early 4-dose combined SSSP group compared to standard _PPP or _SSS schedules at any time point. Current pneumococcal conjugate vaccine formulations do not offer protection from early onset NTHi and pneumococcal colonisation in this high-risk population.

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'

The heterogeneous and highly recombinogenic genus Haemophilus comprises several species, some of which are pathogenic to humans. All share an absolute requirement for blood-derived factors during growth. Certain species, such as the pathogen Haemophilus influenzae and the commensal Haemophilus haemolyticus, are thought to require both haemin (X-factor) and nicotinamide adenine dinucleotide (NAD, V-factor), whereas others, such as the informally classified 'Haemophilus intermedius subsp. intermedius', and Haemophilus parainfluenzae, only require V-factor. These differing growth requirements are commonly used for species differentiation, although a number of studies are now revealing issues with this approach. Here, we perform large-scale phylogenomics of 240 Haemophilus spp. genomes, including five 'H. intermedius' genomes generated in the current study, to reveal that strains of the 'H. intermedius' group are in fact haemin-independent H. haemolyticus (hiHh). Closer examination of these hiHh strains revealed that they encode an intact haemin biosynthesis pathway, unlike haemin-dependent H. haemolyticus and H. influenzae, which lack most haemin biosynthesis genes. Our results suggest that the common ancestor of modern-day H. haemolyticus and H. influenzae lost key haemin biosynthesis loci, likely as a consequence of specialized adaptation to otorhinolaryngeal and respiratory niches during their divergence from H. parainfluenzae. Genetic similarity analysis demonstrated that the haemin biosynthesis loci acquired in the hiHh lineage were likely laterally transferred from a H. parainfluenzae ancestor, and that this event probably occurred only once in hiHh. This study further challenges the validity of phenotypic methods for differentiating among Haemophilus species, and highlights the need for whole-genome sequencing for accurate characterization of species within this taxonomically challenging genus.

Outcomes of protracted bacterial bronchitis in children: A 5-year prospective cohort study

BACKGROUND AND OBJECTIVE

Long-term data on children with PBB has been identified as a research priority. We describe the 5-year outcomes for children with PBB to ascertain the presence of chronic respiratory disease (bronchiectasis, recurrent PBB and asthma) and identify the risk factors for these.

METHODS

Prospective cohort study was undertaken at the Queensland Children's Hospital, Brisbane, Australia, of 166 children with PBB and 28 controls (undergoing bronchoscopy for symptoms other than chronic wet cough). Monitoring was by monthly contact via research staff. Clinical review, spirometry and CT chest were performed as clinically indicated.

RESULTS

A total of 194 children were included in the analysis. Median duration of follow-up was 59 months (IQR: 50-71 months) post-index PBB episode, 67.5% had ongoing symptoms and 9.6% had bronchiectasis. Significant predictors of bronchiectasis were recurrent PBB in year 1 of follow-up (OR_adj = 9.6, 95% CI: 1.8-50.1) and the presence of Haemophilus influenzae in the BAL (OR_adj = 5.1, 95% CI: 1.4-19.1). Clinician-diagnosed asthma at final follow-up was present in 27.1% of children with PBB. A significant BDR (FEV₁ improvement >12%) was obtained in 63.5% of the children who underwent reversibility testing. Positive allergen-specific IgE (OR_adj = 14.8, 95% CI: 2.2-100.8) at baseline and bronchomalacia (OR_adj = 5.9, 95% CI: 1.2-29.7) were significant predictors of asthma diagnosis. Spirometry parameters were in the normal range.

CONCLUSION

As a significant proportion of children with PBB have ongoing symptoms at 5 years, and outcomes include bronchiectasis and asthma, they should be carefully followed up clinically. Defining biomarkers, endotypes and mechanistic studies elucidating the different outcomes are now required.

Hospital surveillance predicts community pneumococcal antibiotic resistance in Vietnam

BACKGROUND

In Vietnam, Streptococcus pneumoniae is a leading cause of disease, including meningitis. Antibiotics are available without physician prescription at community pharmacies and rates of antibiotic non-susceptibility are high. Appropriate treatment and antibiotic stewardship need to be informed by surveillance data.

OBJECTIVES

To report community-based pneumococcal antibiotic susceptibility testing data from children enrolled in a pneumococcal conjugate vaccine trial in Ho Chi Minh City [the Vietnam Pneumococcal Project (ViPP)] and compare these with published hospital-based data from the nationwide Survey of Antibiotic Resistance (SOAR) to determine whether hospital surveillance data provide an informative estimate of circulating pneumococcal resistance.

METHODS

Pneumococcal isolates from 234 nasopharyngeal swabs collected from ViPP participants at 12 months of age underwent antibiotic susceptibility testing using CLSI methods and the data were compared with SOAR data.

RESULTS

Antibiotic susceptibility testing identified penicillin-non-susceptible pneumococci in 93.6% of pneumococcus-positive ViPP swabs (oral, non-meningitis breakpoints). Non-susceptibility to erythromycin, trimethoprim/sulfamethoxazole, clindamycin and tetracycline also exceeded 79%. MDR, defined as non-susceptibility to three or more classes of antibiotic, was common (94.4% of swabs). Low or no resistance was detected for ceftriaxone (non-meningitis breakpoints), ofloxacin and vancomycin. Antibiotic non-susceptibility rates in ViPP and SOAR were similar for several antibiotics tested.

CONCLUSIONS

A very high proportion of pneumococci carried in the community are MDR. Despite wide disparities in population demographics between ViPP and SOAR, the non-susceptibility rates for several antibiotics were comparable. Thus, with some qualification, hospital antibiotic susceptibility testing data in Vietnam can inform circulating pneumococcal antibiotic non-susceptibility in young children, the group at highest risk of pneumococcal disease, to guide antibiotic prescribing and support surveillance strategies.

Acute lower respiratory infections in Indigenous infants in Australia's Northern Territory across three eras of pneumococcal conjugate vaccine use (2006-15): a population-based cohort study

BACKGROUND

The burden of acute lower respiratory infection (ALRI) in Indigenous children of Australia's Northern Territory is among the highest globally. No published data exists on the effect of pneumococcal conjugate vaccine (PCV) introduction on ALRIs in this population beyond 2005. The aim of this study was to describe the rates of ALRI admissions to hospital in Indigenous infants in the Northern Territory from 2006 to 2015, across three periods of different PCV use. We hypothesised that broader valency PCVs would be more effective against hospitalisations for pneumonia.

METHODS

We did a retrospective population-based cohort study of Indigenous infants born in the Northern Territory followed up until age 12 months. Data were from administrative hospital and perinatal datasets. International classification of diseases codes (tenth revision, Australian modification; ICD-10AM) were used to identify respiratory hospitalisations of interest: all-cause ALRI, all-cause pneumonia, bacterial pneumonia, viral pneumonia, influenza-like illness (ILI), respiratory syncytial virus ALRI (RSV-ALRI), and pneumococcal ALRI. Incidence rates were compared between PCV eras (7-valent PCV [PCV7], 2006-09; 10-valent PCV [PCV10], 2009-11; and 13-valent PCV [PCV13], 2011-15) using interrupted time trend analysis and negative binomial regression.

FINDINGS

For children born between Jan 1, 2006, and Dec 31, 2015, 4138 ALRI episodes (31% of all hospitalisations) occurred among 2888 (20%) of the 14 594 infants. The overall ALRI hospitalisation rate was 29·7 episodes per 100 child-years. Prominent risk factors associated with ALRI hospitalisation were living in a remote community or the Central desert region, being born preterm or with low birthweight. ALRI rates were lowest in the PCV13 era, in association with a significant reduction in bacterial pneumonia hospitalisations in the PCV13 era compared with the PCV10 (incidence rate ratio 0·68, 95% CI 0·57-0·81) and PCV7 (0·70, 0·60-0·81) eras. In contrast, RSV-ALRI rates were 4·9 episodes per 100 child-years in each era.

