Multiple-Drug Resistant Nasopharyngeal Streptococcus pneumoniae Isolated in Russia: Serotypes, Antimicrobial Susceptibility, and Molecular Characterization of the Emergent Serotype 13/ST2754 Lineage.

The pneumococcal population structure and drug resistance patterns are constantly changing worldwide. In this study, we described serotypes and antimicrobial susceptibility among 478 multiple-drug resistant (MDR) pediatric nasopharyngeal pneumococci recovered in 2010-2017. The majority of isolates (89.3%; n = 427) carried pneumococcal conjugate vaccine (PCV)13 serotypes, predominantly 6A/B, 14, 19A/F, and 23F. A non-PCV13 serotype capsule was detected in 44 (9.2%) MDR pneumococci, including serotypes 23A (n = 8), 13 (n = 7), 28F (n = 6), 11A (n = 5), and serogroup 35 (n = 10) isolates. The remaining seven (1.5%) MDR isolates were nontypeable. The majority of non-PCV13-serotype isolates were resistant to tetracycline, erythromycin, and clindamycin; most harbored both the ermB and mef genes. Among the 44 serotyped MDR non-PCV13 isolates, multilocus sequence typing analysis revealed 24 different sequence types (STs). ST2754 was the most abundant lineage demonstrating an unusual association with serotypes 13 (n = 7) and 9N (n = 1). The whole-genome sequencing-based analysis demonstrated that the serotype 13/ST2754 lineage was closely related to the serotype 13/ST2754 isolate recovered in Africa (Malawi) in 2013, possessed a Tn6002-like transposon carrying the erm(B) and tet(M) genes, and harbored additional virulence determinants, including arginine metabolism genes and a putative bacteriocin locus. Such a favorable genetic background may provide competitive advantages and potential for spreading and expansion of this clone among pneumococci. These data warrant further molecular monitoring of the genetic composition of the changing pneumococcal population.

Primary Nasopharyngeal Tuberculosis: A Case Report Focused on Nasopharyngoscopic Features and CT Findings.

Primary nasopharyngeal tuberculosis, defined as an isolated tuberculosis infection of the nasopharynx without systemic or pulmonary disease, is rare, even in areas endemic for tuberculosis. It is challenging for ENT specialists to diagnose primary nasopharyngeal tuberculosis at an early stage. In this report, we describe a new case of primary nasopharyngeal tuberculosis, focusing on its nasopharyngoscopic features and radiological findings that can help the understanding and aid in accurate diagnosis of this unusual disease entity. Our experience suggests that although primary nasopharyngeal tuberculosis is a relatively rare disease, it must be included in the differential diagnosis of various nasopharyngeal lesions, particularly in patients with unusual nasopharyngoscopic and computed tomography findings.

Nasopharyngeal colonization with pathobionts is associated with susceptibility to respiratory illnesses in young children.

Some children are more susceptible to viral and bacterial respiratory infections in the first few years of life than others. However, the factors contributing to this susceptibility are incompletely understood. In a retrospective analysis of clinical samples collected from a prospectively-enrolled cohort of 358 children we sought associations between physician-attended illness visits and bacterial colonization in the first five years of life. A subset of children was identified by unsupervised clustering analysis as infection and allergy prone (IAP). Several respiratory infection- and allergy-mediated illnesses co-occurred at higher rates in IAP children, while the rates of other illnesses were not significantly different between the groups. Analyses of nasopharyngeal (NP) pathobionts and microbiota commensals showed that early age of first colonization with pathobionts Streptococcus pneumonia, non-typeable Haemophilus influenzae, and Moraxella catarrhalis was associated with IAP children, and particularly Moraxella abundance was negatively associated with NP microbiome diversity. We conclude that mucosal pathobiont exposures in early life can influence susceptibility to respiratory illnesses in children.

Nasopharyngeal Isolates from a Cohort of Medical Students with or without Pharyngitis.

