Invasive Pneumococcal Infections Among Moroccan Children: Pneumococcal Vaccination Challenges in the Mature Vaccine Era.

BACKGROUND: Streptococcus pneumoniae, a major contributor to global morbidity and mortality, disproportionately affects children, the elderly, and immunocompromised individuals. Despite vaccination efforts, the challenge of serotype replacement highlights the ongoing struggle against invasive pneumococcal diseases (IPD) in Morocco, emphasizing the need for updated public health strategies and vaccine efficacy assessments. METHODS: This study was conducted at the Ibn Rochd University Hospital Center and the Mohammed VI University Hospital Center from 2019 to 2022, focusing on hospitalized children. It involved the analysis of 74 strains of IPD, assessing the distribution of pneumococcal serotypes and their antibiotic sensitivity in the post-vaccination era. RESULTS: The prevalence of meningitis or meningo-encephalitis was found to be 66% among the study subjects, with the most frequent serotypes being 3, 19A, 6B, 14, and 11. These serotypes varied significantly by age and location. Coverage rates for the pneumococcal conjugate vaccines, PCV-10 and PCV-13, were 20.27% and 56.75%, respectively. Notably, 43% of the strains were non-vaccine serotypes, with serotypes 3 and 19 accounting for 36% of the infections in children, indicating a lack of vaccine efficacy against these types. Additionally, 31.3% of the strains were Penicillin non-susceptible Streptococcus pneumoniae (PNSP), with 81.25% associated with non-vaccine serotypes. CONCLUSIONS: This study highlights the persistence of IPD in Moroccan children, revealing significant challenges despite vaccination efforts. With the reintroduction of PCV-13, concerns about the efficacy against non-vaccine serotypes, particularly 3 and 19A, remain. Continuous surveillance and adaptable vaccination strategies are essential to combat these serotype replacements and ensure the effectiveness of future preventive measures.

A case of necrotic pneumonia caused by Streptococcus pneumoniae was diagnosed using a pneumonia antigen test in BALF: A case report.

RATIONALE: Streptococcus pneumoniae is a common cause of community-acquired pneumonia. Currently, it is believed that many cases of pulmonary infection with negative results on pathogenic testing are caused by S. pneumoniae. There have been no reports of the detection of S. pneumoniae antigen in lung lavage fluid. PATIENT CONCERNS: An elderly male patient with suboptimal fasting blood glucose control and a history of liver abscess. DIAGNOSIS: Chest computed tomography (CT) revealed inflammatory lesions in both lungs with consolidation in the middle lobe of the right lung. INTERVENTIONS: After admission, we collected alveolar lavage fluid in a timely manner and performed pneumococcal antigen detection and etiological testing. OUTCOMES: Prompt testing for pneumococcal antigen in bronchoalveolar lavage fluid yielded a positive clinical outcome. Subsequent analysis via bacterial culture of sputum and next-generation sequencing (mNGS) of BALF definitively identified S. pneumoniae as the etiological agent. Following the analysis of drug sensitivity test results from the identified pathogens, adjustments were made to the antibiotic regimen, and appropriate pus puncture drainage was performed. Subsequently, the patient's condition improved, leading to discharge. CONCLUSION: The identification of S. pneumoniae antigen in bronchoalveolar lavage fluid may facilitate earlier and more precise diagnosis of pneumonia attributed to S. pneumoniae.

Etiologic Profile of the Pneumococcus in Ghana: A Systematic Review.