INTERPRETATION

A 30% reduction in bacterial-coded pneumonia hospitalisations in the Northern Territory during the era of PCV13 immunisation supports its ongoing use in the region. Despite the reduction, one in five Indigenous infants born in the region continue to be hospitalised with an ALRI in their first year of life. Future gains require multifaceted environmental and biomedical approaches.

FUNDING

National Health and Medical Research Council of Australia.

Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures

OBJECTIVE

To perform a comprehensive review of otitis media microbiome literature published between 1^st July 2015 and 30th June 2019.

DATA SOURCES

PubMed database, National Library of Medicine.

REVIEW METHODS

Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members.

CONCLUSIONS

Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data.

IMPLICATIONS FOR PRACTICE

Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.

The point prevalence of respiratory syncytial virus in hospital and community-based studies in children from Northern Australia: studies in a 'high-risk' population

INTRODUCTION

Respiratory syncytial virus (RSV) is the leading viral cause of acute lower respiratory infections globally, accounting for high morbidity and mortality burden among children aged less than 5 years. As candidate RSV vaccine trials in pregnant women and infants are underway a greater understanding of RSV epidemiology is now needed, especially in paediatric populations with high rates of acute and chronic respiratory disease. The objective was to identify RSV prevalence in children living in northern Australia, a region with a high respiratory disease burden.

METHODS

Data were sourced from 11 prospective studies (four hospital and seven community-based) of infants and children with acute and chronic respiratory illnesses, as well as otitis media, conducted between 1996 and 2017 inclusive. The data from northern Australian children in these trials were extracted and, where available and consented, their nasopharyngeal swabs (biobanked at -80ºC) were tested by polymerase chain reaction assays for RSV-A and B, 16 other viruses and atypical respiratory bacterial pathogens.

RESULTS

Overall, 1127 children were included. Their median age was 1.8 years (interquartile range 0.5-4.9); 58% were male and 90% Indigenous, with 81% from remote communities. After human rhinoviruses (HRV), RSV was the second most prevalent virus (15%, 95% confidence interval (CI) 13-18). RSV prevalence was greatest amongst children aged less than 2 years hospitalised with bronchiolitis (47%, 95%CI 41.4-52.4), with more than two-thirds with RSV aged less than 6 months. In contrast, the prevalence of RSV was only 1-3.5% in other age groups and settings. In one-third of RSV cases, another respiratory virus was also detected. Individual viruses other than RSV and HRV were uncommon (0-9%).

CONCLUSION

Combined data from 11 hospital and community-based studies of children aged less than 18 years who lived in communities with a high burden of acute and chronic respiratory illness showed that RSV was second only to HRV as the most prevalent virus detected across all settings. RSV was the most frequently detected virus in infants hospitalised with bronchiolitis, including those aged less than 6 months. In contrast, RSV was uncommonly detected in children in community settings. In northern Australia, effective maternal and infant RSV vaccines could substantially reduce RSV bronchiolitis-related hospitalisations, including admissions of Indigenous infants from remote communities.

Antimicrobial susceptibility and impact of macrolide antibiotics on Moraxella catarrhalis in the upper and lower airways of children with chronic endobronchial suppuration

INTRODUCTION

Moraxella catarrhalis is an important but insufficiently studied respiratory pathogen.

AIM

To determine antibiotic susceptibility and impact of recent antibiotics on M. catarrhalis from children with chronic endobronchial suppuration.

METHODOLOGY

We cultured nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) fluids collected from children who were prospectively enrolled in studies of chronic cough and had flexible bronchoscopy performed. Recent β-lactam or macrolide antibiotic use was recorded. M. catarrhalis isolates stored at -80 °C were re-cultured and susceptibility determined to a range of antibiotics including the macrolide antibiotic erythromycin.

RESULTS

Data from concurrently collected NP and BAL specimens were available from 547 children (median age 2.4 years) enrolled from 2007 to 2016. M. catarrhalis NP carriage was detected in 149 (27  %) children and lower airway infection (≥10⁴ c.f.u. ml^-1 BAL) in 67 (12  %) children. In total, 91  % of 222 M. catarrhalis isolates were β-lactamase producers, and non-susceptibility was high to benzylpenicillin (98 %), cefaclor (39 %) and cotrimoxazole (38 %). Overall, >97  % isolates were susceptible to cefuroxime, chloramphenicol, erythromycin and tetracycline; three isolates were erythromycin-resistant (MIC >0.5 mg l^-1). Recent macrolide antibiotics (n=152 children, 28 %) were associated with significantly reduced M. catarrhalis carriage and lower airway infection episodes compared to children who did not receive macrolides; odds ratios 0.19 (95  % CI 0.10-0.35) and 0.15 (0.04-0.41), respectively.

CONCLUSION

Despite the frequent use of macrolides, few macrolide-resistant isolates were detected. This suggests a fitness cost associated with macrolide resistance in M. catarrhalis. Macrolide antibiotics remain an effective choice for treating M. catarrhalis lower airway infection in children with chronic endobronchial suppuration.

Do combined upper airway cultures identify lower airway infections in children with chronic cough?

BACKGROUND

Obtaining lower airway specimens is important for guiding therapy in chronic lung infection but is difficult in young children unable to expectorate. While culture-based studies have assessed the diagnostic accuracy of nasopharyngeal or oropharyngeal specimens for identifying lower airway infection, none have used both together. We compared respiratory bacterial pathogens cultured from nasopharyngeal and oropharyngeal swabs with bronchoalveolar lavage (BAL) cultures as the "gold standard" to better inform the diagnosis of lower airway infection in children with chronic wet cough.

METHODS

Nasopharyngeal and oropharyngeal swabs and BAL fluid specimens were collected concurrently from consecutive children undergoing flexible bronchoscopy for chronic cough and cultured for bacterial pathogens.

RESULTS

In cultures from 309 children (median age, 2.3 years) with chronic endobronchial suppuration, all main pathogens detected (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) were more prevalent in nasopharyngeal than oropharyngeal swabs (37%, 34%, and 23% vs 21%, 6.2%, and 3.2%, respectively). Positive and negative predictive values for lower airway infection by any of these three pathogens were 63% (95% confidence interval [95% CI] 55, 70) and 85% (95% CI, 78, 91) for nasopharyngeal swabs, 65% (95% CI, 54, 75), and 66% (95% CI, 59, 72) for oropharyngeal swabs, and 61% (95% CI, 54,68), and 88% (95% CI, 81, 93) for both swabs, respectively.

CONCLUSIONS

Neither nasopharyngeal nor oropharyngeal swabs, alone or in combination, reliably predicted lower airway infection in children with chronic wet cough. Although upper airway specimens may be useful for bacterial carriage studies and monitoring antimicrobial resistance, their clinical utility in pediatric chronic lung disorders of endobronchial suppuration is limited.

How low can we go? The implications of low bacterial load in respiratory microbiota studies

Background

Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present.

Main body

Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed.

Conclusion

Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.

