Etiological and Radiological Profile of Acute Lower Respiratory Infections during the Pre-COVID Period in the Paediatric Ward of the Teaching Hospital of Mali and in the Community Health Centre of Yirimadio in Bamako

Introduction: Every year, nearly 4 million people pass away from acute respiratory infections. 98% of such deaths are due to lower respiratory tract infections. Even though studies have been carried on lower respiratory infections x-ray aspects in Mali, very few studies have been done to reveal bacteriological and virological evidence of this disease. Materials and methods: It is about a descriptive prospective study carried out from January to December 2018 having involved patients of all ages, coming for medical consultation at the Yirimadio Community-based health center as well as children from 6 months to 15 years old coming at the pediatric department of UHC Hôpital du Mali for a lower respiratory infection. They had all undergone chest X-ray and a PCR. The purpose: of this work is to study etiological and x-ray aspects of acute lower respiratory infections at the Yirimadio Community-based Health Center and at the UHC pediatric department of Hôpital du Mali. Findings: From January to December 2018, we recorded a frequency of 1.19%. The age group 0 - 5 years was the most represented (64.5%) with a sex ratio of 0.97 for women. Cough was the most common clinical sign (98.7%) followed by fever (58.9%). Standard frontal chest X-ray was pathological in 70% of our patients. It was bronchitis in 75.4% of cases, pneumonia (13.5%), and bronchopneumonia (12.3%). PCR positive was in 83.9% of patients. It revealed a co-infection in more than half of the patients (52.5%), bacterial infection (16.1%) and viral infection (15.2%). Pathogens isolated ranked by frequency were Streptococcus pneumoniaa (87.6%) followed by Staphylococcus aureus (24.9%) and human rhinovirus (17%). The most common viral causes were human rhinovirus (17%), followed by influenza A and B virus (7%) and human parainfluenza virus (7%). Conclusion: It stemed from the study that lower respiratory infections were mainly due to Streptococcus pneumonea and human rhinovirus during pre-COVID at the Yirimadio Community-based health center and UHC Hôpital du Mali.

Analysis of the Current Situation and Risk Factors of Lower Respiratory Tract Infection among ICU Patients in Guizhou,China During 2019-2022

Objective:This study aims to explore the prevalence,features,and risk factors of lower respiratory tract infections(LRTIs)in the intensive care unit(ICU)of a newly established hospital in Zunyi City.The goal is to devise strategies for preventing LRTIs in the ICU of new hospitals,thereby mitigating the incidence of nosocomial LRTIs in ICU patients.Methods:A case-control study was conducted from March 2019 to December 2022 to investigate the incidence rate of LRTIs in the ICU of a newly constructed hospital in Zunyi City.Patients with LRTIs constituted the case group,while those without LRTIs constituted the control group,where a 1:1 matching principle was adhered to.A single-factor chi-square(χ2)test was employed to analyze the risk factors,with independent risk factors being explored using a multivariate logistic regression analysis.Results:A total of 169 strains of pathogenic bacteria were isolated,comprising 66.28%gram-negative bacteria,17.75%gram-positive bacteria,and 15.97%fungi.The most prevalent pathogens included Acinetobacter baumannii(43.20%),Candida albicans(10.65%),and Pseudomonas aeruginosa(8.88%).Of the 82 strains infected by multidrug-resistant bacteria in patients with LRTIs,81.7%were carbapenem-resistant Acinetobacter baumannii,9.8%were multidrug-resistant Pseudomonas aeruginosa,and 6.1%were carbapenem-resistant Escherichia coli.Identified risk factors included smoking history,total hospitalization days,ICU stay length,hypoproteinemia,indwelling gastric tube,intubation type,duration of mechanical ventilation,usage of antibacterial drugs,and administration of protein drugs(P<0.05).Multivariate logistic regression analysis demonstrated that these factors were independent risk factors for nosocomial LRTIs in ICU patients(P<0.05).Conclusion:ICU patients in our hospital were mainly infected by carbapenem-resistant Acinetobacter baumannii.To prevent LRTIs in patients,tailored preventive measures should be developed and the rational use of antibacterial drugs should be promoted.