Objective: To describe the profile of Streptococcus pneumoniae, identify research gaps, and provide in-depth insights into various aspects related to the pathogen. Methods: Google Scholar, PubMed, and ScienceDirect were searched for all studies on the pneumococcus in Ghana that reported on specimen collected, population and sample size, carriage prevalence, incidence of pneumococcal diseases, age of the study population, types of test performed, serotypes identified, antimicrobial susceptibilities, or molecular analysis on the pneumococci for data extraction. Results: Overall, a total of 7954 results were obtained from the three-database search, and of this, 24 articles were selected after screening. A total of 924 isolates were accounted for by serotyping/serogrouping. The prevalence of pneumococcal carriage in Ghana ranges from 11.0% to 51.4% in the population depending on the age (≤ 24-80 years), sickle cell disease (SCD), human immunodeficiency virus (HIV) status, or health of the study population, and penicillin (Pen)-nonsusceptible isolates ranged from 17% to 63%. The prevalence of pneumococci found as the etiologic agent of diseases among Ghanaians ranges from 3.4% for otitis media to 77.7% for meningitis. Overall, the 13-valent pneumococcal conjugate vaccine (PCV) (PCV-13) carriage serotypes accounted for 28.4% of the reported pneumococcal isolates. PCV-13 invasive serotypes accounted for 22.4% of the reported isolates. The non-PCV-13 carriage serotypes accounted for most (43.9%) of the reported isolates. In the pre-PCV-13 era, the nontypeable (NT) (5.5%) and other nonvaccine types (NVTs) (6.4%) were reported as being predominant. The non-PCV-13 serotypes accounted for 4.4% of the reported isolates in invasive pneumococcal disease (IPD) cases. Multidrug resistance (MDR) ranged from 7.8% to 100%. Conclusion: Predicting the invasiveness of pneumococci using molecular typing is the way to go in the future as this will provide answers to the extent to which capsular switching is contributing to the pneumococcal disease burden in Ghana almost a decade after introducing PCV-13. Continuous monitoring of antibiotic resistance patterns at both phenotypic and genotypic levels, along with serotyping and molecular typing, should be a standard practice in the surveillance of pneumococcal disease burden in Ghana.

Molecular epidemiology of Streptococcus pneumoniae isolates causing invasive and noninvasive infection in Ethiopia.

Streptococcus pneumoniae, a medically important opportunistic bacterial pathogen of the upper respiratory tract, is a major public health concern, causing a wide range of pneumococcal illnesses, both invasive and noninvasive. It is associated with significant global morbidity and mortality, including pneumonia, meningitis, sepsis, and acute otitis media. The major purpose of this study was to determine the molecular epidemiology of Streptococcus pneumoniae strains that cause invasive and noninvasive infections in Ethiopia. A prospective study was undertaken in two regional hospitals between January 2018 and December 2019. Whole-genome sequencing was used to analyze all isolates. Serotypes and multilocus sequence types (MLST) were derived from genomic data. The E-test was used for antimicrobial susceptibility testing. Patient samples obtained 54 Streptococcus pneumoniae isolates, 33 from invasive and 21 from noninvasive specimens. Our findings identified 32 serotypes expressed by 25 Global Pneumococcal Sequence Clusters (GPSCs) and 42 sequence types (STs), including 21 new STs. The most common sequence types among the invasive isolates were ST3500, ST5368, ST11162, ST15425, ST15555, ST15559, and ST15561 (2/33, 6% each). These sequence types were linked to serotypes 8, 7 C, 15B/C, 16 F, 10 A, 15B, and 6 A, respectively. Among the noninvasive isolates, only ST15432, associated with serotype 23 A, had numerous isolates (4/21, 19%). Serotype 14 was revealed as the most resistant strain to penicillin G, whereas isolates from serotypes 3, 8, 7 C, and 10 A were resistant to erythromycin. Notably, all serotype 6 A isolates were resistant to both erythromycin and penicillin G. Our findings revealed an abnormally significant number of novel STs, as well as extremely diversified serotypes and sequence types, implying that Ethiopia may serve as a breeding ground for novel STs. Recombination can produce novel STs that cause capsular switching. This has the potential to influence how immunization campaigns affect the burden of invasive pneumococcal illness. The findings highlight the importance of continuous genetic surveillance of the pneumococcal population as a vital step toward enhancing future vaccine design.

