Molecular etiological profile of atypical bacterial pathogens, viruses and coinfections among infants and children with community acquired pneumonia admitted to a national hospital in Lima, Peru

Evaluation of the FPMC respiratory panel for detection of respiratory tract pathogens in nasopharyngeal swab and sputum specimens

OBJECTIVES

The performance of the new Respiratory Pathogen panel (fluorescent probe melting curve, FPMC) for the qualitative detection of 12 organisms (chlamydia pneumoniae, mycoplasma pneumoniae, adenovirus, influenza A virus, influenza B virus, parainfluenza virus, rhinovirus, etc.) was assessed.

METHODS

Prospectively collected nasopharyngeal swab (NPS) and sputum specimens (n = 635) were detected by using the FPMC panel, with the Sanger sequencing method as the comparative method.

RESULTS

The overall percent concordance between the FPMC analysis method and the Sanger sequencing method was 100% and 99.66% for NPS and sputum specimens, respectively. The FPMC testified an overall positive percent concordance of 100% for both NPS and sputum specimens. The FPMC analysis method also testified an overall negative percent concordance of 100% and 99.38% for NPS and sputum specimens, respectively.

CONCLUSIONS

The FPMC analysis method is a stable and accurate assay for rapid, comprehensive detecting for respiratory pathogens.

Mayaro Virus as the cause of Acute Febrile Illness in the Colombian Amazon Basin

Introduction

Mayaro Fever (MF) is a tropical disease caused by the Mayaro virus (MAYV), with outbreaks documented in Latin America.

Methods

A hospital-based fever surveillance in Leticia, Colombian Amazon, collected sera from 1,460 patients aged 5-89 between December 2020 and April 2023.

Results

Dengue and malaria were the main diagnoses (19.4 and 5.8%, respectively), leaving 71.4% of cases unidentified after testing. Metagenomic sequencing and real-time RT-qPCR testing identified MAYV in two patients (25-year-old male and an 80-year-old female) exhibiting typical symptoms, of MF including rash, joint pain, and fever. Phylogenetics analysis of these two viruses revealed a close relationship to Peruvian strains within the MAYV D genotype.

Discussion

The study of AFI in Leticia, Colombia, identified dengue as prevalent, with malaria, COVID-19, Influenza, and Zika viruses also detected. Despite extensive testing, most cases remained unexplained until metagenomic sequencing revealed MAYV, previously unseen in Colombia but known in neighboring countries.

Conclusion

This study presents the first near full-length genomes of MAYV in Colombia, highlighting the need for further seroprevalence studies and enhanced surveillance to understand and control the spread of the virus in the region.

Chlamydophila pneumoniae-associated community-acquired pneumonia in paediatric patients of a tertiary care hospital in Mexico: molecular diagnostic and clinical insights

Chlamydophila pneumoniae is a cause of community-acquired pneumonia (CAP) and responsible for 1-2% of cases in paediatric patients. In Mexico, information on this microorganism is limited. The aim of this study was to detect C. pneumoniae using two genomic targets in a real-time PCR and IgM/IgG serology assays in paediatric patients with CAP at a tertiary care hospital in Mexico City and to describe their clinical characteristics, radiological features, and outcomes. A total of 154 hospitalized patients with diagnosis of CAP were included. Detection of C. pneumoniae was performed by real-time PCR of the pst and arg genes. Complete blood cell count, C-reactive protein measurement and IgM and IgG detection were performed. Clinical-epidemiological and radiological data from the patients were collected. C. pneumoniae was detected in 25 patients (16%), of whom 88% had underlying disease (P = 0.014). Forty-eight percent of the cases occurred in spring, 36% in girls, and 40% in children older than 6 years. All patients had cough, and 88% had fever. Interstitial pattern on chest-X-ray was the most frequent (68%), consolidation was observed in 32% (P = 0.002). IgM was positive in 7% and IgG in 28.6%. Thirty-six percent presented complications. Four percent died. A high proportion showed co-infection with Mycoplasma pneumoniae (64%). This is the first clinical report of C. pneumoniae as a cause of CAP in Mexican paediatric patients, using two genomic target strategy and serology. We found a frequency of 16.2% with predominance in children under 6 years of age. In addition; cough and fever were the most common symptoms. Early detection of this pathogen allows timely initiation of specific antimicrobial therapy to reduce development of complications. This study is one of the few to describe the presence of C. pneumoniae in patients with underlying diseases.

Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit

Background

Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection.

Methods

Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection.

Results

A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021.

Conclusions

Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.

