The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis

Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan

Our understanding of the normal variation in the upper respiratory tract (URT) microbiota across the human lifespan and how these relate to host, environment, and health is limited. We studied the microbiota of 3,104 saliva (<10 year-olds)/oropharynx (≥10 year-olds) and 2,485 nasopharynx samples of 3,160 Dutch individuals 0-87 years of age, participating in a cross-sectional population-wide study (PIENTER-3) using 16S-rRNA sequencing. The microbiota composition was strongly related to age, especially in the nasopharynx, with maturation occurring throughout childhood and adolescence. Clear niche- and age-specific associations were found between the microbiota composition and host/environmental factors and health outcomes. Among others, social interaction, sex, and season were associated with the nasopharyngeal microbial community. By contrast, the oral microbiota was more related to antibiotics, tobacco, and alcohol use. We present an atlas of the URT microbiota across the lifespan in association with environment and health, establishing a baseline for future research.

Limited protection of pneumococcal vaccines against emergent Streptococcus pneumoniae serotype 14/ST876 strains

PURPOSE

Streptococcus pneumoniae (Spn) is a major cause of child death. We investigated the epidemiology of S. pneumoniae in a pediatric fever clinic and explored the genomics basis of the limited vaccine response of serotype 14 strains worldwide.

METHODS

Febrile disease and pneumonia were diagnosed following criteria from the WHO at the end of 2019 at a tertiary children's hospital. Spn was isolated by culture from nasopharyngeal (NP) swabs. The density was determined by lytA-base qPCR. Isolates were serotyped by Quellung and underwent antimicrobial susceptibility testing. Whole-genome sequencing was employed for molecular serotyping, MLST, antibiotic gene determination, SNP calling, recombination prediction, and phylogenetic analysis.

RESULTS

The presence of pneumococcus in the nasopharynx (87.5%, 7/8, p = 0.0227) and a high carriage (100%, 7/7, p = 0.0123) were significantly associated with pneumonia development. Living with siblings (73.7%, 14/19, p = 0.0125) and non-vaccination (56.0%, 28/50, p = 0.0377) contributed significantly to the Spn carriage. Serotype 14 was the most prevalent strain (16.67%, 5/30). The genome analysis of 1497 serotype 14 strains indicated S14/ST876 strains were only prevalent in China, presented limited vaccine responses with higher recombination activities within its cps locus, and unique variation patterns in the genes wzg and lrp.

CONCLUSION

With the lifting of the one-child policy, it will be crucial for families with multiple children to get PCV vaccinations in China. Due to the highly variant cps locus and distinctive variation patterns in capsule shedding and binding proteins genes, the prevalent S14/ST876 strains have shown poor response to current vaccines. It is necessary to continue monitoring the molecular epidemiology of this vaccine escape clone.

Bacitracin agar vs. oleandomycin disk supplemented chocolate agar for the recovery of Haemophilus influenzae in diagnostic samples: A prospective comparison

Haemophilus influenzae is an important pathogen able to cause various forms of respiratory and invasive disease. To provide high sensitivity for detection, culture media must inhibit growth of residential flora from the respiratory tract. This study aimed to identify and compare the diagnostic and economic advantages of using bacitracin containing selective agar (SEL) or oleandomycin disk supplemented chocolate agar (CHOC). Growth and semi-quantitative abundance of H. influenzae and growth suppression of residential flora was prospectively assessed in a 28-week period. H. influenzae was identified in 164 (5 %) of all included samples: CHOC and SEL, CHOC only, and SEL only were positive in 95, 24, and 45 cases. Diagnostic superiority of SEL was primarily attributable to the results of throat swabs. However, on average, € 200 had to be spent for the detection of each additional isolate that was recovered only because of additional incubation on SEL.