Meningitis and encephalitis in Poland in 2022. / Zapalenia opon mózgowo-rdzeniowych i zapalenia mózgu w Polsce w 2022 roku.

INTRODUCTION: Monitoring of meningitis and/or encephalitis regardless of etiology is part of routine epidemiological surveillance in Poland. In this study, we discuss in detail meningitis and/or encephalitis in 2022 caused by Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae, and tick-borne encephalitis virus. OBJECTIVE: The aim of this study was an epidemiological assessment of the occurrence of meningoencephalitis and encephalitis in Poland in 2022, taking into account the analysis of the impact of the COVID-19 pandemic. MATERIAL AND METHODS: To analyze the epidemiological situation of neuroinfections in Poland, we used data sent to NIPH NIH-NRI by the Sanitary and Epidemiological Stations and published in the annual bulletins: "Infectious Diseases and Poisons in Poland in 2022" and "Vaccinations in Poland in 2022" as well as individual epidemiological interviews registered in the EpiBase system. RESULTS: In 2022, a total of 1747 cases of meningitis and/or encephalitis were registered in Poland. This was a 79.4% increase in the number of cases compared to 2021, when 974 cases were recorded. For infections of bacterial etiology, including cases of neuroborreliosis, the number of cases increased by 62.3% . The incidence of meningitis and/or encephalitis of N. meningitidis etiology meningitidis increased by 30.8%, with etiology of H. influenzae compared to 2021 increased by 300%, and for S. pneumoniae by 71.9%. Infections of viral etiology accounted for 52% of all registered cases. There was an increase in their number by 99.1% compared to 2021. Among viral infections, tick-borne encephalitis was the most numerous group, with 466 cases compared to 210 in 2021. SUMMARY AND CONCLUSIONS: The year 2022 showed an overall upward trend in the number of registered cases of bacterial and viral meningitis and/or encephalitis compared to 2021. Still, the observed number of cases of meningitis and/or encephalitis of both bacterial and viral origin remains below the levels observed in the period before the COVID-19 pandemic.

Predictive signature of murine and human host response to typical and atypical pneumonia.

BACKGROUND: Pneumonia due to typical bacterial, atypical bacterial and viral pathogens can be difficult to clinically differentiate. Host response-based diagnostics are emerging as a complementary diagnostic strategy to pathogen detection. METHODS: We used murine models of typical bacterial, atypical bacterial and viral pneumonia to develop diagnostic signatures and understand the host's response to these types of infections. Mice were intranasally inoculated with Streptococcus pneumoniae, Mycoplasma pneumoniae, influenza or saline as a control. Peripheral blood gene expression analysis was performed at multiple time points. Differentially expressed genes were used to perform gene set enrichment analysis and generate diagnostic signatures. These murine-derived signatures were externally validated in silico using human gene expression data. The response to S. pneumoniae was the most rapid and robust. RESULTS: Mice infected with M. pneumoniae had a delayed response more similar to influenza-infected animals. Diagnostic signatures for the three types of infection had 0.94-1.00 area under the receiver operator curve (auROC). Validation in five human gene expression datasets revealed auROC of 0.82-0.96. DISCUSSION: This study identified discrete host responses to typical bacterial, atypical bacterial and viral aetiologies of pneumonia in mice. These signatures validated well in humans, highlighting the conserved nature of the host response to these pathogen classes.

Molecular and phenotypic characterization of Streptococcus pneumoniae isolates in a Japanese tertiary care hospital.