OBJECTIVES: Few studies have investigated pharyngeal colonisation in the United Arab Emirates (UAE). This study aims to identify the pharyngeal organisms present in a cohort of medical students with and without symptomatic pharyngitis. METHODS: This study was conducted between September 2016 and June 2018 at the College of Medicine and Health Sciences, UAE University, Al-Ain. Nasopharyngeal swabs were collected from preclinical and clinical medical students attending the college during the study period. The specimens were tested for 16 viral and nine bacterial pathogens using a real-time polymerase chain reaction assay. RESULTS: A total of 352 nasopharyngeal swabs were collected from 287 students; of these, 22 (7.7%) had pharyngitis symptoms. Overall, the most common isolates were human rhinovirus, Streptococcus pneumoniae and Haemophilus influenzae, with no significant differences in terms of gender, year of study or stage of study. The prevalence of S. pyogenes in asymptomatic and symptomatic students was 1.1% and 0%, respectively. A Centor score of ≥2 was not associated with S. pyogenes-positive samples. Six pathogens were isolated from symptomatic students including H. influenzae. Fusobacterium necrophorum was not detected in any of the samples. CONCLUSION: The diagnosis and management of pharyngitis should be tailored to common pathogens in the region. This study found that S. pyogenes and F. necrophorum were not detected among students with symptoms of pharyngitis; moreover, Centor scores of ≥2 were not associated with the presence of S. pyogenes. This cut-off score therefore should not be employed as an empirical measure to initiate penicillin therapy in this population.

Longitudinal investigation of nasopharyngeal pneumococcal carriage in early childhood: The PATCH birth cohort study.

Streptococcus pneumoniae is a common cause of infectious diseases such as pneumonia and sepsis. Its colonization is thought to be the first step in the development of invasive pneumococcal diseases. This study aimed to investigate pneumococcal colonization patterns in early childhood. A longitudinal birth cohort study was conducted for investigating nasopharyngeal colonized pneumococci at 1, 6, 12, 18, 24, and 36 months of age, particularly focusing on the serotype distribution and antimicrobial susceptibilities. Pneumococcal conjugate vaccine (PCV) effect on nasopharyngeal colonization was also assessed. During 2013-2017, 855 infants were enrolled and a total of 107 isolates were recovered from 95 infants during the first three years of life. In this period, the prevalence of pneumococcal colonization increased, with values ranging from 0.2% (2/834) at 1 month of age to 5.9% (19/323) at 36 months of age. The investigation of serotype revealed that 81.1% (73/90) belonged to the non-PCV13 serotypes-23A, 15A, 15C, and 15B. Moreover, PCV13 serotypes significantly decreased during 2014-2015, when routine PCV13 vaccination was initiated in Taiwan. PCV13 introduction may lead to the reduction in the rates of pneumococcal isolates resistant (R) to penicillin. Under conditional PCV13 vaccination, pneumococcal isolates primarily belonged to non-PCV13 serotypes. This non-PCV13 serotype replacement exhibited lower rates of penicillin R isolates, suggesting that PCV13 administration may reduce the antibiotic-nonsusceptible pneumococcal disease burden and antibiotic use.

A Mouse Nasopharyngeal Colonization Model for Group A Streptococcus.

Group A Streptococcus (GAS) often exists as an asymptomatic colonizer of the upper respiratory tract in humans. Unsurprisingly, a high proportion of symptomatic infections caused by GAS include pharyngitis. While not usually life-threatening, these infections cause significant morbidity and economic burden/loss of productivity, and can have downstream life-threatening autoimmune consequences. Modeling asymptomatic colonization in animals is, therefore, a useful tool to dissect host-bacteria interactions and to evaluate efficacy of vaccines aimed at reducing the burden of carriage. Here we describe a mouse model of nasopharyngeal colonization using nasal challenge of susceptible mice and the evaluation of subsequent bacterial burden.

Nasopharyngeal tuberculosis: report of four cases and review of the literature.

Even if tuberculosis is a major cause of morbidity and mortality, nasopharyngeal location is unusual and extremely rare. We report four new cases observed with short time interval suggesting a trend towards increased frequency. The diagnosis was confirmed by histological analysis after a biopsy. The evolution was favorable after anti tuberculosis chemotherapy. In the light of those observations and a review of the literature, we will discuss different characteristics of this disease and we will highlight the need of a systematic biopsy in order to confirm diagnosis and exclude undifferentiated carcinoma especially in endemic regions for both diseases.

Different upper airway microbiome and their functional genes associated with asthma in young adults and elderly individuals.