MV130 in the Prevention of Recurrent Respiratory Tract Infections: A Retrospective Real-World Study in Children and Adults

Respiratory tract infections (RTIs) are among the most common and important problems in clinical medicine, making antibiotics the gold standard therapeutic option regardless of their frequent viral etiology. Their excessive and inappropriate use contributes to the rapid rise of antibiotic resistance and underscores the need for alternative strategies, especially when dealing with recurrent RTIs. Prevention is the ideal alternative, but specific vaccines targeting a wide range of respiratory pathogens are scarce. MV130 is a sublingual bacterial vaccine that induces trained immunity and provides non-specific protection against respiratory pathogens in various clinical settings according to the concept of TIbV (Trained Immunity-based Vaccine). A retrospective real-world study (RWS) was conducted to evaluate the annual incidence of RTIs and the consumption of antibiotics before and after the administration of MV130, using data sourced from the medical records of 599 patients (186 children and 413 adults) who suffered from recurrent RTIs. The median number of infectious episodes in children was significantly reduced by more than 70% from 5 episodes (interquartile range (IQR) 4.0-6.0) to 1 (IQR, 0.0-2.0) (p < 0.001) after MV130. Similarly, in adults, the median number of episodes before MV130 immunization was 5 (IQR, 4.0-6.0), which dropped by more than 80% to 1 (IQR, 0.0-1.0) during the year following MV130 immunization (p < 0.001). The median number of antibiotic courses also significantly decreased for both children and adults by over 80% (p < 0.001). This RWS showed that MV130 is an effective strategy for the prevention of respiratory infections and the reduction of associated antibiotic consumption.

Viral and bacterial microorganisms in Vietnamese children with severe and non-severe pneumonia

To investigate potential respiratory pathogens in children with community-acquired pneumonia (CAP) and risk factors for severe disease. This prospective study was conducted among 467 children at the Thai Binh Paediatric Hospital, Vietnam between 1 July 2020 and 30 June 2021. Clinical data and laboratory results were collected. Twenty-four respiratory microorganisms were tested from nasopharyngeal swabs using real-time PCR. Logistical regression was used to estimate a factor's adjusted odd ratios of the severity of disease. Mean age of patients = 15.4 ± 13.3 months, 63.0% were male. Over 97% of patients had a positive PCR result. 87% of patients were positive for multiple (up to eight) microorganisms. Rhinovirus (46%), respiratory syncytial virus (RSV) (24%), enterovirus (17%), and parainfluenza viruses-3 (13%) were the most frequent viruses. H. influenzae (61%), S. pneumoniae (45%) and M. catarrhalis (30%) were the most common bacteria. 128 (27%) cases were classified as severe pneumonia. Presence of smokers at home (aOR 2.11, 95% CI 1.27-3.52, P value = 0.004), CRP level ≥ 50 mg/dL (aOR  6.11, 95% CI  3.86-9.68, P value < 0.0001), RSV (aOR  1.78, 95% CI  1.07-2.96, P value = 0.03) and H. influenzae (aOR  1.66, 95% CI  1.03-2.67, P value = 0.04) PCR detection associated with a higher risk of severe pneumonia; ,. Causative agents of pneumonia in children are complex. Children positive with RSV and H. influenzae need to be closely monitored to prevent severe pneumonia.

Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage

Background

Targeted next-generation sequencing (tNGS) has emerged as a rapid diagnostic technology for identifying a wide spectrum of pathogens responsible for pulmonary infections.

Methods

Sputum samples were collected from patients unable or unwilling to undergo bronchoalveolar lavage. These samples underwent tNGS analysis to diagnose pulmonary infections. Retrospective analysis was performed on clinical data, and the clinical efficacy of tNGS was compared to conventional microbiological tests (CMTs).