This study aimed to investigate the bacterial characteristics of pneumococcal isolates obtained from a tertiary care hospital in Japan. We analyzed the antimicrobial susceptibility, possession of macrolide resistance genes, pneumococcal serogroup/serotype, and sequence type (ST) of pneumococcal isolates from patients aged 15 years or older between 2011 and 2020 at Nagasaki University Hospital. Of the 73 isolates analyzed, 86.3% showed resistance to macrolides, and 28.8%, 46.6%, and 11.0% harbored mefA, ermB, and both, respectively. Of the isolates possessing ermB, 97.6% showed high levels of macrolide resistance [minimal inhibitory concentration (MIC) range, > 16 µg/mL]. Solithromycin (MIC range, 0.03-0.25 µg/mL), regardless of the presence of macrolide resistance genes, and lascufloxacin (MIC range, 0.06-0.5 µg/mL) showed potent in vitro activity against pneumococci. Serotype 19A was the most prevalent (six isolates), followed by serotypes 10A, 15A, and 15B/C (five isolates each). Four serotypes (11A, 19A, 22F, and 23B) and five STs (36, 99, 433, 558, and 3111) were significantly correlated with the presence of macrolide resistance genes. All four isolates with serotype 11A/ST99 and three isolates with serotype 19A/ST3111 harbored both mefA and ermB. No macrolide resistance genes were detected in either of the two isolates with serotype 22F/ST433, while all ten isolates with serogroup 15 (serotypes 15A and 15B/C, five isolates each) possessed ermB alone. Our study revealed the bacterial characteristics of the pneumococcal isolates obtained from our hospital. In vitro activity of solithromycin and lascufloxacin against these isolates was confirmed.

Effect of pneumococcal conjugate vaccine six years post-introduction on pneumococcal carriage in Ulaanbaatar, Mongolia.

Limited data from Asia are available on long-term effects of pneumococcal conjugate vaccine introduction on pneumococcal carriage. Here we assess the impact of 13-valent pneumococcal conjugate vaccine (PCV13) introduction on nasopharyngeal pneumococcal carriage prevalence, density and antimicrobial resistance. Cross-sectional carriage surveys were conducted pre-PCV13 (2015) and post-PCV13 introduction (2017 and 2022). Pneumococci were detected and quantified by real-time PCR from nasopharyngeal swabs. DNA microarray was used for molecular serotyping and to infer genetic lineage (Global Pneumococcal Sequence Cluster). The study included 1461 infants (5-8 weeks old) and 1489 toddlers (12-23 months old) enrolled from family health clinics. We show a reduction in PCV13 serotype carriage (with non-PCV13 serotype replacement) and a reduction in the proportion of samples containing resistance genes in toddlers six years post-PCV13 introduction. We observed an increase in pneumococcal nasopharyngeal density. Serotype 15 A, the most prevalent non-vaccine-serotype in 2022, was comprised predominantly of GPSC904;9. Reductions in PCV13 serotype carriage will likely result in pneumococcal disease reduction. It is important for ongoing surveillance to monitor serotype changes to potentially inform new vaccine development.

Long-term effect of pneumococcal conjugate vaccines on invasive pneumococcal disease incidence among people of all ages from national, active, laboratory-based surveillance in South Africa, 2005-19: a cohort observational study.