Bacteria and viruses in the nasopharynx immediately prior to onset of acute lower respiratory infections in Indigenous Australian children

Acute lower respiratory infection (ALRI) is a major cause of hospitalization for Indigenous children in remote regions of Australia. The associated microbiology remains unclear. Our aim was to determine whether the microbes present in the nasopharynx before an ALRI were associated with its onset. A retrospective case-control/crossover study among Indigenous children aged up to 2 years. ALRI cases identified by medical note review were eligible where nasopharyngeal swabs were available: (1) 0–21 days before ALRI onset (case); (2) 90–180 days before ALRI onset (same child controls); and (3) from time and age-matched children without ALRI (different child controls). PCR assays determined the presence and/or load of selected respiratory pathogens. Among 104 children (182 recorded ALRI episodes), 120 case-same child control and 170 case-different child control swab pairs were identified. Human adenoviruses (HAdV) were more prevalent in cases compared to same child controls (18 vs 7%; OR = 3.08, 95% CI 1.22–7.76, p = 0.017), but this association was not significant in cases versus different child controls (15 vs 10%; OR = 1.93, 95% CI 0.97–3.87 (p = 0.063). No other microbes were more prevalent in cases compared to controls. Streptococcus pneumoniae (74%), Haemophilus influenzae (75%) and Moraxella catarrhalis (88%) were commonly identified across all swabs. In a pediatric population with a high detection rate of nasopharyngeal microbes, HAdV was the only pathogen detected in the period before illness presentation that was significantly associated with ALRI onset. Detection of other potential ALRI pathogens was similar between cases and controls.

Recommendations for application of Haemophilus influenzae PCR diagnostics to respiratory specimens for children living in northern Australia: a retrospective re-analysis

OBJECTIVE

Haemophilus haemolyticus can be misidentified as nontypeable Haemophilus influenzae (NTHi) due to their phenotypic similarities in microbiological culture. This study aimed to determine the prevalence of misidentified NTHi in respiratory specimens from children living in northern Australia.

RESULTS

Among respiratory specimens collected in studies between 2010 and 2013, retrospective PCR analysis found that routine culture misidentified H. haemolyticus as NTHi in 0.3% (3/879) of nasal specimens, 25% (14/55) of bronchoalveolar lavage and 40% (12/30) of throat specimens. Therefore, in this population, PCR-based NTHi diagnostics are indicated for throat and bronchoalveolar specimens, but not for nasal specimens.

Defining lower airway bacterial infection in children with chronic endobronchial disorders

BACKGROUND

Differentiating lower airway bacterial infection from possible upper airway contamination in children with endobronchial disorders undergoing bronchoalveolar lavage (BAL) is important for guiding management. A diagnostic bacterial load threshold based on inflammatory markers has been determined to differentiate infection from upper airway contamination in infants with cystic fibrosis, but not for children with protracted bacterial bronchitis (PBB), chronic suppurative lung disease (CSLD), or bronchiectasis.

METHODS

BAL samples from children undergoing bronchoscopy underwent quantitative bacterial culture, cytologic examination, and respiratory virus testing; a subset also had interleukin-8 examined. Geometric means (GMs) of total cell counts (TCCs) and neutrophil counts were plotted by respiratory pathogen bacterial load. Logistic regression determined associations between age, sex, Indigenous status, antibiotic exposure, virus detection and bacterial load, and elevated TCCs (>400 × 10³ cells/mL) and airway neutrophilia (neutrophils >15% BAL leukocytes).

RESULTS

From 2007 to 2016, 655 children with PBB, CSLD, or bronchiectasis were enrolled. In univariate analyses, Indigenous status and bacterial load ≥10⁵ colony-forming units (CFU)/mL were positively associated with high TCCs. Viruses and bacterial load ≥10⁴ CFU/mL were positively associated with neutrophilia; negative associations were seen for Indigenous status and macrolides. In children who had not received macrolide antibiotics, bacterial load was positively associated in multivariable analyses with high TCCs at ≥10⁴ CFU/mL and with neutrophilia at ≥10⁵ CFU/mL; GMs of TCCs and neutrophil counts were significantly elevated at 10⁴ and 10⁵ CFU/mL compared to negative cultures.

CONCLUSIONS

Our findings support a BAL threshold ≥10⁴ CFU/mL to define lower airway infection in children with chronic endobronchial disorders.

Streptococcus pneumoniae and chronic endobronchial infections in childhood

Streptococcus pneumoniae (pneumococcus) is the main cause of bacterial pneumonia worldwide and has been studied extensively in this context. However, its role in chronic endobronchial infections and accompanying lower airway neutrophilic infiltration has received little attention. Severe and recurrent pneumonia are risk factors for chronic suppurative lung disease (CSLD) and bronchiectasis; the latter causes considerable morbidity and, in some populations, premature death in children and adults. Protracted bacterial bronchitis (PBB) is another chronic endobronchial infection associated with substantial morbidity. In some children, PBB may progress to bronchiectasis. Although nontypeable Haemophilus influenzae is the main pathogen in PBB, CSLD and bronchiectasis, pneumococci are isolated commonly from the lower airways of children with these diagnoses. Here we review what is known currently about pneumococci in PBB, CSLD and bronchiectasis, including the importance of pneumococcal nasopharyngeal colonization and how persistence in the lower airways may contribute to the pathogenesis of these chronic pulmonary disorders. Antibiotic treatments, particularly long-term azithromycin therapy, are discussed together with antibiotic resistance and the impact of pneumococcal conjugate vaccines. Important areas requiring further investigation are identified, including immune responses associated with pneumococcal lower airway infection, alone and in combination with other respiratory pathogens, and microarray serotyping to improve detection of carriage and infection by multiple serotypes. Genome wide association studies of pneumococci from the upper and lower airways will help identify virulence and resistance determinants, including potential therapeutic targets and vaccine antigens to treat and prevent endobronchial infections. Much work is needed, but the benefits will be substantial.

Simultaneous identification of Haemophilus influenzae and Haemophilus haemolyticus using real-time PCR

AIM

To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic near-neighbor Haemophilus haemolyticus.

MATERIALS & METHODS

A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed.

RESULTS & DISCUSSION

PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT. These two assays were multiplexed with the recently described fucP assay for further differentiation among H. influenzae.

CONCLUSION

The triplex assay provides rapid, unambiguous, sensitive and highly specific genotyping results for the simultaneous detection of hypD and siaT, including fucose-positive H. influenzae (fucP), in a single PCR.

Culture of non-typeable Haemophilus influenzae from the nasopharynx: Not all media are equal

The efficacy of chocolate agar, versus bacitracin, vancomycin, clindamycin, chocolate agar (BVCCA) for the isolation of non-typeable Haemophilus influenzae (NTHi) from nasopharyngeal swabs was determined. BVCCA cultured NTHi from 97.3% of NTHi-positive swabs, compared to 87.1% for chocolate agar. To maximise culture sensitivity, the use of both media is recommended.

Propensity of pneumococcal carriage serotypes to infect the lower airways of children with chronic endobronchial infections

BACKGROUND

Chronic endobronchial infections in children are responsible for a high disease burden. Streptococcus pneumoniae is frequently isolated; however, few publications have described serotypes associated with non-invasive lower airway infection.

METHODS

Paired nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) fluids were collected from children undergoing bronchoscopy for chronic cough. NP swabs were also collected from asymptomatic children in otitis media surveillance studies (controls). Specimens were processed and lower airway infection defined (⩾10⁴ colony forming units/mL BAL) as previously described. Serotype-specific odds ratios (ORs) were calculated (as described for invasive pneumococcal disease) to indicate propensity for infection.

RESULTS

From 2007-2015, paired specimens were processed from 435 children with protracted bacterial bronchitis (PBB), chronic suppurative lung disease (CSLD) or bronchiectasis. S. pneumoniae lower airway infection was detected in 95 children: 27% with PBB and 20% with CSLD/bronchiectasis. Most (91%) children were vaccinated with ⩾2 doses of 7-valent, 10-valent or 13-valent pneumococcal conjugate vaccine. Paired NP and BAL serotype distributions were very similar; prevalent serotypes (>10 isolates) were 19A (9%), 19F, 6C, 35B, 15B, 16F, 15A, 15C, 23A, 23F and 11A. For 21 serotypes found in both NP and BAL specimens, ORs for infection were low; range 0.46 (serotype 23B) to 2.15 (serotype 6A). In the 2008-2013 surveillance studies, NP swabs were collected from 1565 asymptomatic children; 74% were pneumococcal carriers. For 21 of 22 serotypes found in both control NP swabs and BAL specimens, ORs for infection were similarly low; range 0.33 (serotype 23B) to 3.29 (serotype 22F); none was significantly different from 1. The exception was serotype 7B with OR 8.84 (95% CI 1.46, 38.1).