Results

This study included 209 pediatric and adult patients with confirmed pulmonary infections. tNGS detected 45 potential pathogens, whereas CMTs identified 23 pathogens. The overall microbial detection rate significantly differed between tNGS and CMTs (96.7% vs. 36.8%, p < 0.001). Among the 76 patients with concordant positive results from tNGS and CMTs, 86.8% (66/76) exhibited full or partial agreement. For highly pathogenic and rare/noncolonized microorganisms, tNGS, combined with comprehensive clinical review, directly guided pathogenic diagnosis and antibiotic treatment in 21 patients. This included infections caused by Mycobacterium tuberculosis complex, certain atypical pathogens, Aspergillus, and nontuberculous Mycobacteria. Among the enrolled population, 38.8% (81/209) of patients adjusted their treatment based on tNGS results. Furthermore, tNGS findings unveiled age-specific heterogeneity in pathogen distribution between children and adults.

Conclusion

CMTs often fall short in meeting the diagnostic needs of pulmonary infections. This study highlights how tNGS of sputum samples from patients who cannot or will not undergo bronchoalveolar lavage yield valuable insights into potential pathogens, thereby enhancing the diagnosis of pulmonary infections in specific cases.

Analysis of the Sputum Culture Spectrum of Children with Respiratory Tract Infection in Wuxi Between 2014 and 2021

Objective

We retrospectively analysed related clinical data to determine the influencing factors to better prevent and treat children's respiratory tract infection.

Methods

The study participants were children with respiratory tract infection who had sputum cultured in our hospital between 2014 and 2021. Sputum samples were extracted using negative suction pressure and sent to the hospital microbiological laboratory for testing. The testing results were analysed.

Results

A total of 4610 sputum samples were collected, and 508 positive samples were detected. The positive rate of pathogenic bacteria was 11.02%. Escherichia coli infection was more common in male patients (11.11%), whereas Haemophilus influenzae infection was more common in female patients (17.54%); the infection rates of these 2 bacteria are increasing annually. There were 304 (59.84%) strains of gram-negative bacteria, 172 (33.86%) strains of gram-positive bacteria and 32 (6.3%) strains of fungi. In children between 0 and 3 years old, the proportions of gram-negative bacteria were significantly higher than those of gram-positive bacteria in 2016-2017, 2018-2019 and 2020-2021 (p < 0.01). In every age group, the constituent ratio of gram-negative bacteria was significantly higher than that of gram-positive bacteria (p < 0.01) except for the 3-6-year age group. The proportion of Staphylococcus aureus in 2014-2015, 2016-2017, 2018-2019 and 2020-2021 was 25.64%, 25.20%, 22.98% and 16.44%, respectively. The proportion of H. influenzae in 2014-2015 was significantly lower than that in other years (p < 0.01). Haemolyticus staphylococcus and E. coli were more common in newborns, accounting for 19.12%.

Conclusion

The pathogens of respiratory tract infection in children change dynamically. There are significant differences in pathogens of respiratory tract infections among different age groups, years and seasons. Clinicians should pay attention to changes in the pathogen spectrum and improve drug resistance monitoring.

Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children

Introduction. Respiratory tract infection, which is associated with high morbidity and mortality, occurs frequently in children. At present, the main diagnostic method is culture. However, the low pathogen detection rate of the culture approach prevents timely and accurate diagnosis. Fortunately, next-generation sequencing (NGS) can compensate for the deficiency of culture, and its application in clinical diagnostics has become increasingly available.Gap Statement. Targeted NGS (tNGS) is a platform that can select and enrich specific regions before data enter the NGS pipeline. However, the performance of tNGS in the detection of respiratory pathogens and antimicrobial resistance genes (ARGs) in infections in children is unclear.Aim and methodology. In this study, we estimated the performance of tNGS in the detection of respiratory pathogens and ARGs in 47 bronchoalveolar lavage fluid (BALF) specimens from children using conventional culture and antimicrobial susceptibility testing (AST) as the gold standard.Results. RPIP (Respiratory Pathogen ID/AMR enrichment) sequencing generated almost 500 000 reads for each specimen. In the detection of pathogens, RPIP sequencing showed targeted superiority in detecting difficult-to-culture bacteria, including Mycoplasma pneumoniae. Compared with the results of culture, the sensitivity and specificity of RPIP were 84.4 % (confidence interval 70.5-93.5 %) and 97.7 % (95.9 -98.8%), respectively. Moreover, RPIP results showed that a single infection was detected in 10 of the 47 BALF specimens, and multiple infections were detected in 34, with the largest number of bacterial/viral coinfections. Nevertheless, there were also three specimens where no pathogen was detected. Furthermore, we analysed the drug resistance genes of specimens containing Streptococcus pneumoniae, which was detected in 25 out of 47 specimens in the study. A total of 58 ARGs associated with tetracycline, macrolide-lincosamide-streptogramin, beta-lactams, sulfonamide and aminoglycosides were identified by RPIP in 19 of 25 patients. Using the results of AST as a standard, the coincidence rates of erythromycin, tetracycline, penicillin and sulfonamides were 89.5, 79.0, 36.8 and 42.1 %, respectively.Conclusion. These results demonstrated the superiority of RPIP in pathogen detection, particularly for multiple and difficult-to-culture pathogens, as well as in predicting resistance to erythromycin and tetracycline, which has significance for the accurate diagnosis of pathogenic infection and in the guidance of clinical treatment.