BACKGROUND: In South Africa, 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2009 and 13-valent PCV (PCV13) was introduced in 2011, both in a two plus one schedule. We evaluated the ongoing effects of PCV on the prevention of invasive pneumococcal disease (IPD) over 15 years of sustained surveillance in South Africa before the COVID-19 pandemic. METHODS: We conducted national, active, laboratory-based surveillance for IPD among all ages in South Africa, including isolate serotyping and susceptibility testing. We fitted linear regression models with vaccine covariates to imputed IPD case counts each year by serotype and age to compare expected and actual IPD cases in 2019, which was the main outcome. Vaccine effects were set to zero to identify expected incidence after the introduction of PCV7 and PCV13. FINDINGS: From Jan 1, 2005, to Dec 31, 2019, surveillance identified 52 957 IPD cases. Among the 50 705 individuals with age data available, 9398 (18·5%) were infants aged younger than 2 years. Compared with expected case numbers (no vaccination) predicted using all available data, overall IPD rates among children younger than 2 years declined by 76·0% (percentage risk difference; 95% CI -79·0 to -72·8%) in 2019; notably, PCV7 and additional PCV13 serotype IPD rates declined by 95·5% (-97·0 to -93·4%) and 93·8% (-96·2 to-90·5%), respectively, whereas non-vaccine serotypes (NVTs) did not change significantly. Among adults aged 25-44 years, overall IPD declined by 50·4% (-54·2 to -46·3%), and PCV7 and additional PCV13 serotype IPD rates declined by 86·1% (-88·7 to -83·1%) and 77·2% (-80·9 to -73·0%), respectively, whereas NVTs increased by 78·5% (56·8 to 103·4%). Individuals aged older than 64 years also benefited from declines in IPD (-30·2%; -41·9 to -16·2%), but NVTs increased (234·9%; 138·1 to 379·4%). INTERPRETATION: We documented sustained direct and indirect benefits of PCV across age groups, and NVT increases in adults older than 24 years. Higher valency PCVs would have the added benefit of preventing this residual disease. FUNDING: National Institute for Communicable Diseases of the National Health Laboratory Service (South Africa) and US Agency for International Development Antimicrobial Resistance Initiative, US Centers for Disease Control and Prevention.

A DAMP-Based Assay for Rapid and Affordable Diagnosis of Bacterial Meningitis Agents: Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae.

The rapid and accurate diagnosis of meningitis is critical for preventing severe complications and fatalities. This study addresses the need for accessible diagnostics in the absence of specialized equipment by developing a novel diagnostic assay. The assay utilizes dual-priming isothermal amplification (DAMP) with unique internal primers to significantly reduce non-specificity. For fluorescence detection, the dye was selected among Brilliant Green, Thioflavin T, and dsGreen. Brilliant Green is preferred for this assay due to its availability, high fluorescence level, and optimal sample-to-background (S/B) ratio. The assay was developed for the detection of the primary causative agents of meningitis (Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae), and tested on clinical samples. The developed method demonstrated high specificity, no false positives, sensitivity comparable to that of loop-mediated isothermal amplification (LAMP), and a high S/B ratio. This versatile assay can be utilized as a standalone test or an integrated assay into point-of-care systems for rapid and reliable pathogen detection.

Multicentre case-control study of pneumococcal infections among children with pneumonia in Peninsular Malaysia (MY-Pneumo): a study protocol.

BACKGROUND: S. pneumoniae (SPN) is the most common cause of pneumonia. The disease can be effectively prevented through immunisation. Since December 2020, the Malaysian Government has included the 10-valent pneumococcal conjugate vaccine (PCV10) for all infants born on or after 1 January 2020 as part of the National Immunisation Programme (NIP). However, the epidemiology of pneumonia remains poorly understood. To fill the knowledge gap, we established a multicentre surveillance study to understand the burden of pneumococcal pneumonia among young children in Peninsular Malaysia. METHODS: MY-Pneumo is a multicentre prospective case-control study conducted in three sentinel sites located in three different states of Peninsular Malaysia - Kuala Lumpur, Pahang, and Kelantan. A cohort of at least 500 incident cases and 500 controls is enrolled beginning in October 2021 and matched for age. Cases are hospitalised children < 5 years with radiologically confirmed pneumonia, and the controls are children without any features suggestive of pneumonia. Clinical samples, including nasopharyngeal swabs (NPS) and urine, are collected according to the study protocol. Biological fluids such as blood, cerebrospinal fluid (CSF) and pleural fluid are obtained from invasive pneumonia disease (IPD) patients, if available. All children are tested for SPN using polymerase chain reaction (PCR) and pneumococcal urine antigen test (PUAT) using BinaxNow. DISCUSSION: Surveillance data, including carriage rate, serotype variations and the phylogeny data structure of SPN among young children in Malaysia during PCV implementation, will be generated from this study. Trends and patterns of pneumococcal serotypes by different regions are important for targeted public health strategies. Our data will provide baseline information for estimating the impact of PCV10 implementation and will influence policymakers' decisions regarding the upgrade from PCV10 to a higher-valency conjugate vaccine in Malaysia. TRIAL REGISTRATION: This project was registered at ClinicalTrials.gov (NCT04923035) on 2021, June 11. The study protocol was approved by the International Medical University Joint-Committee on Research & Ethics (4.15/JCM-216/2021) and the Institutional Review Board at sentinel sites (USM/JEPeM/21020190, IREC 2021-114, MREC ID No: 2021128-9769) and University of Southampton's Ethics and Research Governance (ERGo II 64844).