Respiratory Virus Multiplex RT-PCR Assay Sensitivities and Influence Factors in Hospitalized Children with Lower Respiratory Tract Infections

Multiplex RT-PCR assays have been widely used tools for detection and differentiation of a panel of respiratory viral pathogens. In this study, we evaluated the Qiagen ResPlex lI V2.0 kit and explored factors influencing its sensitivity. Nasopharyngeal swab （NPS） specimens were prospectively collected from pediatric inpatients with lower respiratory tract infections at the time of admission in the Shenzhen Children＇s Hospital from May 2009 to April 2010. Total nucleic acids were extracted using the EZ1 system （Qiagen, Germany） and 17 respiratory viruses and genotypes including influenza A virus （FluA）, FluB, parainfluenza virus 1 （PIV1）, PIV2, PIV3, PIV4, respiratory syncytial virus （RSV）, human metapneumovirus （hMPV）, rhinoviruses （RhV）, enteroviruses （EnV）, human bocaviruses （hBoV）, adenoviruses （AdV）, four coronaviruses （229E, OC43, NL63 and HKU1）, and FluA 2009 pandemic H1NI（H1NI-p） were detected and identified by the ResPlex II kit. In parallel, 16 real-time TaqMan quantitative RT-PCR assays were used to quantitatively detect each virus except for RhV. Influenza and parainfluenza viral cultures were also performed. Among the total 438 NPS specimens collected during the study period, one or more viral pathogens were detected in 274 （62.6%） and 201（45.9%） specimens by monoplex TaqMan RT-PCR and multiplex ResPlex, respectively. When results from monoplex PCR or cell culture were used as the reference standard, the multiplex PCR possessed specificities of 92.9-100.0%. The sensitivity of multiplex PCR for PIV3, hMPV, PIV1 and BoV were 73.1%, 70%, 66.7% and 55.6%, respectively, while low sensitivities （11.1%-40.0%） were observed for FluA, EnV, OC43, RSV and H1N1. Among the seven viruses/genotypes detected with higher frequencies, multiplex PCR sensitivities were correlated significantly with viral loads determined by the TaqMan RT-PCR in FluA, H 1N 1-p and RSV （p=0.011-0.000） The Qiagen ResPlex II multiplex RT-PCR kit possesses excellent specificity for simultaneous detection of 17 viral pathogens in NPS specimens in pediatric inpatients at the time of admission. The sensitivity of multiplex RT-PCR was influenced by viral loads, specimen process methods, primer and probe design and amplification condition.

Prevalence and antimicrobial susceptibility patterns of bacteria in ICU patients with lower respiratory tract infection: A cross-sectional study

Objective: To investigate the prevalence of isolated organisms in patients with lower respiratory tract infections and the antibiotic susceptibilities at a tertiary care center. Methods: In this observational and cross-sectional analysis, 114 patients admitted in the intensive care unit were enrolled. The endotracheal aspirates and bronchoalveolar lavage were collected. The bacteria were isolated and identified, and finally, antimicrobial sensitive pattern of the isolated bacteria was examined. Results: The prevalence of infection was 72.72% in male patients and 27.28% in females. The predominant bacteria were Klebsiella pneumoniae (37.50%) followed by Acinetobacter spp. (36.36%), Pseudomonas aeruginosa (7.95%),Escherichia coli (6.81%), Proteus mirabilis (2.27%), atypical Escherichia coli (1.13%), Enterococcus spp. (1.13%),Elizabethkingia meningoseptica (1.13%),Staphylococcus aureus (1.13%),Proteus vulgaris (1.13%), Citrobacter freundii (1.13%), and Citrobacter koseri (1.13%). High resistance to cephalosporins (82.18%) was demonstrated in all Gram-negative bacteria. Bacteria showed susceptibility to colistin (88.75%) followed by tigecycline (83.11%), gentamycin (36.18%), and amikacin (49.23%). Conclusions: As the most frequent respiratory organisms, Klebsiella pneumoniae and Acinetobacter spp. have increased resistance to cephalosporins and susceptibility to colistin followed by tigecycline.