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

BACKGROUND

Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa.

METHODS

We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months.

RESULTS

Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae.

CONCLUSIONS

In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.

Investigation of Upper Respiratory Carriage of Bacterial Pathogens among University Students in Kampar, Malaysia

The carriage of bacterial pathogens in the human upper respiratory tract (URT) is associated with a risk of invasive respiratory tract infections, but the related epidemiological information on this at the population level is scarce in Malaysia. This study aimed to investigate the URT carriage of Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Staphylococcus aureus, Klebsiella pneumoniae and Pseudomonas aeruginosa among 100 university students by nasal and oropharyngeal swabbing. The presence of S. aureus, K. pneumoniae and P. aeruginosa was assessed via swab culture on selective media and PCR on the resulting isolates. For S. pneumoniae, H. influenzae and N. meningitidis, their presence was assessed via multiplex PCR on the total DNA extracts from chocolate agar cultures. The carriage prevalence of H. influenzae, S. aureus, S. pneumoniae, K. pneumoniae, N. meningitidis and P. aeruginosa among the subjects was 36%, 27%, 15%, 11%, 5% and 1%, respectively, by these approaches. Their carriage was significantly higher in males compared to females overall. The S. aureus, K. pneumoniae and P. aeruginosa isolates were also screened by the Kirby-Bauer assay, in which 51.6% of S. aureus were penicillin-resistant. The outcomes from carriage studies are expected to contribute to informing infectious disease control policies and guidelines.

Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) first emerged in 2019 in China and has resulted in millions of human morbidities and mortalities across the globe. Evidence has been provided that this novel virus originated in animals, mutated, and made the cross-species jump to humans. At the time of this communication, the Coronavirus disease (COVID-19) may be on its way to an endemic form; however, the threat of the virus is more for susceptible (older and immunocompromised) people. The human body has millions of bacterial cells that influence health and disease. As a consequence, the bacteriomes in the human body substantially influence human health and disease. The bacteriomes in the body and the immune system seem to be in constant association during bacterial and viral infections. In this review, we identify various bacterial spp. In major bacteriomes (oral, nasal, lung, and gut) of the body in healthy humans and compare them with dysbiotic bacteriomes of COVID-19 patients. We try to identify key bacterial spp. That have a positive effect on the functionality of the immune system and human health. These select bacterial spp. Could be used as potential probiotics to counter or prevent COVID-19 infections. In addition, we try to identify key metabolites produced by probiotic bacterial spp. That could have potential anti-viral effects against SARS-CoV-2. These metabolites could be subject to future therapeutic trials to determine their anti-viral efficacies.

Nasopharyngeal detection of atypical bacteria by multiplex polymerase chain reaction panel in acutely ill children was associated with an increased risk of pneumonia

AIM

We aimed to assess whether detection of respiratory bacteria by multiplex polymerase chain reaction (PCR) testing associates with clinical outcomes in acutely ill children.