Acute Streptococcus pneumoniae Meningitis: A Case Report.

A 69-year-old woman without significant medical history presented to an emergency department for evaluation and management of altered mental status and a 10-day history of worsening symptoms of upper respiratory infection. Two days previously, she had been evaluated at an urgent care center, where she reported productive cough and neck pain. Evaluation in the emergency department aroused suspicions of sepsis and meningitis, and computed tomography of the head revealed nontraumatic pneumocephalus with evidence of bony erosion of the sinus into the brain. Culture results revealed disseminated Streptococcus pneumoniae. Cerebral vasculopathy secondary to the meningitis caused bilateral acute ischemic strokes in areas of the brain, with the potential to lead to significant disability.

Nasopharyngeal carriage, antimicrobial susceptibility patterns, and associated factors of Gram-positive bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia.

BACKGROUND: Gram-positive bacteria residing in the nasopharynx can lead to severe illnesses in children, such as otitis media, pneumonia, and meningitis. Despite the potential threat, there is a lack of comprehensive data regarding the carriage rates of these bacteria among children in outpatient departments in the study area. OBJECTIVE: This study aimed to assess the nasopharyngeal carriage, antimicrobial resistance patterns, and associated factors of Gram-positive bacteria among children attending the outpatient department at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. METHODS: A hospital-based cross-sectional study was conducted from May 1, 2023, to August 30, 2023. A total of 424 nasopharyngeal swab samples were collected using sterile nasopharyngeal swabs, inoculated on Blood Agar and Mannitol Salt Agar plates, and identified through colony morphology, Gram stain, and biochemical tests. Antimicrobial susceptibility of the identified bacterial isolates was determined employing both the Kirby-Bauer and modified Kirby-Bauer methods. D-tests were conducted using clindamycin and erythromycin discs to detect inducible clindamycin resistance, while cefoxitin disc tests were utilized to ascertain methicillin resistance. Data entry was executed using Epi-Data version 4.6, and subsequent analysis was performed utilizing SPSS version 25. Bivariable and multivariable logistic regression analyses were employed to identify associated factors. An adjusted odds ratio at a 95% confidence interval with a P-value of < 0.05 was considered statistically significant. RESULTS: The overall nasopharyngeal carriage rate of Gram-positive bacteria was 296/424 (69.8%, 95% CI: 65.3-74.0). Staphylococcus aureus was the most prevalent 122/424 (28.8%), followed by Streptococcus pneumoniae 92/424 (21.7%). Methicillin resistance was observed in 19/122 (15.6%) of S. aureus and 3/60 (5%) of coagulase-negative staphylococcus (CoNS) species. Inducible clindamycin resistance was 10/122 (8.2%) in S. aureus and 4/53 (7.5%) in coagulase-negative staphylococcus species. Multidrug resistance was found in 146/296 (49.3%, 95% CI: 43.6-55.0) of the isolates. Associated factors with a bacterial carriage were large family size (AOR = 3.061, 95% CI: 1.595-5.874, P = 0.001), having siblings under five years old (AOR = 1.991, 95% CI: 1.196-3.313, P = 0.008), indoor cooking (AOR = 2.195, 95% CI: 1.275-3.778, P = 0.005), an illiterate mother (AOR = 3.639, 95% CI: 1.691-7.829, P = 0.001), and hospital visits (AOR = 2.690, 95% CI: 1.405-5.151, P = 0.003). CONCLUSION: The study found a high nasopharyngeal carriage of Gram-positive bacteria in outpatient children, including notable levels of methicillin-resistant S. aureus and multi-drug-resistant isolates. Clindamycin, rifampin, and erythromycin were the most effective antimicrobials for the tested isolates. Factors contributing to bacterial carriage include visits to healthcare facilities, larger family sizes, having younger siblings, maternal illiteracy, and indoor cooking. This emphasizes the need for methicillin-resistant S. aureus surveillance in pediatric outpatient settings and community health education, especially for children's guardians. Additionally, improving household ventilation by separating kitchens from sleeping areas and regular screening of younger siblings in healthcare environments were recommended to reduce bacterial transmission within family members. The study also called for studies with advanced procedures like minimum inhibitory concentration testing and molecular characterization to better comprehend the resistance patterns and genes in circulating bacteria.

