Muhamed-Kheir Taha

Background: Haemophilus influenzae resistance to β-lactams is mediated by β-lactamase and amino acid alterations in penicillin-binding protein 3 encoded by ftsI gene, which shows incomplete phenotype–genotype concordance. Objectives: To develop and evaluate a genomic classification framework to predict clinically relevant β-lactam resistance categories. Methods: We analysed 5288 H. influenzae isolates collected in eight European countries and Canada. Among these, 4833 isolates had phenotypic β-lactam susceptibility that were classified into three categories: susceptible to amoxicillin (AMX), resistant to AMX but susceptible to cefotaxime and resistant to both. A 621 bp DNA fragments of the whole ftsI gene (between codons 326 and 532) were analysed to construct category-specific k-mer vocabulary and an allele classifier using Python scripts. Performance was assessed using independent allele validation and agreement with phenotypic classification was evaluated using Cohen’s κ coefficient. An additional 455 isolates lacked phenotypic data and were used for external genomic application. Results: Forty-seven frequent ftsI alleles and 34 additional alleles were used for the implementation and the refinement of the vocabulary. Subsequently, 23 other alleles were used for independent allele validation and resulted in correctly predicted resistance categories for 21 alleles (accuracy 91.3%). Agreement with phenotypic classification was high (Cohen’s κ 0.853; weighted κ 0.880). Application of the classifier to 455 UK isolates predicted resistance distributions consistent with those observed in phenotypically characterized datasets. Conclusions: A recurrence-filtered k-mer–based vocabulary provides a promising standardized genomic framework that complements phenotypic AST, particularly when phenotypic testing is unavailable, incomplete or heterogeneous.

Abdominal symptoms are increasingly reported in invasive meningococcal disease (IMD), but the underlying mechanisms remain unclear. We aimed to explore the

Background/Objectives: Re-emergence of Haemophilus influenzae serotype b (Hib) was reported in several European countries. We aimed to characterize the age distribution of H. influnezae carriage before and after Hib vaccination. Methods: We conducted a systematic review and meta-analysis to reassess H. influenzae carriage dynamics in the pre- and post-Hib vaccination eras, focusing on age-specific patterns in childhood. Searches were performed with no date restriction and included PubMed/MEDLINE, Scopus, Web of Science, WHO Global Index Medicus, and the Cochrane Library. Eligible studies reported nasopharyngeal and/or oropharyngeal carriage prevalence and serotype distribution. Pooled estimates with 95% confidence intervals (CIs) were calculated using random-effects models, with age-stratified analyses. Results: Twenty-two studies were included (12 pre- and 10 post-Hib vaccination). Pre-vaccination, pooled H. influenzae carriage prevalence was 24.3% (95% CI, 18.9–30.7%), including 6% (95% CI, 3.4–12.8%) for Hib and 17.5% (95% CI, 12.6–23.9%) for non–type b strains. Post-vaccination, overall carriage remained similar (21.8%; 95% CI, 14.6–31.2%), but Hib carriage declined markedly to 0.67% (95% CI, 0.26–1.71%), while non–type b strains predominated (16.7%; 95% CI, 10.4–25.6%). Meta-analysis showed that carriage peaked around 4–5 years of age and persisted into later childhood. Conclusions: Hib vaccination has reduced Hib carriage, but overall H. influenzae carriage persists due to non–type b strains. Age-related persistence of carriage may have implications for herd protection, particularly in the context of evolving vaccination schedules with early childhood boosters. Continued surveillance integrating carriage and immunological data is needed to inform optimization of vaccination strategies.