METHODS

This cross-sectional study enrolled children under the age of 18 with a suspected respiratory infection treated in a paediatric emergency department of Oulu University Hospital, Finland from January 2015 through December 2015. Nasopharyngeal samples were routinely analysed for 16 respiratory viruses and later, after storage, analysed with a multiplex PCR panel for seven respiratory bacteria.

RESULTS

At least one bacterial pathogen was detected in 600 out of the 1195 children (50%). The mean age was 3.3 (SD 3.7) years and 54% were boys. Atypical bacteria were associated with a risk of pneumonia (adjusted odds ratio [aOR] 14.1, 95% CI 3.98-50.1). Co-detection of rhinovirus with Streptococcus pneumoniae was not associated with risk of pneumonia (aOR 2.39, 95% CI 0.78-7.30). Detection of Streptococcus pneumoniae, Haemophilus influenzae or both was not associated with the risk of hospital admission or prescription of antibiotics.

CONCLUSION

Nasopharyngeal detection of atypical bacteria in acutely ill children was associated with a markedly increased risk of pneumonia. The clinical utility of wide testing for other respiratory bacteria needs further evaluation.

Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units

PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors.

Prevalence and Antibiogram Pattern of Klebsiella pneumoniae in a Tertiary Care Hospital in Makkah, Saudi Arabia: An 11-Year Experience

Infectious disease is one of the greatest causes of morbidity and mortality worldwide, and with the emergence of antimicrobial resistance, the situation is worsening. In order to prevent this crisis, antimicrobial resistance needs to be monitored carefully to control the spread of multidrug-resistant bacteria. Therefore, in this study, we aimed to determine the prevalence of infection caused by Klebsiella pneumoniae and investigate the antimicrobial profile pattern of K. pneumoniae in the last eleven years. This retrospective study was conducted in a tertiary hospital in Makkah, Saudi Arabia. Data were collected from January 2011 to December 2021. From 2011 to 2021, a total of 61,027 bacterial isolates were collected from clinical samples, among which 14.7% (n = 9014) were K. pneumoniae. The antibiotic susceptibility pattern of K. pneumoniae revealed a significant increase in the resistance rate in most tested antibiotics during the study period. A marked jump in the resistance rate was seen in amoxicillin/clavulanate and piperacillin/tazobactam, from 33.6% and 13.6% in 2011 to 71.4% and 84.9% in 2021, respectively. Ceftazidime, cefotaxime, and cefepime resistance rates increased from 29.9%, 26.2%, and 53.9%, respectively, in 2011 to become 84.9%, 85.1%, and 85.8% in 2021. Moreover, a significant increase in the resistance rate was seen in both imipenem and amikacin, with an average resistance rate rise from 6.6% for imipenem and 11.9% for amikacin in 2011 to 59.9% and 62.2% in 2021, respectively. The present study showed that the prevalence and drug resistance of K. pneumoniae increased over the study period. Thus, preventing hospital-acquired infection and the reasonable use of antibiotics must be implemented to control and reduce antimicrobial resistance.

The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections

Objective

Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce.

Methods

A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms.

Results

The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group.

Conclusion

In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.

Analysis of Tonsil Tissues from Patients Diagnosed with Chronic Tonsillitis-Microbiological Profile, Biofilm-Forming Capacity and Histology

Chronic tonsillitis (CT) is a global health issue which can impair patient's quality of life and has an important socioeconomic impact due to the nonrational use of antibiotics, increased antimicrobial resistance and frequent need for surgical treatment. In order to isolate and identify the causing agents of CT, a total of 79 postoperative palatine and adenoid tissue samples were obtained from the ENT Clinic, KBC Zvezdara, Belgrade, Serbia. Culture identification was performed by MALDI-TOF MS and the Staphylococcus aureus isolates were tested for biofilm forming capability and antibiotic susceptibility. Additionally, a histological examination of palatine and adenoid tissue was performed in order to detect the presence of CT-causing bacteria. The slight majority of participants were females with median age of 28 years for adult patients (group I) and 6 years for children (group II). Analysis of the incidence of bacteria isolated from tissue samples in both groups showed the highest prevalence of S. aureus, Streptococcus oralis and Streptococcus parasanquinis. In addition to interfollicular hyperplasia, colonies of species S. aureus were detected in histological material. The presence of biofilm might be the reason for the recurrence of infection. Therefore, searching for a new treatment of CT is of great importance.