Epidemiology and surveillance implications of community-acquired pneumonia in children

Community-acquired pneumonia (CAP) is the single largest infectious cause of hospitalization and death in children worldwide. With improved immunizations, the incidence of bacterial pneumonia and the number of colonized bacteria have decreased. However, respiratory viruses are still an important cause of CAP, especially as new infectious agents such severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge. The SARS-CoV-2 virus emerged in 2019 and caused the current coronavirus disease 2019 pandemic. Therefore, it is necessary to elucidate the epidemiology and causative pathogens of CAP. Recently, the Pneumonia and Respiratory Disease Study Group, affiliated with the Korean Academy of Pediatric Allergy and Respiratory Disease, investigated the causative pathogens of respiratory infections in children hospitalized with CAP, the serotype of Streptococcus pneumoniae, and the prevalence of Mycoplasma pneumoniae with gene mutations. Antibiotic resistance and serotype test results can determine the use of empirical antibiotics. Moreover, it is possible to help develop future vaccines by comparing bacterial culture results with vaccine serotype and identifying the changes and prevalence of each serotype. Therefore, we will perform continuous national surveillance and monitor the epidemiology of respiratory pathogens in Korea and worldwide. The surveillance of these respiratory infections can play a role in monitoring the emergence of new infectious diseases such as SARS-CoV-2.

Characteristics of Respiratory Syncytial Virus versus Influenza Infection in Hospitalized Patients of Peru: A Retrospective Observational Study

Respiratory syncytial virus (RSV) and influenza infections are important causes of respiratory illness associated with hospitalizations in children in Peru; however, comparisons of RSV and influenza hospitalization across all age groups are not available in Peru. Therefore, we conducted an observational, retrospective study between May 2015 and October 2021 using hospitalization from RSV and influenza infection data obtained from SUSALUD (open data) in Peru to compare the baseline characteristics of sex, age, region, and infection type. For the study, 2696 RSV-infected and 1563 influenza-infected hospitalized patients from different age groups were included. Most hospitalizations from RSV infection and the influenza virus occurred in children <5 years of age (86.1% vs. 32.2%, respectively). Compared with influenza infection, RSV infection was less likely to occur in individuals ≥5 years of age (adjusted odds ratio (aOR) = 0.07; 95% confidence interval (CI), 0.06−0.08; p < 0.0001; compared to <5 years of age), and more likely to occur in highlands (aOR = 1.75; 95% CI, 1.46−2.07; p < 0.0001, compared to coast region), and jungle region (aOR = 1.75; 95% CI, 1.27−2.41; p = 0.001, compared to coast region). Among the respiratory complications, RSV pneumonia was less likely to occur between different age groups (aOR = 0.29; 95% CI, 0.22−0.37; p < 0.0001, compared to <5 years of age), compared with influenza pneumonia. These findings on the RSV-hospitalization and its complications are helpful for health services planning and may increase awareness of the Peruvian population’s RSV and influenza disease burden.

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.

The clinical application of Filmarray respiratory panel in children especially with severe respiratory tract infections

BACKGROUND

Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children.

METHODS

Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated.

RESULTS

A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0-2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3-5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6-14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05).

CONCLUSIONS

This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.

Prevalence and clinical characteristics of hospitalized children with community-acquired Mycoplasma pneumoniae pneumonia during 2017/2018, Chengde, China

Community acquired-pneumonia (CAP) has varying causative pathogens and clinical characteristics. This study investigated the prevalence of Mycoplasma pneumoniae (M pneumoniae) and evaluated the clinical characteristics in infected hospitalized children by disease severity.From throat swabs of hospitalized children (5 months to 14 years) with CAP collected between November 2017 and May 2018, M pneumoniae and other CAP pathogens were identified using polymerase chain reaction (PCR). Differences in clinical and laboratory test data were compared between severe and mild case groups.Of 333 hospitalized children enrolled, 221/333 (66.4%) tested positive for M pneumoniae and 24/221 (10.9%) patients were (n = 9, aged <5 years vs n = 15, ≥5 years) single infection by PCR, however, only 170/333 (51.1%) patients were presented with M pneumoniae IgM-positive. M pneumoniae detection rate by PCR was higher than by immunoglobulin (IgM) serology. In 123/221 (55.7%) M pneumoniae infected patients, coinfection with bacterial pathogens (n = 61, <5 years vs n = 62, ≥5 years) occurred. Children (aged 3-8 years) had most M pneumoniae infection. Severe M pneumoniae pneumonia (MPP) in children occurred mostly in older age (7 [interquartile ranges {IQR}, 6-8] years; P < .0001), with longer cough days (14 [IQR, 10-19.5] days; P = .002) and hospitalization duration (9.5 [IQR, 7-12.3] days; P < .0001), lower lymphocyte ratio (24.1, [IQR, 20.0-31.1] %; P = .001), higher neutrophils ratio (66.0, [IQR, 60.2-70.3]%; P < .0001), and serum C-reactive protein (CRP) level (3.8, [IQR, 1.3-10.9] mg/L; P = .027).M pneumoniae is the most commonly detected pathogen in CAP. High coinfection prevalence increases diagnosis difficulty by clinically nonspecific characteristics. M pneumoniae detection by PCR with IgM may improve precise and reliable diagnosis of community-acquired MPP.