CONCLUSIONS

Most NP carriage serotypes have a similar propensity to cause lower airway infection in children with suppurative lung diseases. Further development of pneumococcal vaccines is needed to prevent non-invasive disease caused by commonly carried serotypes.

Geographic consistency in dominant, non-typeable Haemophilus influenzae genotypes colonising four distinct Australian paediatric groups: a cohort study

Non-typeable Haemophilus influenzae (NTHi)-associated ear and respiratory diseases (including pneumonia) represent a major health burden in many parts of the world. NTHi strains retrieved from the upper airways commonly reflect those found in the lower airways. Despite growing genomic and genotyping data on NTHi, there remains a limited understanding of global and regional NTHi population structures. The aim of this study was to determine whether nasopharyngeal carriage in four Australian paediatric groups at varying risk of NTHi colonisation was dominated by the same NTHi genotypes. Genotyping data generated by PCR-ribotyping were evaluated for 3070 NTHi isolates colonising the nasopharynges of Aboriginal and non-Aboriginal children enrolled in four longitudinal studies in three separate urban and remote regions of Australia. Several NTHi PCR-ribotypes dominated in nasopharyngeal carriage, irrespective of study setting. Principal coordinates analysis confirmed a cluster of common PCR-ribotypes among all cohorts. In conclusion, we identified dominant PCR-ribotypes common to geographically disparate Australian paediatric populations. Future genomic analyses will shed further light on the precise factors underlying the dominance of certain NTHi strains in nasopharyngeal carriage.

Cord blood vitamin D and the risk of acute lower respiratory infection in Indigenous infants in the Northern Territory

OBJECTIVES

To assess vitamin D status in Indigenous mothers and infants in the Northern Territory, and to determine whether cord blood vitamin D levels are correlated with the risk of infant hospitalisation for acute lower respiratory infection (ALRI).

DESIGN AND PARTICIPANTS

Within a nested cohort of 109 Indigenous mother-infant pairs recruited between 2006 and 2011, we used liquid chromatography-mass spectrometry to measure vitamin D (25(OH)D3) levels in maternal blood during pregnancy (n = 33; median gestation, 32 weeks [range, 28-36 weeks]) and at birth (n = 106; median gestation, 39 weeks [range, 34-41 weeks]), in cord blood (n = 84; median gestation, 39 weeks [range, 36-41 weeks]), and in infant blood at age 7 months (n = 37; median age, 7.1 months [range, 6.6-8.1 months]).

MAIN OUTCOME MEASURE

ALRI hospitalisations during the first 12 months of infancy, identified using International Classification of Diseases coding (J09-J22, A37-A37.9).

RESULTS

Compared with mean 25(OH)D3 levels in maternal blood during pregnancy (104 nmol/L), mean levels were 23% lower in maternal blood at birth (80 nmol/L) and 48% lower in cord blood samples (54 nmol/L). The mean cord blood 25(OH)D3 concentration in seven infants subsequently hospitalised for an ALRI was 37 nmol/L (95% CI, 25-48 nmol/L), lower than the 56 nmol/L (95% CI, 51-61 nmol/L) in the 77 infants who were not hospitalised with an ALRI (P = 0.025).

CONCLUSIONS

Cord blood 25(OH)D3 concentrations were about half those in maternal blood during the third trimester of pregnancy (about 7 weeks earlier). Most cord blood levels (80%) were classified as vitamin D insufficient (< 75 nmol/L) by existing guidelines, and were lower among infants who were subsequently hospitalised with an ALRI.

Respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough

Identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. Flexible bronchoscopy with bronchoalveolar lavage (BAL) is used to obtain lower-airway specimens in young children. The first lavage (lavage-1) is typically used for bacterial culture. However, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. BAL fluid was collected from two sequential lavages of the same lobe in 79 children enrolled in our prospective studies of chronic cough. The respiratory bacteria Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and Haemophilus parainfluenzae were isolated and identified using standard published methods. H. influenzae was differentiated from Haemophilus haemolyticus using PCR assays. Lower-airway infection was defined as ≥ 104 c.f.u. ml- 1 BAL fluid. We compared cultivable bacteria from lavage-1 with those from the second lavage (lavage-2) using the κ statistic. Lower-airway infections by any pathogen were detected in 46% of first lavages and 39% of second lavages. Detection was similar in both lavages for all pathogens; the κ statistic was 0.7-0.8 for all bacteria except H. parainfluenzae. Of all infections detected in either lavage, 90% were detected in lavage-1 and 78  in lavage-2. However, culture of lavage-2 identified infections that would have been missed in 8% of children, including infections by additional Streptococcus pneumoniae serotypes. Our findings support the continued use of lavage-1 for bacterial culture; however, culture of lavage-2 may yield additional identifications of bacterial pathogens in lower-airway infections.

The microbiome of otitis media with effusion in Indigenous Australian children

INTRODUCTION

Indigenous Australian children have a high prevalence of otitis media with effusion (OME) and associated conductive hearing loss. Only three microbiological studies of middle ear fluid (MEF) from Indigenous Australian children with OME have been reported. All of these were reliant on culture or species-specific PCR assays. The aim of this study was to characterise the middle ear fluid (MEF), adenoid and nasopharyngeal (NP) microbiomes of Indigenous Australian children, using culture-independent 16S rRNA gene sequencing.

METHODS

MEF, NP swabs and adenoid specimens were collected from 11 children in the Alice Springs region of Central Australia. Bacterial communities in these specimens were characterised using 16S rRNA gene sequencing.

RESULTS

The microbiota in MEF samples were dominated (>50% relative abundance) by operational taxonomic units (OTUs) consistent with Alloiococcus otitidis (6/11), Haemophilus influenzae (3/11) or Streptococcus sp. (specifically, Mitis group streptococci which includes Streptococcus pneumoniae) (1/11). Anatomical site selectivity was indicated by the presence of a single conserved Haemophilus OTU in 7/11 MEF samples. In comparison, there were ten distinct Haemophilus OTUs observed across the NP and adenoid samples. Despite significant differences between the MEF and NP/adenoid microbiomes, Streptococcus sp., H. influenzae and Moraxella catarrhalis OTUs were common to all sample types. Co-occurrence of classical otopathogens in paired MEF and NP/Adenoid samples is consistent with earlier culture-based studies.

CONCLUSION

These data highlight the need to further assess H. influenzae traits important in otitis media and to understand the role of canal flora, especially A. otitidis, in populations with a high prevalence of tympanic membrane perforation.

Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen

Background

Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance, accurate identification of H. influenzae is a non-trivial endeavour. H. haemolyticus can be misidentified as H. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. On the molecular level, frequent genetic exchange amongst Haemophilus spp. has confounded accurate identification of H. influenzae, leading to both false-positive and false-negative results with existing speciation assays.

Results

Whole-genome single-nucleotide polymorphism data from 246 closely related global Haemophilus isolates, including 107 Australian isolate genomes generated in this study, were used to construct a whole-genome phylogeny. Based on this phylogeny, H. influenzae could be differentiated from closely related species. Next, a H. influenzae-specific locus, fucP, was identified, and a novel TaqMan real-time PCR assay targeting fucP was designed. PCR specificity screening across a panel of clinically relevant species, coupled with in silico analysis of all species within the order Pasteurellales, demonstrated that the fucP assay was 100 % specific for H. influenzae; all other examined species failed to amplify.

