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

Rapid and sensitive detection of Haemophilus influenzae using multiple cross displacement amplification combined with CRISPR-Cas12a-based biosensing system

Haemophilus influenzae (H. influenzae, Hi) is an opportunistic bacterium that colonizes the upper respiratory tract of humans and frequently causes meningitis, pneumonia, sepsis, and other severe infections in children. Early and accurate detection of H. influenzae is essential for effective diagnosis and treatment. In this study, we established a novel diagnostic method by integrating the CRISPR-Cas12a detection platform with multiple cross-displacement amplification (MCDA), termed the Hi-MCDA-CRISPR assay. This method offers an efficient and highly precise diagnostic tool for the identification of H. influenzae. In the Hi-MCDA-CRISPR system, the outer membrane protein (OMP) P6 of H. influenzae was pre-amplified using the MCDA assay. The CRISPR-Cas12a-gRNA complex specifically recognized and bound to the amplified gene, forming a ternary complex that triggered the nonspecific trans-cleavage of the Cas12a effector, which subsequently degraded the fluorescent-quenched single-stranded DNA (ssDNA) probes, resulting in the emission of detectable fluorescent signals. After optimizing the reaction conditions, the Hi-MCDA-CRISPR assay proved capable of completing H. influenzae detection within 45 min, including a 40 min MCDA pre-amplification at 62 °C and a 5 min CRISPR-Cas12a cleavage at 37 °C. The assay was able to detect H. influenzae genomic DNA at concentrations as low as 50 fg and showed no cross-reactivity with non-H. influenzae pathogens. Furthermore, the Hi-MCDA-CRISPR assay successfully analyzed 65 clinical sputum samples. These findings suggest that the Hi-MCDA-CRISPR assay is a promising new detection tool for the rapid and reliable diagnosis of H. influenzae infection.

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.