Incidence and Mortality Trends of Upper Respiratory Infections in China and Other Asian Countries from 1990 to 2019

Respiratory infections remain a major public health problem, affecting people of all age groups, but there is still a lack of studies analyzing the burden of upper respiratory infections (URIs) in Asian countries. We used the data from the Global Burden of Diseases Study 2019 results to assess the current status and trends of URI burden from 1990 to 2019 in Asian countries. We found that Thailand had the highest age-standardized incidence rate (ASIR) of URI both in 1990 (354,857.14 per 100,000) and in 2019 (344,287.93 per 100,000); and the highest age-standardized mortality rate (ASMR) was in China in 1990 (2.377 per 100,000), and in Uzbekistan in 2019 (0.418 per 100,000). From 1990 to 2019, ASIRs of URI slightly increased in several countries, with the speediest in Pakistan (estimated annual percentage change [EAPC] = 0.404%, 95% CI, 0.322% to 0.486%); and Kuwait and Singapore had uptrends of ASMRs, at a speed of an average 3.332% (95% CI, 2.605% to 4.065%) and 3.160% (95% CI, 1.971% to 4.362%) per year, respectively. The age structure of URI was similar at national, Asian and Global levels. Children under the age of five had the highest incidence rate, and the elderly had the highest mortality rate of URI. Asian countries with a Socio-demographic Index between 0.5 and 0.7 had relatively lower ASIRs but higher ASMRs of URIs. The declined rate of URI ASMR in Asian countries was more pronounced in higher baseline (ASMR in 1990) countries. Our findings suggest that there was a huge burden of URI cases in Asia that affected vulnerable and impoverished people's livelihoods. Continuous and high-quality surveillance data across Asian countries are needed to improve the estimation of the disease burden attributable to URIs, and the best public health interventions are needed to curb this burden.

Klebsiella pneumoniae Lower Respiratory Tract Infection in a South African Birth Cohort: a Longitudinal Study

OBJECTIVES

The role of Klebsiella pneumoniae (KP) in lower respiratory tract infection (LRTI) is not well studied. We longitudinally investigated KP colonization and its association with LRTI in a South African birth cohort.

METHODS

We conducted a case-control study of infants who developed LRTI and age-matched controls, followed twice weekly through infancy. Nasopharyngeal swabs taken fortnightly and at LRTI for 33-multipex Quantitative multiplex real-time polymerase chain reaction were tested at LRTI and twice weekly from 90 days preceding LRTI. Controls were tested over the equivalent period. Multivariate models investigated the factors associated with LRTI or with KP-associated LRTI (KP-LRTI).

RESULTS

Among 885 infants, there were 439 LRTI episodes, of which 68 (15.5%) were KP-LRTI (OR 1.93; 95% CI 1.25-3.03). Infants with KP-LRTI were younger than those without KP-LRTI (median [IQR] 3.7 [2.1-5.9] vs 4.7 [2.8-7.9] months, P-value=0.009). Clinical features of KP and non-KP-LRTI were similar with 114 (26%) infants hospitalized. Prematurity (adjusted odds ratio [aOR] 11.86; 95% CI 5.22-26.93), HIV exposure (aOR 3.32; 95% CI 1.69-6.53), lower birthweight (aOR 0.68; 95% CI 0.51-0.91), and shorter breastfeeding time (aOR 0.79; 95% CI 0.65-0.96) were associated with KP-LRTI versus non-LRTI. These factors and younger age were associated with KP-LRTI versus non-KP-LRTI.