Conclusions

This study is the first of its kind to use large-scale comparative genomic analysis of Haemophilus spp. to accurately delineate H. influenzae and to identify a species-specific molecular signature for this species. The fucP assay outperforms existing H. influenzae targets, most of which were identified prior to the next-generation genomics era and thus lack validation across a large number of Haemophilus spp. We recommend use of the fucP assay in clinical and research laboratories for the most accurate detection and diagnosis of H. influenzae infection and colonisation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1857-x) contains supplementary material, which is available to authorized users.

Detection of biofilm in bronchoalveolar lavage from children with non-cystic fibrosis bronchiectasis

BACKGROUND

The presence of Pseudomonas aeruginosa biofilms in lower airway specimens from cystic fibrosis (CF) patients is well established. To date, biofilm has not been demonstrated in bronchoalveolar lavage (BAL) from people with non-CF bronchiectasis. The aim of this study was to determine (i) if biofilm was present in BAL from children with and without bronchiectasis, and (ii) if biofilm detection differed between sequentially collected BAL.

METHODS

Testing for biofilm in two sequentially collected BAL from children with and without bronchiectasis was done using BacLight™ live-dead staining and lectin staining for extracellular polymeric biofilm matrices. Bacterial culture and cytological measures were performed on the first and second lavages, respectively. Clinically important BAL infection was defined as >10⁴  cfu of respiratory pathogens/ml BAL.

RESULTS

Biofilm was detected in BAL from seven of eight (87.5%) children with bronchiectasis (aged 0.8-6.9 years), but was not detected in any of three controls (aged 1.3-8.6 years). The biofilms contained both live and dead bacteria irrespective of antibiotic use prior to bronchoscopy. Biofilm was detected more frequently in the second lavage than the first. Three of the seven biofilm-positive BAL were culture-positive for respiratory pathogens at clinically important levels.

CONCLUSIONS

Biofilm is present in BAL from children with non-CF bronchiectasis even when BAL-defined clinically important infection was absent. Studies to characterize lower airway biofilms and determine how biofilm contributes to bronchiectasis disease progression and treatment outcomes are necessary. Pediatr Pulmonol. 2015; 50:284-292. © 2014 Wiley Periodicals, Inc.

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

BACKGROUND

The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spurious signal that is characteristic of samples with low levels of bacteria and high levels of non-bacterial DNA. We have developed a workflow based on the paired-end read Illumina MiSeq-based approach, which enables significant improvement in data quality, post-sequencing. We demonstrate the efficacy of this methodology through its application to paediatric upper-respiratory samples from several anatomical sites.

RESULTS

A workflow for processing sequence data was developed based on commonly available tools. Data generated from different sample types showed a marked variation in levels of non-bacterial signal and 'contaminant' bacterial reads. Significant differences in the ability of reference databases to accurately assign identity to operational taxonomic units (OTU) were observed. Three OTU-picking strategies were trialled as follows: de novo, open-reference and closed-reference, with open-reference performing substantially better. Relative abundance of OTUs identified as potential reagent contamination showed a strong inverse correlation with amplicon concentration allowing their objective removal. The removal of the spurious signal showed the greatest improvement in sample types typically containing low levels of bacteria and high levels of human DNA. A substantial impact of pre-filtering data and spurious signal removal was demonstrated by principal coordinate and co-occurrence analysis. For example, analysis of taxon co-occurrence in adenoid swab and middle ear fluid samples indicated that failure to remove the spurious signal resulted in the inclusion of six out of eleven bacterial genera that accounted for 80% of similarity between the sample types.

CONCLUSIONS

The application of the presented workflow to a set of challenging clinical samples demonstrates its utility in removing the spurious signal from the dataset, allowing clinical insight to be derived from what would otherwise be highly misleading output. While other approaches could potentially achieve similar improvements, the methodology employed here represents an accessible means to exclude the signal from contamination and other artefacts.

Vitamin D insufficiency among hospitalised children in the Northern Territory

AIM

Acute lower respiratory infections (ALRIs) are the most common reason for hospitalisation of young children in the Northern Territory of Australia. International studies have linked vitamin D deficiency with increased risk of ALRI in paediatric populations, but this has not been explored in tropical regions such as the Top End of the Northern Territory. The aim of this study is to determine the prevalence of vitamin D insufficiency among children hospitalised with ALRI in the Northern Territory.

METHODS

Vitamin D serum metabolite (25OHD3) levels were retrospectively measured using liquid chromatography-mass spectrometry in 74 children (64% male; 57% Indigenous) aged less than 3 years admitted to Royal Darwin Hospital in the Northern Territory of Australia between May 2008 and May 2010.

RESULTS

There were 44 (59%) ALRI-classified hospitalisations and 30 (41%) non-ALRI-classified hospitalisations. The most common ALRI diagnoses were bronchiolitis (n = 22, 30%) and pneumonia (n = 21, 28%), whereas the most common non-ALRI diagnosis was gastroenteritis (n = 20, 27%). Overall, 24/74 (32%) children had 25OHD3 levels <75 nmol/L (insufficiency). For children hospitalised with ALRI, 23% (10/44) had vitamin D insufficiency compared with 47% (14/30) among children hospitalised for other reasons (odds ratio 0.34, 95% confidence interval 0.11-1.03; P = 0.043). Twelve of the 20 (60%) children hospitalised for gastroenteritis had vitamin D insufficiency.

CONCLUSIONS

Vitamin D insufficiency was observed in almost one-third of these hospitalised children. Children hospitalised with an ALRI were less likely to have vitamin D insufficiency compared with children hospitalised for other conditions (predominantly gastroenteritis).

Adenovirus species C is associated with chronic suppurative lung diseases in children

Background. The role of human adenoviruses (HAdVs) in chronic respiratory disease pathogenesis is recognized. However, no studies have performed molecular sequencing of HAdVs from the lower airways of children with chronic endobronchial suppuration. We thus examined the major HAdV genotypes/species, and relationships to bacterial coinfection, in children with protracted bacterial bronchitis (PBB) and mild bronchiectasis (BE).

Methods. Bronchoalveolar lavage (BAL) samples of 245 children with PBB or mild (cylindrical) BE were included in this prospective cohort study. HAdVs were genotyped (when possible) in those whose BAL had HAdV detected (HAdV⁺). Presence of bacterial infection (defined as ≥10⁴ colony-forming units/mL) was compared between BAL HAdV⁺ and HAdV negative (HAdV⁻) groups. Immune function tests were performed including blood lymphocyte subsets in a random subgroup.

Results. Species C HAdVs were identified in 23 of 24 (96%) HAdV⁺ children; 13 (57%) were HAdV-1 and 10 (43%) were HAdV-2. An HAdV⁺ BAL was significantly associated with bacterial coinfection with Haemophilus influenzae, Moraxella catarrhalis, or Streptococcus pneumoniae (odds ratio [OR], 3.27; 95% confidence interval, 1.38–7.75; P = .007) and negatively associated with Staphylococcus aureus infection (P = .03). Young age was related to increased rates of HAdV⁺. Blood CD16 and CD56 natural killer cells were significantly more likely to be elevated in those with HAdV (80%) compared with those without (56.1%) (P = .027).

Conclusions. HAdV-C is the major HAdV species detected in the lower airways of children with PBB and BE. Younger age appears to be an important risk factor for HAdV⁺ of the lower airways and influences the likelihood of bacterial coinfection.

Dominance of Haemophilus influenzae in ear discharge from Indigenous Australian children with acute otitis media with tympanic membrane perforation

Background

Indigenous Australian children living in remote communities experience high rates of acute otitis media with tympanic membrane perforation (AOMwiP). Otitis media in this population is associated with dense nasopharyngeal colonization of three primary otopathogens; Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis. Little is known about the relative abundance of these pathogens during infection. The objective of this study was to estimate the abundance and concordance of otopathogens in ear discharge and paired nasopharyngeal swabs from children with AOMwiP (discharge of not more than 6 weeks’ duration and perforation size <2%).