Human bocavirus infection in children hospitalized with lower respiratory tract infections:Does viral load affect disease course?

Objective:To examine the effects of human bocavirus type 1(HBoV1)on the course of lower respiratory tract infections in cases of monoinfection and coinfection,and the effects of HBoV1 viral load on the disease in children under six years old hospitalized with a diagnosis of HBoV1-associated lower respiratory tract infections.Methods:Children under six years of age,who were hospitalized with the diagnosis of lower respiratory tract infection due to HBoV1 between 1 January 2021 and 1 January 2022 were included in the study.Laboratory confirmation of the respiratory pathogens was performed using polymerase chain reaction(PCR).Results:Fifty-four(16.4%)children with HBoV1 among 329 children whose PCR was positive with bacterial/viral agent in nasopharyngeal swab samples were included in the study.There were 28(51.9%)males and 26(48.1%)females with a median age 23.4 months[interquartile range(IQR):13.2,30.0 months](min-max:1 month-68 months).HBoV1 was detected as a monoinfecton in 26(48.1%)children,and as a coinfection with other respiratory agents in 28 children(51.9%).In multiple regression analysis,coinfection(P=0.032)was associated with the length of hospitalization(P<0.001;R^(2)=0.166).There was a negative correlation(r=−0.281,P=0.040)between cough and cycle threshold.Fever was found to be positively correlated with C-reactive protein(r=0.568,P<0.001)and procalcitonin(r=0.472;P=0.001).Conclusions:Although we found a higher HBoV1 viral load in children with more cough symptoms in our study,it had no effect on the severity of the disease,such as length of hospital stay and need for intensive care.Coinfection was found to affect the length of hospitalization.

Association between early viral lower respiratory tract infections and subsequent asthma development

BACKGROUND The association between hospitalization for human respiratory syncytial virus(HRSV)bronchiolitis in early childhood and subsequent asthma is well established.The long-term prognosis for non-bronchiolitis lower respiratory tract infections(LRTI)caused by viruses different from HRSV and rhinovirus,on the other hand,has received less interest.AIM To investigate the relationship between infant LRTI and later asthma and examine the influence of confounding factors.METHODS The PubMed and Global Index Medicus bibliographic databases were used to search for articles published up to October 2021 for this systematic review.We included cohort studies comparing the incidence of asthma between patients with and without LRTI at≤2 years regardless of the virus responsible.The meta-analysis was performed using the random effects model.Sources of heterogeneity were assessed by stratified analyses.RESULTS This review included 15 articles(18 unique studies)that met the inclusion criteria.LRTIs at≤2 years were associated with an increased risk of subsequent asthma up to 20 years[odds ratio(OR)=5.0,95%CI:3.3-7.5],with doctor-diagnosed asthma(OR=5.3,95%CI:3.3-8.6),current asthma(OR=5.4,95%CI:2.7-10.6),and current medication for asthma(OR=1.2,95%CI:0.7-3.9).Our overall estimates were not affected by publication bias(P=0.671),but there was significant heterogeneity[I 2=58.8%(30.6-75.5)].Compared to studies with hospitalized controls without LRTI,those with ambulatory controls had a significantly higher strength of association between LRTIs and subsequent asthma.The strength of the association between LRTIs and later asthma varied significantly by country and age at the time of the interview.The sensitivity analyses including only studies with similar proportions of confounding factors(gender,age at LRTI development,age at interview,gestational age,birth weight,weight,height,smoking exposure,crowding,family history of atopy,and family history of asthma)between cases and controls did not alter the overall estimates.CONCLUSION Regardless of the causative virus and confounding factors,viral LRTIs in children<2 years are associated with an increased risk of developing a subsequent asthma.Parents and pediatricians should be informed of this risk.