CONCLUSION

KP was associated with a substantial proportion of LRTI, particularly in premature or HIV-exposed infants in whom strategies for treatment and prevention should be strengthened.

The microbiota in respiratory tract infections: from association to intervention

PURPOSE OF REVIEW

The respiratory microbiota has a role in respiratory tract infection (RTI) pathogenesis. On the mucosa, the respiratory microbiota interacts with potential pathogenic viruses, bacteria and the host immune system, including secretory IgA (sIgA). This review discusses the role of the respiratory microbiota and its interaction with the (mucosal) immune system in RTI susceptibility, as well as the potential to exploit the microbiota to promote health and prevent RTIs.

RECENT FINDINGS

Recent studies confirm that specific microbiota profiles are associated with RTI susceptibility and during susceptibility and found accompanying RTIs, although clear associations have not yet been found for SARS-CoV-2 infection. sIgA plays a central role in RTI pathogenesis: it stands under control of the local microbiota, while at the same time influencing bacterial gene expression, metabolism and defense mechanisms. Respiratory microbiota interventions are still newly emerging but promising candidates for probiotics to prevent RTIs, such as Corynebacterium and Dolosigranulum species, have been identified.

SUMMARY

Improved understanding of the respiratory microbiota in RTIs and its interplay with the immune system is of importance for early identification and follow-up of individuals at risk of infection. It also opens doors for future microbiota interventions by altering the microbiota towards a healthier state to prevent and/or adjunctively treat RTIs.

Role of Microbiota in Viral Infections and Pathological Progression

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.

Distribution and Drug Resistance of Bacterial Pathogens Associated with Lower Respiratory Tract Infection in Children and the Effect of COVID-19 on the Distribution of Pathogens