Risk factors associated with meningitis outbreak in the Upper West Region of Ghana: A matched case-control study.

The Northern part of Ghana lies within the African meningitis belt and has historically been experiencing seasonal meningitis outbreaks. Despite the continuous meningitis outbreak in the region, the risk factors contributing to the occurrence of these outbreaks have not been clearly identified. This study, therefore, sought to describe the clinical characteristics and possible risk factors associated with meningitis outbreaks in the Upper West Region (UWR). A 1:2 matched case-control study was conducted in May-December 2021 to retrospectively investigate possible risk factors for meningitis outbreak in the UWR of Ghana between January and December 2020. Cases were persons with laboratory confirmed meningitis, and controls were persons of similar age and sex without meningitis living in the same house or neighborhood with a confirmed case. Both primary and secondary data including clinical, socio-demographic and laboratory information were collected and entered on standard questionnaires. Data was analyzed using descriptive statistics and conditional logistic regression. Meningitis cases were mostly due to Streptococcus pneumoniae (67/98; 68.37%), followed by Neisseria meningitides serogroup X (27/98; 27.55%). Fever occurred in 94.03% (63/67) of Streptococcus pneumoniae cases and 100% in both Neisseria meningitidis serogroup X (27/27) and Neisseria meningitidis serogroup W groups (3/3). CSF white cell count was significantly associated with the causative agents of meningitis. Conditional logistic regression analysis showed that, passive exposure to tobacco [AOR = 3.65, 95%CI = 1.03-12.96], bedrooms with 3 or more people [AOR = 4.70, 95%CI = 1.48-14.89] and persons with sore throat infection [AOR = 8.97, 95%CI = 2.73-29.43] were independent risk factors for meningitis infection. Headache, fever and neck pain continue to be the most common symptoms reported by meningitis patients. Education and other preventive interventions targeting exposure to tobacco smoke and crowded rooms would be helpful in reducing meningitis outbreaks in the Upper West Region of Ghana.

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.

Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.

Biochemical characterization of actinomycete from Namibia rocky crest mountainous soil and analyzing their bioactive metabolites for antagonistic effect against human respiratory pathogens.