Background: Invasive meningococcal disease (IMD) remains a rare but severe condition associated with high mortality and a significant risk of long-term sequelae. Despite global vaccination efforts, the epidemiology of Neisseria meningitidis continues to evolve, with serogroup B (MenB) representing the predominant cause of IMD in many high-income countries. Methods: This consensus document reviews current evidence on MenB epidemiology and the role of the multicomponent meningococcal serogroup B vaccine (4CMenB), with a focus on immunogenicity, strain coverage, real-world effectiveness, and remaining challenges. Results: Protein-based MenB vaccines have overcome the limitations of polysaccharide approaches, demonstrating robust immunogenicity across age groups. Real-world data confirm substantial vaccine effectiveness, particularly in infant immunization programs and outbreak settings, with significant reductions in disease incidence. For example, in England in the 3 years after vaccine introduction, MenB IMD incidence declined by 75% in immunized infants compared to unvaccinated controls. Adjusted vaccine efficacy was 52.7% after the two-dose primary series and 59.1% following the booster dose, highlighting the contribution of the booster. However, protection is influenced by antigenic variability among circulating strains, resulting in incomplete and geographically variable coverage. In addition, antibody waning over time and the limited impact on nasopharyngeal carriage reduce the potential for long-term and indirect protection. These factors highlight the need to optimize vaccination strategies, including the timing of booster doses, particularly in adolescents, and the role of vaccination in different epidemiological contexts. In this regard, it is not precisely defined whether infants who were immunized in the first year of life need a booster dose in the preschool period, especially in countries with a high incidence of MenB disease. Moreover, it is not established whether and when adolescents who were vaccinated both in infancy and during the preschool period need a booster dose. Economic considerations and variability in national immunization policies further contribute to heterogeneity in vaccine implementation. Emerging evidence suggests possible cross-protection against other meningococcal serogroups and Neisseria gonorrhoeae, although findings remain inconsistent across different risk groups and do not allow us to recommend 4CMenB vaccine beyond MenB IBD prevention. Conclusions: 4CMenB is an effective tool for preventing MenB IMD, although further studies are needed. Future strategies should prioritize age-targeted boosting and enhanced genomic surveillance to maximize impact.

Background: Prediction of antimicrobial resistance from genomic data could support phenotypic susceptibility testing for large-scale surveillance. In Haemophilus influenzae, resistance to β-lactam antibiotics is mediated by β- lactamase and amino acid alterations in penicillin-binding protein 3 (PBP3) encoded by ftsI gene. But the latter shows incomplete phenotype- genotype concordance, limiting alteration-based resistance prediction. We developed and evaluated a genomic classification framework to predict clinically relevant β-lactam resistance categories.Methods: We analysed 5,288 H. influenzae isolates collected in eight European countries and Canada. Among these, 4,833 isolates had phenotypic β-lactam susceptibility data and 455 isolates from the United Kingdom lacked phenotypic data and were used for independent testing. The ftsI alleles based on a 621 bp DNA fragment of the whole ftsI gene were analysed using a recurrence-filtered genomic model. Training was restricted to ftsI alleles represented by at least 10 isolates from at least three countries. Category-specific k-mer signatures were extracted from ftsI allele sequences and used to build a genomic classifier. Model performance was assessed using independent validation alleles and agreement with phenotypic classification was evaluated using Cohen’s kappa coefficient.Findings: Forty-seven frequent ftsI alleles were used for model implementation. The validation of the model with 23 other alleles resulted in correctly predicted resistance categories for 21 alleles (accuracy 91·3%). Agreement with phenotypic classification was high (Cohen’s κ 0·853; weighted κ 0·880). Misclassifications occurred only between susceptible and aminopenicillins resistance categories, and no alleles conferring resistance to both aminopenicillins and cefotaxime were misclassified. Application of the classifier to 455 UK isolates predicted resistance distributions consistent with those observed in phenotypically characterised datasets.Interpretation: A recurrence-filtered k-mer–based genomic framework enables robust prediction of β-lactam resistance categories in H. influenzae across multinational datasets. This approach may support scalable genomic surveillance of antimicrobial resistance where phenotypic testing is incomplete or heterogeneous.

Background: Non-typeable Haemophilus influenzae (NTHi) is a major cause of acute respiratory tract infections and chronic airway disease, despite its clinical importance, no licensed vaccine is available, largely due to the extensive genetic and antigenic diversity among circulating isolates. We previously identified conserved outer membrane proteins capable of inducing systemic protection against NTHi. Methods: In this study, we evaluated whether a multi-antigen protein vaccine composed of conserved NTHi antigens (P5 and P26) could protect against pulmonary infection. Transgenic mice expressing human transferrin and factor H were immunized via the intraperitoneal or intranasal route and challenged intranasally with a clinical NTHi isolate. Bacterial clearance, antigen-specific mucosal and systemic antibody responses, and recruitment of innate immune cells to the airways were assessed. Results: Both immunization routes significantly reduced bacterial loads compared with controls. Vaccination induced robust mucosal and systemic IgG and IgA responses and enhanced early recruitment of macrophages, monocytes, dendritic cells, and neutrophils to the airways. Intranasal immunization elicited strong mucosal antibody responses and was associated with improved local bacterial clearance. Conclusions: These findings demonstrate that multi-antigen vaccines targeting conserved NTHi proteins can elicit effective mucosal and systemic immunity and represent promising candidates for the prevention against NTHi respiratory infections.