BACKGROUND: Microbes in the airway have been shown to be associated with the pathogenesis of asthma. The upper airway microbiome influences the dysbiosis of the lower airway microbiome. However, to date, the influence of upper airway microbiome for adult and elderly asthma has not been fully elucidated. Here, the metagenome of upper airway microbiome of young adults and elderly was analyzed to identify their association with adult asthma. METHODS: Nasopharyngeal swabs were collected from young adult and elderly asthma patients and non-asthmatic subjects. The compositions and functional genes of airway microbiome were analyzed by high-throughput sequencing. RESULTS: The composition of microbiota differed between young adult and elderly, and it was different between asthmatics and non-asthmatics in each age group. Different bacteria were related to FEV1% predicted in each age group. Genes related to lysine degradation, N-glycan biosynthesis, caprolactam degradation, and PPAR signaling pathway, which could be related to the reduction in inflammation and degradation of air pollutants, were higher in non-asthmatics. Genes related to pentose phosphate pathway, lipopolysaccharide biosynthesis, flagella assembly, and bacterial chemotaxis-which may all be related to increased inflammation and colonization of pathogenic bacteria-were higher in young adult asthmatic patients. However, the functional genes of airway microbiome in elderly patients were not significantly different according to asthma morbidity. CONCLUSIONS: These results suggest that the composition and function of upper airway microbiome could influence asthma pathogenesis, and the microbiome could play various roles depending on the age group.

Brain abscess caused by chronic invasive actinomycosis in the nasopharynx: A case report and literature review.

RATIONALE: Actinomycosis is a rare anaerobic, gram-positive bacterial infection caused by Actinomyces, which is part of the normal flora in the oral cavity and respiratory and female genitourinary tracts. The cervicofacial area is the most common site of involvement, and involvement of the central nervous system is rare. PATIENT CONCERNS: We report a case involving a 51-year-old woman who developed an actinomycotic brain abscess 15 months after the treatment of noninvasive nasopharyngeal actinomycosis, which recurred as an invasive form. DIAGNOSES: Histopathological examination of the surgical specimens revealed actinomycosis. INTERVENTIONS: The patient was treated by surgical drainage of the brain abscess and long-term antibiotic treatment. OUTCOMES: Follow-up brain imaging performed 12 months after surgery showed complete resolution of the brain abscess, and there were no further signs or symptoms of infection. LESSONS: Physicians should be aware of the typical clinical presentations of cervicofacial actinomycosis. Moreover, they should know that actinomycosis may mimic the process of malignancy at various anatomical locations.

Chemotherapy with Phage Lysins Reduces Pneumococcal Colonization of the Respiratory Tract.

Bacteriophage-borne lytic enzymes, also named lysins or enzybiotics, are efficient agents for the killing of bacterial pathogens. The colonization of the respiratory tract by Streptococcus pneumoniae is a prerequisite for the establishment of the infection process. Hence, we have evaluated the antibacterial activities of three different lysins against pneumococcal colonization using human nasopharyngeal and lung epithelial cells as well as a mouse model of nasopharyngeal colonization. The lysins tested were the wild-type Cpl-1, the engineered Cpl-7S, and the chimera Cpl-711. Moreover, we included amoxicillin as a comparator antibiotic. Human epithelial cells were infected with three different multidrug-resistant clinical isolates of S. pneumoniae followed by a single dose of the corresponding lysin. The antimicrobial activities of these lysins were also evaluated using a mouse nasopharyngeal carriage model. The exposure of the infected epithelial cells to Cpl-7S did not result in the killing of any of the pneumococcal strains investigated. However, the treatment with Cpl-1 or Cpl-711 increased the killing of S. pneumoniae organisms adhered to both types of human epithelial cells, with Cpl-711 being more effective than Cpl-1, at subinhibitory concentrations. In addition, a treatment with amoxicillin had no effect on reducing the carrier state, whereas mice treated by the intranasal route with Cpl-711 showed significantly reduced nasopharyngeal colonization, with no detection of bacterial load in 20 to 40% of the mice. This study indicates that Cpl-1 and Cpl-711 lysins might be promising antimicrobial candidates for therapy against pneumococcal colonization.

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

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

Streptococcus pneumoniae burden and nasopharyngeal inflammation during acute otitis media.

Streptococcus pneumoniae (Spn) is a common respiratory pathogen and a frequent cause of acute otitis media (AOM) in children. The first step in bacterial pathogenesis of AOM is the establishment of asymptomatic colonization in the nasopharynx. We studied Spn bacterial burden in conjunction with neutrophil recruitment and inflammatory gene transcription and cytokine secretion in samples of nasal wash collected from normal and otitis-prone children during health, viral upper respiratory infection without middle ear involvement (URI) and AOM. We found no significant associations between otitis-prone status and any of the measured parameters. However, Spn bacterial burden was significantly correlated with neutrophil recruitment, transcription of IL-8, TNF-α and SOD2, and secretion of TNF-α. We also found that transcription of IL-8 and TNF-α mRNA by neutrophils was significantly correlated with the secretion of these cytokines into the nasopharynx. We conclude that Spn bacterial burden in the NP is a major determinant of neutrophil recruitment to the NP and activity during URI and AOM, and that neutrophils are contributors to the secretion of IL-8 and TNF-α in the NP when the Spn burden is high.