Consensus Document on Community-Acquired Pneumonia in Children. SENP-SEPAR-SEIP

Community-acquired pneumonia (CAP) is a prevalent disease among children and is frequently associated with both diagnostic and therapeutic uncertainties. Consensus has been reached between SEPAR, SENP and SEIP, and their conclusions are as follows.

Efficacy and Safety of Intravenous-to-oral Lefamulin, a Pleuromutilin Antibiotic, for the Treatment of Community-acquired Bacterial Pneumonia: The Phase III Lefamulin Evaluation Against Pneumonia (LEAP 1) Trial

BACKGROUND

Lefamulin, a pleuromutilin antibiotic, is active against pathogens commonly causing community-acquired bacterial pneumonia (CABP). The Lefamulin Evaluation Against Pneumonia (LEAP 1) study was a global noninferiority trial to evaluate the efficacy and safety of lefamulin for the treatment of CABP.

METHODS

In this double-blind study, adults with CABP of Pneumonia Outcomes Research Team risk class ≥III were randomized 1:1 to receive lefamulin at 150 mg intravenously (IV) every 12 hours or moxifloxacin at 400 mg IV every 24 hours. After 6 doses, patients could be switched to an oral study drug if prespecified improvement criteria were met. If methicillin-resistant Staphylococcus aureus was suspected, either linezolid or placebo was added to moxifloxacin or lefamulin, respectively. The US Food and Drug Administration primary endpoint was an early clinical response (ECR) 96 ± 24 hours after the first dose of the study drug in the intent-to-treat (ITT) population (noninferiority margin, 12.5%). The European Medicines Agency co-primary endpoints were an investigator assessment of clinical response (IACR) 5-10 days after the last dose of the study drug in the modified ITT (mITT) and clinically evaluable (CE) populations (noninferiority margin, 10%).

RESULTS

There were 551 patients randomized (n = 276 lefamulin; n = 275 moxifloxacin). Lefamulin was noninferior to moxifloxacin for ECR (87.3% vs 90.2%, respectively; difference -2.9%, 95% confidence interval [CI] g -8.5 to 2.8) and IACR (mITT, 81.7% vs 84.2%, respectively; difference -2.6%, 95% CI -8.9 to 3.9; CE, 86.9% vs 89.4%, respectively; difference -2.5%, 95% CI -8.4 to 3.4). Rates of study drug discontinuation due to treatment-emergent adverse events were 2.9% for lefamulin and 4.4% for moxifloxacin.

CONCLUSIONS

Lefamulin was noninferior to moxifloxacin for the primary efficacy endpoints and was generally safe and well tolerated.

CLINICAL TRIALS REGISTRATION

NCT02559310.

Reverse vaccinology and subtractive genomics reveal new therapeutic targets against Mycoplasma pneumoniae: a causative agent of pneumonia

Pneumonia is an infectious disease caused by bacteria, viruses or fungi that results in millions of deaths globally. Despite the existence of prophylactic methods against some of the major pathogens of the disease, there is no efficient prophylaxis against atypical agents such as Mycoplasma pneumoniae, a bacterium associated with cases of community-acquired pneumonia. Because of the morphological peculiarity of M. pneumoniae, which leads to an increased resistance to antibiotics, studies that prospectively investigate the development of vaccines and drug targets appear to be one of the best ways forward. Hence, in this paper, bioinformatics tools were used for vaccine and pharmacological prediction. We conducted comparative genomic analysis on the genomes of 88 M. pneumoniae strains, as opposed to a reverse vaccinology analysis, in relation to the capacity of M. pneumoniae proteins to bind to the major histocompatibility complex, revealing seven targets with immunogenic potential. Predictive cytoplasmic proteins were tested as potential drug targets by studying their structures in relation to other proteins, metabolic pathways and molecular anchorage, which identified five possible drug targets. These findings are a valuable addition to the development of vaccines and the selection of new in vivo drug targets that may contribute to further elucidating the molecular basis of M. pneumoniae-host interactions.