Invasive meningococcal disease (IMD) is classically associated with meningitis and septic shock, but an increasing proportion of cases present with atypical, extra-meningeal manifestations. Following the COVID-19 pandemic, major epidemiological shifts have occurred in France, including a rebound in IMD incidence and changes in circulating serogroups and clonal complexes. We conducted a nationwide retrospective study including all laboratory-confirmed IMD cases analysed by the French National Reference Centre between July 2014 and June 2025. Clinical presentations were coded as non-exclusive entities. Associations with age, serogroup, clonal complex, antimicrobial susceptibility and early mortality (≤72 h) were assessed using descriptive analyses and multivariable logistic regression models. Among 4328 IMD cases, sepsis/shock (61.1%) and meningeal involvement (54.9%) predominated, while atypical forms were frequent, including bacteraemic pneumonia (7.7%), abdominal presentations (8.0%) and arthritis (6.0%). Bacteraemic pneumonia was strongly associated with older age and serogroups W and Y, whereas abdominal forms predominated in adolescents and young adults and were independently associated with serogroups W and Y and clonal complex (cc) cc11. Abdominal presentations were independently associated with early mortality (adjusted odds ratio [aOR] 2.40) but not meningococcal pneumonia. Abdominal presentations were associated with serogroup W (aOR 2.27; 95% CI 1.35–3.83) and serogroup Y (aOR 2.92; 95% CI 1.79–4.75) and with cc11 (aOR 1.77; 95% CI 1.07–2.94). In contrast, cc23 was associated with lower odds of abdominal involvement (aOR 0.42; 95% CI 0.25–0.70). Overall, atypical presentations now represent a substantial proportion of IMD in France and are strongly shaped by age and meningococcal lineage. These findings highlight diagnostic challenges, prognostic heterogeneity and the need for continued integrated clinical, microbiological and genomic surveillance in the context of evolving vaccination strategies.

Background/Objectives: Streptococcus pneumoniae (S. pneumoniae) remains a leading cause of invasive bacterial disease in children worldwide. In Tunisia, the 10-valent pneumococcal conjugate vaccine (PCV10) was introduced into the national immunization program in 2019 for children under two years of age. This study aimed to assess molecular epidemiology, antimicrobial resistance, and vaccine impact on pediatric invasive pneumococcal disease (IPD) before and after PCV10 introduction. Methods: A retrospective study was conducted at Bechir Hamza Children’s Hospital (Tunis, Tunisia) between 2016 and 2022. IPD isolates were characterized by multiplex PCR, antimicrobial susceptibility testing, and whole-genome sequencing. Serotyping was performed using three approaches: multiplex PCR, SeroBA, and a novel cpsB gene-based algorithm. Genomic diversity and population structure were analyzed through molecular typing approaches. Incidence trends were calculated using national population data. Results: Among 150 confirmed IPD isolates, vaccine-type (VT-PCV10) strains decreased significantly from 69.8% before to 47.2% after vaccine introduction (p = 0.013), with serotype 14 showing the largest decline. Genomic analysis identified 43 sequence types and 27 global pneumococcal sequence clusters, reflecting high genetic heterogeneity. The cpsB approach demonstrated strong concordance with PCR (κ = 0.67) and SeroBA (κ = 0.85). The mean annual incidence of VT disease in children aged 0–4 years declined from 1.28 to 0.86 cases per 100,000 population, while non-vaccine serotypes showed a modest increase. Conclusions: PCV10 introduction was associated with a marked reduction in vaccine-type IPD among young children, supporting its public health benefit. Ongoing genomic surveillance remains essential to monitor serotype replacement and antimicrobial resistance in Tunisia.

Invasive meningococcal disease (IMD) in older adults frequently presents with atypical clinical manifestations, including bacteremic pneumonia, often without classical meningeal signs or sepsis, which presents clinicians with diagnostic challenges, and may delay treatment, which contributes to the high mortality observed in older adults. Within the broader resurgence of IMD observed since relaxation of quarantine measures introduced to mitigate the impact of the COVID-19 pandemic, there has been a notable increase in reporting of such atypical cases. The aim of this review is to summarize epidemiological, diagnostic, and treatment aspects of non-meningeal forms of IMD in older patients, with a focus on meningococcal pneumonia. By convention, laboratory confirmation requires N. meningitidis detection by culture, polymerase chain reaction (PCR), or antigen detection. In most cases, presentation of meningococcal pneumonia is similar to that of other forms of community-acquired pneumonia, and cerebrospinal fluid sampling may be non-informative. This places a premium on early blood culture for N. meningitidis, allied with testing of respiratory samples (e.g., broncho-alveolar washes). Many cases are linked to isolates of serogroups Y and W. When confirmed, treatment with third-generation cephalosporins is generally preferred. Chemoprophylaxis and vaccination of close contacts is essential for controlling onward meningococcal disease transmission and prevention of further cases.