Simultaneous Detection of 13 Key Bacterial Respiratory Pathogens by Combination of Multiplex PCR and Capillary Electrophoresis

Objective Lower respiratory tract infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory bacteria. To compensate for the limits of current respiratory bacteria detection methods, we developed a combination of multiplex polymerase chain reaction （PCR） and capillary electrophoresis （MPCE） assay to detect thirteen bacterial pathogens responsible for lower respiratory tract infections, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catorrholis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Mycoplasma pneumoniae, Legionella spp., Bordetella pertussis, Mycobacterium tuberculosis complex, Corynebactefium diphthefiae, and Streptococcus pyogenes. Methods Three multiplex PCR reactions were built, and the products were analyzed by capillary electrophoresis using the high-throughput DNA analyzer. The specificity of the MPCE assay was examined and the detection limit was evaluated using DNA samples from each bacterial strain and the simulative samples of each strain. This assay was further evaluated using 152 clinical specimens and compared with real-time PCR reactions. For this assay, three nested-multiplex-PCRs were used to detect these clinical specimens. Results The detection limits of the MPCE assay for the 13 pathogens were very low and ranged from 10-7 to 10-2 ng/μL. Furthermore, analysis of the 252 clinical specimens yielded a specificity ranging from 96.5%-100.0%, and a sensitivity of 100.0% for the 13 pathogens. Conclusion This study revealed that the MPCE with high specificity and sensitivity. This assay survey of respiratory pathogens. assay is a rapid, reliable, and high-throughput method has great potential in the molecular epidemiological.

Lung Function in Wheezing Infants after Acute Lower Respiratory Tract Infection and Its Association with Respiratory Outcome

Background： Wheezing is common in early childhood and remains an important health concern. The aim of this study was to assess the lung function of wheezing infants and to investigate the relationship between lung function and respiratory outcome. Methods： Infants 〈2 years of age with acute lower respiratory tract infection （ALRTI） who had undergone lung function tests were included in the study. They were assigned to wheeze or no wheeze group based on physical examination. Infants without any respiratory diseases were enrolled as controls. Lung function was measured during the acute phase and 3 months after ALRTI. One-year follow-up for infants with ALRTI was achieved. Results： A total of 252 infants with ALRTI who had acceptable data regarding tidal breathing were included in the final analysis. Compared with the control and the no wheeze groups, infants in the wheeze group had significantly decreased time to peak tidal expiratory flow as a percentage of total expiratory time （TPTEF/TE） （20.1 1 6.4% vs. 34.4 ± 6.2% and 26.4 ±8.3%, respectively, P 〈 0.0001） and significantly increased peak tidal expiratory flow （PTEF） （90.7 ± 26.3 ml/s vs. 79.3 ± 18.4 ml/s and 86.1 ± 28.0 ml/s, respectively, P 〈 0.01）, sReff and Reff. The infants in the wheeze group still had lower TPTEF/TE and volume to peak tidal expiratory flow as a percentage of total expiratory volume （VPTEF/VE） than the no wheeze infants 3 months after the ALRT1. Moreover, there was a significant inverse relationship between TPTEF/TE, VPTEF/VE, and the recurrence of wheezing and pneumonia. Conclusions： Impaired lung function was present in wheezing infants with ALRTI and the deficits persisted. In addition, the lower level of TPTEF/TE and VPTEF/VE was a risk factor for poor respiratory outcome.

Diagnostic Value of Nasopharyngeal Aspirates in Children with Lower Respiratory Tract Infections