By studying the distribution and drug resistance of bacterial pathogens associated with lower respiratory tract infection (LRTI) in children in Chengdu and the effect of the COVID-19 on the distribution of pathogens and by analyzing the epidemic trend and drug resistance changes of the main pathogens of LRTI, this research is supposed to provide a useful basis for the prevention of LRTI in children and the rational use of drugs in clinical practice. Hospitalized children clinically diagnosed with LRTI in Chengdu Women and Children's Central Hospital from 2011 to 2020 were selected as the study subjects. The pathogens of LRTI in children and the distribution of pathogens in different ages, genders, seasons, years, and departments and before and after the pandemic situation of COVID-19 were counted. The drug resistance distribution of the top six pathogens with the highest infection rate in the past three years and the trend of drug resistance in the past decade were analyzed. A total of 26,469 pathogens were isolated. Among them, 6240 strains (23.6%) were Gram-positive bacteria, 20152 strains (76.1%) were Gram-negative bacteria, and 73 strains (0.3%) were fungi. Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Staphylococcus aureus were highly isolated in the group of infants aged 0-1 (P < 0.01), Moraxella catarrhalis and Streptococcus pneumoniae were highly isolated in children aged 1–6 (P < 0.01), and Haemophilus influenzae was highly isolated in children over 1 (P < 0.01). The isolation rates of Enterobacteriaceae, Acinetobacter baumannii, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Staphylococcus aureus, and Candida albicans in the lower respiratory tract of 0-1 year-old male infants were higher than those of female infants (p < 0.05). Haemophilus influenzae was highly isolated in spring and summer, and Moraxella catarrhalis was highly isolated in autumn and winter, while the infection of Streptococcus pneumoniae was mainly concentrated in winter. This difference was statistically significant (P < 0.01). Affected by the COVID-19 pandemic, the isolation rates of Haemophilus influenzae and Streptococcus pneumoniae were significantly lower than those before the pandemic, and the isolation rate of Moraxella catarrhalis was significantly higher. The difference was statistically significant (P < 0.01). The proportion of isolated negative bacteria in NICU and PICU was higher than that in positive bacteria, and the infection rates of Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Acinetobacter baumannii were higher than those in other departments. The differences were statistically significant (P < 0.01). The results of drug sensitivity test showed that the drug resistance of Haemophilus influenzae and Moraxella catarrhalis was mainly concentrated in Ampicillin, First- and Second-generation cephalosporins, and Cotrimoxazole, with stable sensitivity to Third-generation cephalosporins, while the drug resistance of Streptococcus pneumoniae was concentrated in Macrolides, Sulfonamides, and Tetracyclines, with stable sensitivity to Penicillin. Staphylococcus aureus is highly resistant to penicillins and macrolides and susceptible to vancomycin. Enterobacteriaceae resistance is concentrated in cephalosporins, with a low rate of carbapenem resistance. From 2018 to 2020, 1557 strains of Staphylococcus aureus were isolated, of which 416 strains were MRSA, accounting for 27% of the isolates; 1064 strains of Escherichia coli were isolated, of which 423 strains were ESBL and 23 strains were CRE, accounting for 40% and 2% of the isolates, respectively; and 1400 strains of Klebsiella pneumoniae were isolated, of which 385 strains were ESBL and 402 strains were CRE, accounting for 28% and 29% of the isolates, respectively. Since 2011, the resistance of Escherichia coli and Klebsiella pneumoniae to Third-generation cephalosporins has increased, peaking in 2017, and has decreased after 2018, years after which carbapenem resistance has increased significantly, corresponding to an increase in the detection rate of Carbapenem-resistant Enterobacteriaceae CRE. Findings from this study revealed that there are significant differences in community-associated infectious pathogens before and after the COVID-19 pandemic, and there are significant age differences, seasonal epidemic trends, and high departmental correlation of pathogens related to lower respiratory tract disease infection in children. There was a significant gender difference in the isolation rate of pathogens associated with LRTI in infants under one year. Vaccination, implementation of isolation measures and social distance, strengthening of personal protective measures, aseptic operation of invasive medical treatment, hand hygiene, and environmental disinfection are beneficial to reducing community-associated pathogen infection, opportunistic pathogen infection, and an increase in resistant bacteria. The strengthening of bacterial culture of lower respiratory tract samples by pediatricians is conducive to the diagnosis of respiratory tract infections caused by different pathogens, contributing to the selection of effective drugs for treatment according to drug susceptibility results, which is important for the rational use of antibiotics and curbing bacterial resistance.

Analysis of national surveillance of respiratory pathogens for community-acquired pneumonia in children and adolescents

Background

Respiratory infections among children, particularly community-acquired pneumonia (CAP), is a major disease with a high frequency among outpatient and inpatient visits. The causes of CAP vary depending on individual susceptibility, the epidemiological characteristics of the community, and the season. We performed this study to establish a nationwide surveillance network system and identify the causative agents for CAP and antibiotic resistance in Korean children with CAP.

Methods

The monitoring network was composed of 28 secondary and tertiary medical institutions. Upper and lower respiratory samples were assayed using a culture or polymerase chain reaction (PCR) from August 2018 to May 2020.

Results

A total of 1023 cases were registered in patients with CAP, and PCR of atypical pneumonia pathogens revealed 422 cases of M. pneumoniae (41.3%). Respiratory viruses showed a positivity rate of 65.7% by multiplex PCR test, and human rhinovirus was the most common virus, with 312 cases (30.5%). Two hundred sixty four cases (25.8%) were isolated by culture, including 131 cases of S. aureus (12.8%), 92 cases of S. pneumoniae (9%), and 20 cases of H. influenzae (2%). The cultured, isolated bacteria may be colonized pathogen. The proportion of co-detection was 49.2%. The rate of antibiotic resistance showed similar results as previous reports.

Conclusions

This study will identify the pathogens that cause respiratory infections and analyze the current status of antibiotic resistance to provide scientific evidence for management policies of domestic respiratory infections. Additionally, in preparation for new epidemics, including COVID-19, monitoring respiratory infections in children and adolescents has become more important, and research on this topic should be continuously conducted in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07263-z.