Competitive Dominance within Biofilm Consortia Regulates the Relative Distribution of Pneumococcal Nasopharyngeal Density.

Streptococcus pneumoniae is a main cause of child mortality worldwide, but strains also asymptomatically colonize the upper airways of most children and form biofilms. Recent studies have demonstrated that ∼50% of colonized children carry at least two different serotypes (i.e., strains) in the nasopharynx; however, studies of how strains coexist are limited. In this work, we investigated the physiological, genetic, and ecological requirements for the relative distribution of densities, and spatial localization, of pneumococcal strains within biofilm consortia. Biofilm consortia were prepared with vaccine type strains (i.e., serotype 6B [S6B], S19F, or S23F) and strain TIGR4 (S4). Experiments first revealed that the relative densities of S6B and S23F were similar in biofilm consortia. The density of S19F strains, however, was reduced to ∼10% in biofilm consortia, including either S6B, S23F, or TIGR4, in comparison to S19F monostrain biofilms. Reduction of S19F density within biofilm consortia was also observed in a simulated nasopharyngeal environment. Reduction of relative density was not related to growth rates, since the Malthusian parameter demonstrated similar rates of change of density for most strains. To investigate whether quorum sensing (QS) regulates relative densities in biofilm consortia, two different mutants were prepared: a TIGR4ΔluxS mutant and a TIGR4ΔcomC mutant. The density of S19F strains, however, was similarly reduced when consortia included TIGR4, TIGR4ΔluxS, or TIGR4ΔcomC Moreover, production of a different competence-stimulating peptide (CSP), CSP1 or CSP2, was not a factor that affected dominance. Finally, a mathematical model, confocal experiments, and experiments using Transwell devices demonstrated physical contact-mediated control of pneumococcal density within biofilm consortia.IMPORTANCEStreptococcus pneumoniae kills nearly half a million children every year, but it also produces nasopharyngeal biofilm consortia in a proportion of asymptomatic children, and these biofilms often contain two strains (i.e., serotypes). In our study, we investigated how strains coexist within pneumococcal consortia produced by vaccine serotypes S4, S6B, S19F, and S23F. Whereas S6B and S23F shared the biofilm consortium, our studies demonstrated reduction of the relative density of S19F strains, to ∼10% of what it would otherwise be if alone, in consortial biofilms formed with S4, S6B, or S23F. This dominance was not related to increased fitness when competing for nutrients, nor was it regulated by quorum-sensing LuxS/AI-2 or Com systems. It was demonstrated, however, to be enhanced by physical contact rather than by a product(s) secreted into the supernatant, as would naturally occur in the semidry nasopharyngeal environment. Competitive interactions within pneumococcal biofilm consortia regulate nasopharyngeal density, a risk factor for pneumococcal disease.

Enhanced nasopharyngeal infection and shedding associated with an epidemic lineage of emm3 group A Streptococcus.

BACKGROUND: A group A Streptococcus (GAS) lineage of genotype emm3, sequence type 15 (ST15) was associated with a 6 month upsurge in invasive GAS disease in the UK. The epidemic lineage (Lineage C) had lost 2 typical emm3 prophages, Φ315.1 and Φ315.2 associated with the superantigen ssa, but gained a different prophage (ΦUK-M3.1) associated with a different superantigen, speC and a DNAse spd1. METHODS AND RESULTS: The presence of speC and spd1 in Lineage C ST15 strains enhanced both in vitro mitogenic and DNase activities over non-Lineage C ST15 strains. Invasive disease models in Galleria mellonella and SPEC-sensitive transgenic mice, revealed no difference in overall invasiveness of Lineage C ST15 strains compared with non-Lineage C ST15 strains, consistent with clinical and epidemiological analysis. Lineage C strains did however markedly prolong murine nasal infection with enhanced nasal and airborne shedding compared with non-Lineage C strains. Deletion of speC or spd1 in 2 Lineage C strains identified a possible role for spd1 in airborne shedding from the murine nasopharynx. CONCLUSIONS: Nasopharyngeal infection and shedding of Lineage C strains was enhanced compared with non-Lineage C strains and this was, in part, mediated by the gain of the DNase spd1 through prophage acquisition.

Corynebacterium species nasopharyngeal carriage in asymptomatic individuals aged ≥ 65 years in Germany.