Introduction: the present study aimed at isolating and characterizing actinomycete from unexplored Windhoek rocky crest mountainous soil and extracting bioactive metabolites as possible therapeutics against common life-threatening Streptococcus pneumonia (S. pneumonia) and Stachybotrys chartarum (S. chartarum). Methods: chemotaxonomy and biochemical methods were used to identify the isolates. The solvent extraction method was used to extract bioactive compounds. Agar overlay and disc diffusion methods were used to determine the antimicrobial activity of isolates and extracted bioactive metabolites against S. pneumonia and S. chartarum. The antioxidant activity of the extracted bioactive metabolites was determined using 2.2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method with ascorbic acid as a positive control. Comparison between groups was done using a Two-way ANOVA, followed by Bonferroni post-test. Results: three distinct isolates from 3 soil samples were identified on starch casein agar and distinguished using biochemical tests. All three isolates showed strong inhibitory activity against S. pneumonia with average growth inhibition zones between 18.0±1.00 and 27±0.00 mm p< 0.005. All isolates showed potent inhibitory activity against S. chartarum with the average inhibition zones ranging between 42.0±1.00 and 48±0.00 mm, p< 0.005. The chloroform extracts showed potent DPPH activity of up to 73± 1.41%. Conclusion: growth conditions and extraction solvents can influence the antimicrobial and antioxidant properties of bioactive metabolites.

Pneumococcal carriage and changes in serotype distribution post- PCV13 introduction in children in Matiari, Pakistan.

BACKGROUND: In early 2021, the 10-valent Pneumococcal conjugate vaccine (PCV10) was replaced with 13-valent (PCV13) by the federal directorate of immunization (FDI), Pakistan. We assessed the impact of a higher valent vaccine, PCV13, on the serotype distribution of nasopharyngeal carriage in rural Pakistan. METHODS: Children <2 years were randomly selected from two rural union councils of Matiari, Sindh in Pakistan between September-October,2022. Clinical, sociodemographic and vaccination histories were recorded. Nasopharyngeal swabs were collected and processed at Infectious Disease Research Laboratory, Aga Khan University, Karachi. Whole genome sequencing was performed on the culture positive isolates. RESULTS: Of the 200 children enrolled, pneumococcus was detected in 140(70 %) isolates. Majority of age-eligible children (60.1 %,110/183) received 3 PCV13 doses. PCV10 carriage declined from 13.2 %(78/590) in 2017/18 to 7.2 % (10/140) in 2022, additional PCV13 serotypes (3, 6A/6C and 19A) decreased from 18.5 %(109/590) to 11.4 %(16/140) while non-PCV13 serotypes increased from 68.3 %(403/590) to 81.4 %(114/140). There were 88.5 %(n = 124), 80.7 %(n = 113), 55.0 %(n = 77), and 46.0 %(n = 65) isolates predicted to be resistant to cotrimoxazole, penicillin(meningitis cut-off), tetracycline, and erythromycin respectively. CONCLUSION: Replacing PCV10 with PCV13 rapidly decreased prevalence of PCV13 carriage among vaccinated children in Matiari, Pakistan. Vaccine-driven selection pressure may have been responsible for the increase of non-PCV13 serotypes.

A review of the value of point-of-care testing for community-acquired pneumonia.

INTRODUCTION: Community-acquired pneumonia (CAP) is an infectious disease associated with high mortality worldwide. Although Streptococcus pneumoniae remains the most frequent pathogen in CAP, data from recent studies using molecular tests have shown that respiratory viruses play a key role in adults with pneumonia. The impact of difficult-to-treat pathogens on the outcomes of pneumonia is also important even though they represent only a small proportion of overall cases. Despite improvements in the microbiological diagnosis of CAP in recent decades, the identification of the causative pathogen is often delayed because of difficulties in obtaining good-quality sputum samples, issues in transporting samples, and slow laboratory processes. Therefore, the initial treatment of CAP is usually empirical. Point-of-care testing (POCT) was introduced to avoid treatment delays and reduce reliance on empirical antibiotics. AREAS COVERED: This review summarizes the main scientific evidence on the role of POCT in the diagnosis and management of patients with CAP. The authors searched for articles on POCT in pneumonia on PubMed from inception to 20 January 2024. The references in the identified articles were also searched. EXPERT OPINION: POCT involves rapid diagnostic assays that can be performed at the bedside especially in cases of severe CAP and immunocompromised patients. These tests can produce results that could help guide initial therapy and management.