Methods

Culture and quantitative PCR (qPCR) estimation of H. influenzae, S. pneumoniae, M. catarrhalis and total bacterial load were performed on paired nasopharyngeal and ear discharge swabs from 55 Indigenous children with AOMwiP aged 3.5 – 45.6 months and resident in remote communities.

Results

By culture, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 80%, 84% and 91% of nasopharyngeal swabs, and 49%, 33% and 4% of ear discharge swabs, respectively. Using qPCR, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 82%, 82%, and 93% of nasopharyngeal swabs, and 89%, 41% and 18% of ear discharge swabs, respectively. Relative abundance of H. influenzae in ear discharge swabs was 0-68% of the total bacterial load (median 2.8%); whereas S. pneumoniae and M. catarrhalis relative abundances were consistently <2% of the total bacterial load. S. pneumoniae and M. catarrhalis abundances were significantly lower in ear discharge compared with nasopharyngeal swabs (p = 0.001, p < 0.001); no significant difference was observed in H. influenzae mean abundance at the two sites.

Conclusions

H. influenzae was the dominant otopathogen detected in ear discharge swabs collected from children with AOMwiP. High prevalence and abundance of S. pneumoniae and M. catarrhalis in the nasopharynx did not predict ear discharge prevalence and abundances of these pathogens. PCR was substantially more sensitive than culture for ear discharge, and a necessary adjunct to standard microbiology. Quantitative methods are required to understand species abundance in polymicrobial infections and may be needed to measure accurately the microbiological impact of interventions and to provide a better understanding of clinical failure in these children.

Longitudinal nasopharyngeal carriage and antibiotic resistance of respiratory bacteria in indigenous Australian and Alaska native children with bronchiectasis

Background

Indigenous children in Australia and Alaska have very high rates of chronic suppurative lung disease (CSLD)/bronchiectasis. Antibiotics, including frequent or long-term azithromycin in Australia and short-term beta-lactam therapy in both countries, are often prescribed to treat these patients. In the Bronchiectasis Observational Study we examined over several years the nasopharyngeal carriage and antibiotic resistance of respiratory bacteria in these two PCV7-vaccinated populations.

Methods

Indigenous children aged 0.5–8.9 years with CSLD/bronchiectasis from remote Australia (n = 79) and Alaska (n = 41) were enrolled in a prospective cohort study during 2004–8. At scheduled study visits until 2010 antibiotic use in the preceding 2-weeks was recorded and nasopharyngeal swabs collected for culture and antimicrobial susceptibility testing. Analysis of respiratory bacterial carriage and antibiotic resistance was by baseline and final swabs, and total swabs by year.

Results

Streptococcus pneumoniae carriage changed little over time. In contrast, carriage of Haemophilus influenzae declined and Staphylococcus aureus increased (from 0% in 2005–6 to 23% in 2010 in Alaskan children); these changes were associated with increasing age. Moraxella catarrhalis carriage declined significantly in Australian, but not Alaskan, children (from 64% in 2004–6 to 11% in 2010). While beta-lactam antibiotic use was similar in the two cohorts, Australian children received more azithromycin. Macrolide resistance was significantly higher in Australian compared to Alaskan children, while H. influenzae beta-lactam resistance was higher in Alaskan children. Azithromycin use coincided significantly with reduced carriage of S. pneumoniae, H. influenzae and M. catarrhalis, but increased carriage of S. aureus and macrolide-resistant strains of S. pneumoniae and S. aureus (proportion of carriers and all swabs), in a ‘cumulative dose-response’ relationship.

Conclusions

Over time, similar (possibly age-related) changes in nasopharyngeal bacterial carriage were observed in Australian and Alaskan children with CSLD/bronchiectasis. However, there were also significant frequency-dependent differences in carriage and antibiotic resistance that coincided with azithromycin use.

Nasopharyngeal microbial interactions in the era of pneumococcal conjugate vaccination

The nasopharynx of children is often colonised by microorganisms such as Streptococcus pneumoniae (the pneumococcus) that can cause infections including pneumonia and otitis media. In this complex environment, bacteria and viruses may impact each other through antagonistic as well as synergistic interactions. Vaccination may alter colonisation dynamics, evidenced by the rise in non-vaccine serotypes following pneumococcal conjugate vaccination. Discovery of an inverse relationship between S. pneumoniae and Staphylococcus aureus carriage generated concern that pneumococcal vaccination could increase S. aureus carriage and disease. Here we review data on co-colonisation of pathogens in the nasopharynx, focusing on S. pneumoniae and the impact of pneumococcal vaccination. Thus far, pneumococcal vaccination has not had a sustained impact on S. aureus carriage but it is associated with an increase in non-typeable Haemophilus influenzae in acute otitis media aetiology. Advances in bacterial and viral detection methodologies have facilitated research in nasopharyngeal microbiology and will aid investigation of potential vaccine-induced changes, particularly when baseline studies can be conducted prior to pneumococcal vaccine introduction.

Quantitative PCR confirms culture as the gold standard for detection of lower airway infection by nontypeable Haemophilus influenzae in Australian Indigenous children with bronchiectasis

Correlation was observed between quantitative PCR and semi-quantitative culture for definition of Haemophilus influenzae infection in bronchoalveolar lavage specimens from 81 children with bronchiectasis. However, qPCR data correlated less well with airway neutrophilia, and supports continued use of culture as the gold standard for defining H. influenzae lower airway infection.

Quantitative PCR of ear discharge from Indigenous Australian children with acute otitis media with perforation supports a role for Alloiococcus otitidis as a secondary pathogen

Background

Otitis media is endemic in remote Indigenous communities of Australia’s Northern Territory. Alloiococcus otitidis is an outer ear commensal and putative middle ear pathogen that has not previously been described in acute otitis media (AOM) in this population. The aims of this study were to determine the presence, antibiotic susceptibility and bacterial load of A. otitidis in nasopharyngeal and ear discharge swabs collected from Indigenous Australian children with AOM with perforation.

Methods

Paired nasopharyngeal and ear discharge swabs from 27 children with AOM with perforation were tested by A. otitidis quantitative PCR (qPCR). Positive swabs were cultured for 21 days. Total and respiratory pathogen bacterial loads in A. otitidis-positive swabs were determined by qPCR.

Results

A. otitidis was detected by qPCR in 11 ear discharge swabs from 10 of 27 (37%) children, but was not detected in paired nasopharyngeal swabs. A. otitidis was cultured from 5 of 11 qPCR-positive swabs from four children. All A. otitidis isolates had minimum inhibitory concentrations consistent with macrolide resistance. All A. otitidis qPCR-positive swabs were culture-positive for other bacteria. A. otitidis bacterial load ranged from 2.2 × 10⁴-1.1 × 10⁸ cells/swab (median 1.8 × 10⁵ cells/swab). The relative abundance of A. otitidis ranged from 0.01% to 34% of the total bacterial load (median 0.7%). In 6 of 11 qPCR-positive swabs the A. otitidis relative abundance was <1% and in 5 of 11 it was between 2% and 34%. The A. otitidis bacterial load and relative abundance measures were comparable to that of Haemophilus influenzae.

Conclusions

A. otitidis can be a dominant species in the bacterial communities present in the ear discharge of Indigenous children with AOM with perforation. The absence of A. otitidis in nasopharyngeal swabs suggests the ear canal as the likely primary reservoir. The significance of A. otitidis at low relative abundance is unclear; however, at higher relative abundance it may be contributing to the associated inflammation. Further studies to better understand A. otitidis as a secondary otopathogen are warranted, particularly in populations at high-risk of progression to chronic suppurative otitis media and where macrolide therapies are being used.