Identfication of viral and bacterial etiologic agents of the pertussis-like syndrome in children under 5 years old hospitalized

BACKGROUND

Acute respiratory infections (ARIs) represent an important cause of morbidity and mortality in children, remaining a major public health concern, especially affecting children under 5 years old from low-income countries. Unfortunately, information regarding their epidemiology is still limited in Peru.

METHODS

A secondary data analysis was performed from a previous cross-sectional study conducted in children with a probable diagnosis of Pertussis from January 2010 to July 2012. All samples were analyzed via Polymerase Chain Reaction (PCR) for the following etiologies: Influenza-A, Influenza-B, RSV-A, RSV-B, Adenovirus, Parainfluenza 1 virus, Parainfluenza 2 virus, Parainfluenza 3 virus, Mycoplasma pneumoniae and Chlamydia pneumoniae.

RESULTS

A total of 288 patients were included. The most common pathogen isolated was Adenovirus (49%), followed by Bordetella pertussis (41%) from our previous investigation, the most prevelant microorganisms were Mycoplasma pneumonia (26%) and Influenza-B (19.8%). Coinfections were reported in 58% of samples and the most common association was found between B. pertussis and Adenovirus (12.2%).

CONCLUSIONS

There was a high prevalence of Adenovirus, Mycoplasma pneumoniae and other etiologies in patients with a probable diagnosis of pertussis. Despite the presence of persistent cough lasting at least two weeks and other clinical characteristics highly suspicious of pertussis, secondary etiologies should be considered in children under 5 years-old in order to give a proper treatment.

A retrospective seroepidemiologic survey of Chlamydia pneumoniae infection in patients in Beijing between 2008 and 2017

Background

Chlamydia pneumoniae (C. pneumoniae) is an obligate intracellular bacterium and a human pathogen that causes respiratory infectious diseases. More than 50% of the adult population worldwide was once infected with C. pneumoniae, but investigations into this topic are insufficient in mainland China.

Methods

Anti-C. pneumoniae IgG and IgM antibodies were detected using micro-immunofluorescence test in serum samples of patients visiting Peking Union Medical College Hospital between 2008 and 2017 for routine medical purposes, and the aim of this retrospective study was to analyze the test results.

Results

Among 12,050 serum specimens tested for anti-C. pneumoniae IgG and IgM antibodies, the overall prevalence of anti-C. pneumoniae IgG antibodies was 86.6%, 87.2% for men and 86.0% for women. Adult men (>20 years) were found to have a significantly higher prevalence of anti-C. pneumoniae IgG than women (χ² = 30.32, P = 0.000). 3 to 5 years old patients were observed to have the lowest prevalence of anti-C. pneumoniae IgG, 42.8%, then increased with age, reaching the highest level of 98.6% in patients over 70 years of age. In the 10,434 specimens with C. pneumoniae IgG antibodies, the total geometric mean titer (GMT) for C. pneumoniae IgG was 45.71. Although GMTs were found to be significantly higher among all men than among all women (t = 5.916, P = 0.000), sex difference actually began in patients over 40 years of age and increased in the elderly. In the total 12,050 specimens, 1.2% had anti-C. pneumoniae IgM, 3.3% had anti-C. pneumoniae IgG with titers equal to or greater than 1:512; 0.39% had ≥4-fold increasing titers of antibodies in acute and convalescent phase paired samples, and 4.4% were finally confirmed to have acute antibodies against C. pneumoniae. 6 to 10 years old patients were found to have the highest rate of both IgM antibodies (3.9%) and acute antibodies (6.2%) against C. pneumoniae. Acute antibodies against C. pneumoniae were found to be more frequent in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD, 14.0%, χ² = 20.43, P = 0.000), patients with pneumonia (7.8%, χ² = 51.87, P = 0.000) and patients with acute respiratory tract infection (12.3%, χ² = 60.91, P = 0.000) than among all patients (4.4%). Both anti-C. pneumoniae IgG and IgM antibodies should be tested for acute antibodies against C. pneumoniae as testing for either alone will underestimate by a maximum of two-thirds the incidence of acute antibodies against C. pneumoniae.

Conclusions

More than 86% of Chinese patients on an average were once infected with C. pneumoniae. Adult men had both a higher prevalence and higher levels of antibodies than women. 6 to10 year old patients were found to have the most frequent acute infection of C. pneumoniae. C. pneumoniae is associated with AECOPD, pneumonia and acute respiratory tract infection. Anti-C. pneumoniae IgG and IgM should be tested simultaneously to avoid underestimation of acute antibodies against C. pneumoniae.