PURPOSE: The prevalence of protective anti-diphtheria toxin antibodies decreases with age. Therefore, the elderly might serve as reservoir for potentially toxigenic Corynebacterium (C.) species (C. diphtheriae, C. ulcerans, and C. pseudotuberculosis). This study aimed to examine the colonization rate of the nasopharynx with corynebacteria of individuals aged 65 years and older. METHODS: In the period from October 2012 to June 2013, nasal and throat swabs were taken from 714 asymptomatic subjects aged 65-106 years (average age 77.2) at three regions in Germany and investigated for Corynebacterium species. RESULTS: A total of 402 strains of Corynebacterium species were isolated from 388 out of 714 asymptomatic subjects (carriage rate 54.3%). The carriage rate was significantly higher in study participants living in retirement homes (68.4%) compared to those living autonomously at home (51.1%). Strains were isolated mostly from the nose (99%). Corynebacterium accolens was the most often isolated species (39.8%), followed by C. propinquum (24.1%), C. pseudodiphtheriticum (19.4%), and C. tuberculostearicum (10.2%). No C. diphtheriae, C. ulcerans, and C. pseudotuberculosis strains were isolated. A subsample of 74 subjects was tested serologically for anti-diphtheria antibodies. Protective anti-diphtheria toxin antibodies were found in 29.7% of the subjects; 70.3% showed no protective immunity. CONCLUSIONS: These results suggest that carriage of potentially toxigenic corynebacteria is very rare among people aged 65 and older in Germany. However, the low prevalence of protective anti-diphtheria toxin antibodies might pose a risk for acquiring diphtheria especially for the elderly.

Identification of a two-component Class IIb bacteriocin in Streptococcus pyogenes by recombinase-based in vivo expression technology.

Streptococcus pyogenes is a globally prominent bacterial pathogen that exhibits strict tropism for the human host, yet bacterial factors responsible for the ability of S. pyogenes to compete within this limited biological niche are not well understood. Using an engineered recombinase-based in vivo expression technology (RIVET) system, we identified an in vivo-induced promoter region upstream of a predicted Class IIb bacteriocin system in the M18 serotype S. pyogenes strain MGAS8232. This promoter element was not active under in vitro laboratory conditions, but was highly induced within the mouse nasopharynx. Recombinant expression of the predicted mature S. pyogenes bacteriocin peptides (designated SpbM and SpbN) revealed that both peptides were required for antimicrobial activity. Using a gain of function experiment in Lactococcus lactis, we further demonstrated S. pyogenes immunity function is encoded downstream of spbN. These data highlight the importance of bacterial gene regulation within appropriate environments to help understand mechanisms of niche adaptation by bacterial pathogens.

Palatopharyngoplasty for treatment of nasopharyngeal stenosis secondary to extra-laryngeal tuberculosis.

Nasopharyngeal stenosis is a rare sequela of extra-laryngeal tuberculosis that can adversely impact the quality of life of afflicted patients. Relying solely on the oropharyngeal airway, patients often complain of inspiratory dryness and decreased sensation of airflow as the nasal mucosa and turbinate complex is entirely excluded from the breathing mechanism. Often times, the oropharyngeal inlet can be narrowed as well, limiting the air flow through the oropharyngeal airway. In those circumstances, patients often require tracheostomy for establishment of a reliable airway. We present the unique case of a previously tracheotomized patient with nasopharyngeal stenosis secondary to tuberculosis successfully treated with a modified palatopharyngoplasty to reestablish a patent naso-oropharyngeal airway. During the follow-up period, the patient was decannulated and highly satisfied with his respiratory status. Although rare and more commonly used in the treatment of sleep apnea, palatopharyngoplasty can be a viable option for the treatment of naso-oropharyngeal stenosis and should be kept in the armamentarium of reconstructive craniofacial surgeons.

Tuberculosis of the cavum revealed by acute facial pain.

An 85-year-old woman presented for assessment of recurring episodes of intense hemifacial pain, mimicking trigeminal neuralgia, associated with tinnitus. A necrotic tumour of the cavum with compression of the left Eustachian tube and skull-base invasion was discovered on brain MRI. Although the tumour was initially thought to be malignant, the histopathological findings on the biopsy were compatible with tuberculosis, later confirmed by the cultures. F-18-fluorodeoxyglucose positron emission tomography (PET)/CT showed an intense signal of the cavum, cervical and mediastinal lymph nodes, and also of two small nodules of the apex of each lung. Currently, after 9 months of combined antituberculosis antibiotics, the initial lesion has almost disappeared from both PET scan and MRI. This case highlights the importance of systematically screening for tuberculosis in the assessment of nasopharyngeal tumours.