Potential use of serum based quantitative real-time PCR for the detection of pneumonia pathogens in a densely colonised population

Molecular methods offer improvement in the detection of causative pneumonia pathogens, but there are concerns of false positive results. Here we validate quantitative real-time PCR (qPCR) assays for the detection of Streptococcus pneumoniae and Haemophilus influenzae in: (a) spiked serum samples and (b) in matched serum and nasopharyngeal swabs from a population of Indigenous Australian children without pneumonia, but with a high nasopharyngeal carriage prevalence of S. pneumoniae and H. influenzae. Matched sera and nasopharyngeal swabs were selected from Indigenous children less than 5 years of age without a diagnosis of pneumonia. Specimens were assayed by qPCR targeting the lytA and glpQ genes from S. pneumoniae and H. influenzae, respectively. Using qPCR, neither S. pneumoniae nor H. influenzae DNA was detected in serum samples, even after concentration of serum DNA. In matched nasopharyngeal swabs, bacterial load was high with up to 106 cells/ml detected by qPCR. In this cohort of children with a high nasopharyngeal carriage, prevalence and bacterial load of pneumonia pathogens, qPCR on sera would not have produced a false pneumonia diagnosis. Thus, qPCR analysis of sera appears to be an appropriate method to aid aetiological diagnosis of pneumonia in this population.

Viability of respiratory pathogens cultured from nasopharyngeal swabs stored for up to 12 years at -70°C in skim milk tryptone glucose glycerol broth

Nasopharyngeal carriage studies are needed to monitor changes in important bacterial pathogens in response to vaccination and antibiotics. The ability to store original specimens frozen in skim milk tryptone glucose glycerol broth (STGGB) allows additional studies to be conducted without the need for further expensive field collection. Although sub-cultured isolates remain viable in this medium for many years, limited data are available to indicate viability of relatively low numbers of organisms present in nasopharyngeal specimens stored frozen over long periods of time. We conducted several studies whereby swabs stored in STGGB at -70°C for up to 12 years were thawed and aliquots cultured. Recovery of Streptococcus pneumoniae (72% positive from 269 swabs), Haemophilus influenzae (62% from 214) and Moraxella catarrhalis (81% from 162) was not significantly different from the original cultures: 69% (Risk Difference [RD] 3.0, 95% Confidence Interval [CI] -4.7, 10.7), 66% (RD -4.7, 95% CI -13.8, 4.4) and 78% (RD 3.1, 95% CI -5.7, 11.9) positive respectively. There was no trend in recovery from swabs stored for increasing lengths of time. We conclude that studies which rely on the viability of these respiratory pathogens can be conducted using original swabs stored at -70°C for at least 12 years.

A variable region within the genome of Streptococcus pneumoniae contributes to strain-strain variation in virulence

The bacterial factors responsible for the variation in invasive potential between different clones and serotypes of Streptococcus pneumoniae are largely unknown. Therefore, the isolation of rare serotype 1 carriage strains in Indigenous Australian communities provided a unique opportunity to compare the genomes of non-invasive and invasive isolates of the same serotype in order to identify such factors. The human virulence status of non-invasive, intermediately virulent and highly virulent serotype 1 isolates was reflected in mice and showed that whilst both human non-invasive and highly virulent isolates were able to colonize the murine nasopharynx equally, only the human highly virulent isolates were able to invade and survive in the murine lungs and blood. Genomic sequencing comparisons between these isolates identified 8 regions >1 kb in size that were specific to only the highly virulent isolates, and included a version of the pneumococcal pathogenicity island 1 variable region (PPI-1v), phage-associated adherence factors, transporters and metabolic enzymes. In particular, a phage-associated endolysin, a putative iron/lead permease and an operon within PPI-1v exhibited niche-specific changes in expression that suggest important roles for these genes in the lungs and blood. Moreover, in vivo competition between pneumococci carrying PPI-1v derivatives representing the two identified versions of the region showed that the version of PPI-1v in the highly virulent isolates was more competitive than the version from the less virulent isolates in the nasopharyngeal tissue, blood and lungs. This study is the first to perform genomic comparisons between serotype 1 isolates with distinct virulence profiles that correlate between mice and humans, and has highlighted the important role that hypervariable genomic loci, such as PPI-1v, play in pneumococcal disease. The findings of this study have important implications for understanding the processes that drive progression from colonization to invasive disease and will help direct the development of novel therapeutic strategies.

The bacteriology of lower respiratory infections in Papua New Guinean and Australian indigenous children

Indigenous children in Australia and children in Papua New Guinea (PNG) share a high burden of respiratory disease. In PNG the focus has been on pneumonia as a major cause of mortality. While pneumonia incidence remains high in Australian Indigenous children, improved access to better health care has resulted in reduced mortality. However, severe and recurrent pneumonia are risk factors for chronic suppurative lung disease or bronchiectasis in Australian Indigenous children. Bronchiectasis is associated with significant morbidity, and early death in adulthood. This paper includes an outline of the disease manifestations of acute and chronic lower respiratory infections. The main bacterial pathogens involved in pneumonia, bronchiolitis, bronchitis and bronchiectasis have been determined. Capsular organisms such as Streptococcus pneumoniae and Haemophilus influenzae type b are more often implicated in acute infections, while chronic infections are frequently associated with nontypeable (noncapsular) H. influenzae. Moraxella catarrhalis is more often isolated from very young children. Possible reasons for the high burden of respiratory disease in Papua New Guinean children and Australian Indigenous (primarily Aboriginal) children include early and dense colonization with multiple species and strains of respiratory pathogens. There is a role for vaccines in preventing lower respiratory infection.

Improving the aetiological diagnosis of bacterial pneumonia and meningitis in Papua New Guinea

Bacterial pneumonia and meningitis are major causes of childhood mortality in Papua New Guinea (PNG). Laboratory techniques for detection of bacterial pathogens have improved in the last decade, particularly molecular techniques that can be applied to culture-negative samples. With adequate training and support, a number of these techniques are readily available to research staff in PNG. In this article we summarize previous studies on the aetiology of pneumonia and meningitis in PNG, describe current diagnostic approaches and discuss available diagnostic tools to enhance surveillance of bacterial pneumonia and meningitis.

Single-dose azithromycin versus seven days of amoxycillin in the treatment of acute otitis media in Aboriginal children (AATAAC): a double blind, randomised controlled trial

OBJECTIVE

To compare the clinical effectiveness of single-dose azithromycin treatment with 7 days of amoxycillin treatment among Aboriginal children with acute otitis media (AOM) in rural and remote communities in the Northern Territory.

DESIGN, SETTING AND PARTICIPANTS

Aboriginal children aged 6 months to 6 years living in 16 rural and remote communities were screened for AOM. Those diagnosed with AOM were randomly allocated to receive either azithromycin (30 mg/kg as a single dose) or amoxycillin (50mg/kg/day in two divided doses for a minimum of 7 days). We used a double-dummy method to ensure blinding. Our study was conducted from 24 March 2003 to 20 July 2005.

MAIN OUTCOME MEASURES

Failure to cure AOM by the end of therapy; nasal carriage of Streptococcus pneumoniae and non-capsular Haemophilus influenzae (NCHi).

RESULTS

We followed 306 of 320 children (96%) allocated to the treatment groups. Single-dose azithromycin did not reduce (or increase) the risk of clinical failure (50% failure rate [82/165]) compared with amoxycillin (54% failure rate [83/155]) (risk difference [RD], - 4% [95% CI, - 15% to 7%]; P = 0.504). Compared with amoxycillin, azithromycin significantly reduced the proportion of children with nasal carriage of S. pneumoniae (27% v 63%; RD, - 36% [95% CI, - 47% to - 26%]; P < 0.001) and NCHi (55% v 85%; RD, - 30% [95% CI, - 40% to - 21%]; P < 0.001). Nasal carriage of S. pneumoniae with intermediate or full resistance to penicillin was lower (but not significantly so) in the azithromycin group (10% v 16%), but this group had significantly increased carriage of azithromycin-resistant S. pneumoniae (10% v 3%; RD, 7% [95% CI, 0.1% to 12%]; P = 0.001). Carriage of beta-lactamase-producing NCHi was about 5% in both groups.

CONCLUSION

Although azithromycin reduced nasal carriage of S. pneumoniae and NCHi, clinical failure was high in both treatment groups. The possibility of weekly azithromycin treatment in children with persistent AOM should be evaluated.

TRIAL REGISTRATION

Australian Clinical Trials Registry ACTRN 12609000691246.

Emerging pneumococcal carriage serotypes in a high-risk population receiving universal 7-valent pneumococcal conjugate vaccine and 23-valent polysaccharide vaccine since 2001

Background

In Australia in June 2001, a unique pneumococcal vaccine schedule commenced for Indigenous infants; seven-valent pneumococcal conjugate vaccine (7PCV) given at 2, 4, and 6 months of age and 23-valent pneumococcal polysaccharide vaccine (23PPV) at 18 months of age. This study presents carriage serotypes following this schedule.

Methods

We conducted cross sectional surveys of pneumococcal carriage in Aboriginal children 0 to 6 years of age living in remote Aboriginal communities (RACs) in 2003 and 2005. Nasal secretions were collected and processed according to published methods.

Results

902 children (mean age 25 months) living in 29 communities in 2003 and 818 children (mean age 35 months) in 17 communities in 2005 were enrolled. 87% children in 2003 and 96% in 2005 had received two or more doses of 7PCV. From 2003 to 2005, pneumococcal carriage was reduced from 82% to 76% and reductions were apparent in all age groups; 7PCV-type carriage was reduced from 11% to 8%, and 23PPV-non-7PCV-type carriage from 31% to 25% respectively. Thus non-23PPV-type carriage increased from 57% to 67%. All these changes were statistically significant, as were changes for some specific serotypes. Shifts could not be attributed to vaccination alone. The top 10 of 40 serotypes identified were (in descending order) 16F, 19A, 11A, 6C, 23B, 19F, 6A, 35B, 6B, 10A and 35B. Carriage of penicillin non-susceptible (MIC > = 0.12 μg/mL) strains (15% overall) was detected in serotypes (descending order) 19A, 19F, 6B, 16F, 11A, 9V, 23B, and in 4 additional serotypes. Carriage of azithromycin resistant (MIC > = 2 μg/mL) strains (5% overall), was detected in serotypes (descending order) 23B, 17F, 9N, 6B, 6A, 11A, 23F, and in 10 additional serotypes including 6C.

Conclusion

Pneumococcal carriage remains high (~80%) in this vaccinated population. Uptake of both pneumococcal vaccines increased, and carriage was reduced between 2003 and 2005. Predominant serotypes in combined years were 16F, 19A, 11A, 6C and 23B. Antimicrobial non-susceptibility was detected in these and 17 additional serotypes. Shifts in serotype-specific carriage suggest a need more research to clarify the association between pneumococcal vaccination and carriage at the serotype level.

The clinical course of acute otitis media in high-risk Australian Aboriginal children: a longitudinal study

BACKGROUND

It is unclear why some children with acute otitis media (AOM) have poor outcomes. Our aim was to describe the clinical course of AOM and the associated bacterial nasopharyngeal colonisation in a high-risk population of Australian Aboriginal children.

METHODS

We examined Aboriginal children younger than eight years who had a clinical diagnosis of AOM. Pneumatic otoscopy and video-otoscopy of the tympanic membrane (TM) and tympanometry was done every weekday if possible. We followed children for either two weeks (AOM without perforation), or three weeks (AOM with perforation), or for longer periods if the infection persisted. Nasopharyngeal swabs were taken at study entry and then weekly.

RESULTS

We enrolled 31 children and conducted a total of 219 assessments. Most children had bulging of the TM or recent middle ear discharge at diagnosis. Persistent signs of suppurative OM (without ear pain) were present in most children 7 days (23/30, 77%), and 14 days (20/26, 77%) later. Episodes of AOM did not usually have a sudden onset or short duration. Six of the 14 children with fresh discharge in their ear canal had an intact or functionally intact TM. Perforation size generally remained very small (<2% of the TM). Healing followed by re-perforation was common. Ninety-three nasophyngeal swabs were taken. Most swabs cultured Streptococcus pneumoniae (82%), Haemophilus influenzae (71%), and Moraxella catarrhalis (95%); 63% of swabs cultured all three pathogens.

CONCLUSION

In this high-risk population, AOM was generally painless and persistent. These infections were associated with persistent bacterial colonisation of the nasopharynx and any benefits of antibiotics were modest at best. Systematic follow up with careful examination and review of treatment are required and clinical resolution cannot be assumed.

Ubiquity of putative type III secretion genes among clinical and environmental Burkholderia pseudomallei isolates in Northern Australia

Type III secretion (TTSI) genes of an HRP (hypersensitivity response and pathogenicity)-like locus were present in all 116 Northern Australian Burkholderia pseudomallei isolates tested but were not detected in other common environmental Burkholderia species. PCR of TTS1 genes may prove valuable as a diagnostic test [corrected].

Modelling of endemic carriage of Haemophilus influenzae in Aboriginal infants in Northern Australia

Aboriginal infants and children in rural communities in Northern Australia have high rates of nasopharyngeal carriage of nonencapsulated Haemophilus influenzae (NCHi), with positive swab rates of 76%. In this population, the acquisition of NCHi from soon after birth is associated with the onset of otitis media and with muco-purulent nasal discharge, while the long-term persistence of NCHi carriage is associated with the acquisition and turnover of large numbers of antigenically diverse strains. Mathematical models have been fitted to data on the acquisition and loss of encapsulated strains of H. influenzae and 43 different strains of NCHi in 10 children followed from early infancy for up to 2 years. Subject to plausible assumptions, the preferred model estimated the mean time to acquisition of a H. influenzae strain to be 7 days after first becoming exposed after birth. For an infant already carrying H. influenzae, each additional strain was acquired after a mean waiting period of 45 days. On average, 1.50 different strains of H. influenzae were detected in four colonies routinely typed from each positive swab, but it was estimated that another 2.55 strains were 'hidden' behind these more frequent strains. With an average of 4.05 strains per carrier, it was estimated that each strain was carried for an average of 137 days, although detected on only 37% of occasions. Thus we have developed mathematical models that provide estimates for duration of colonisation, time to colonisation, and number of colonising strains in a population in which H. influenzae is highly endemic, characterised by sequential and concurrent carriage of multiple strains in each infant.

Low genetic diversity of Haemophilus influenzae type b compared to nonencapsulated H. influenzae in a population in which H. influenzae is highly endemic

Immunization with Haemophilus influenzae type b (Hib) conjugate polysaccharide vaccines has dramatically reduced Hib disease worldwide. As in other populations, nasopharyngeal carriage of Hib declined markedly in Aboriginal infants following vaccination, although carriage has not been entirely eliminated. In this study, we describe the genetic characteristics and the carriage dynamics of longitudinal isolates of Hib, characterized by using several typing methods. In addition, carriage rates of nonencapsulated H. influenzae (NCHi) are high, and concurrent colonization with Hib and NCHi is common; we also observed NCHi isolates which were genetically similar to Hib. There is a continuing need to promote Hib immunization and monitor H. influenzae carriage in populations in which the organism is highly endemic, not least because of the possibility of genetic exchange between Hib and NCHi strains in such populations.