Background： The accuracy of nasopharyngeal aspirate （NPA） specimens in detecting lower respiratory pathogens remains controversial. The objective of this study was to evaluate the diagnostic accuracy of aspirates （NPAs） specimen in lower respiratory tract infections （LRTIs） in children. Methods： The prospective study was designed to collect the data of paired NPAs and bronchoalveolar lavage fluids from children with acute LRTIs from January 2013 to December 2015. All specimens were subjected to pathogen detection： bacterial detection by culture, Mvcoplasma pneumoniae （Mp） detection by polymerase chain reaction assay and virus （influenza A and B viruses, parainfluenza virus [PIV] Types 1 and 3, respiratory syncytial virus, and adenovirus） detection by immunofluorescence assay. The diagnostic accuracy analysis of NPAs was stratified by age ≤3 years （n = 194） and 〉3 years （n = 294）. Results： We collected paired specimens from 488 children. The positive rate of pathogen was 61.6%. For Streptococcus pneumoniae, NPA culture had the specificity of 89.9% and negative predictive value of 100% in age ≤3 years, the specificity of 97.2% and negative predictive value of 98.9% in age 〉3 years. For Mp, the positive predictive values of NPA was 77.4% in children ≤3 years, and 89.1% in children 〉3 years. For PIV III, NPA specimen had the specificity of 99.8% and negative predictive value of 96.5% in children ≤3 years. For adenovirus, NPA had the specificity of 97.8% and negative predictive value of 98.4% in age ≤3 years, the specificity of 98.9% and negative predictive value of 99.3% in age 〉3 years. Conclusions： NPAs are less invasive diagnostic respiratory specimens, a negative NPA result is helpful in ＂rule out＂ lower airway infection; however, a positive result does not reliably ＂rule in＂ the presence of pathogens.

Drug-resistant genes carried by Acinetobacter baumanii isolated from patients with lower respiratory tract infection

Background Acinetobacter baumanii （A. baumanii ） remains an important microbial pathogen resulting in nosocomialacquired infections with significant morbidity and mortality. The mechanism by which nosocomial bacteria, like A. baumanii, attain multidrug resistance to antibiotics is of considerable interest. The aim in this study was to investigate the spread status of antibiotic resistance genes, such as multiple 13-1actamase genes and aminoglycoside-modifying enzyme genes, from A. baumanii strains isolated from patients with lower respiratory tract infections （LRTIs）. Methods Two thousand six hundred and ninety-eight sputum or the bronchoalveolar lavage samples from inpatients with LRTIs were collected in 21 hospitals in the mainland of China from November 2007 to February 2009. All samples were routinely inoculated. The isolated bacterial strains and their susceptibility were analyzed via VITEK-2 expert system. Several kinds of antibiotic resistant genes were further differentiated via polymerase chain reaction and sequencing methods. Results Totally, 39 A. baumanii strains were isolated from 2698 sputum or bronchoalveolar lavage samples. There was not only a high resistant rate of the isolated A. baumanfi strains to ampicillin and first- and second-generation cephalosporins （94.87%, 100% and 97.44%, respectively）, but also to the third-generation cephalosporins （ceftriaxone at 92.31%, ceftazidine at 51.28%） and imipenem （43.59%） as well. The lowest antibiotic resistance rate of 20.51% was found to amikacin. The OXA-23 gene was identified in 17 strains of A. baumanii, and the AmpC gene in 23 strains. The TEM-1 gene was carried in 15 strains. PER-1 and SHV-2 genes were detected in two different strains. Aminoglycoside-modifying enzyme gene aac-3-1a was found in 23 strains, and the aac-6＂lb gene in 19 strains, aac-3-1a and aac-6＂lb genes hibernated in three A. baumanfi strains that showed no drug-resistant phenotype. Conclusions A. baumanii can carry multiple drug-resistant genes at the same time and result in multi-drug resistance. Aminoglycoside-modifying enzyme genes could be hibernating in aminoglycoside sensitive strains without expressing their phenotype.

Clinical characteristics and molecular epidemiology of human metapneumovirus in children with acute lower respiratory tract infections in China, 2017 to 2019: A multicentre prospective observational study

Human metapneumovirus(HMPV) infection is one of the leading causes of hospitalization in young children with acute respiratory illness. In this study, we prospectively collected respiratory tract samples from children who were hospitalized with acute lower respiratory tract infection in six hospitals in China from 2017 to 2019. HMPV was detected in 145 out of 2733 samples(5.3%) from the hospitalized children. The majority of HMPV-positive children were under the age of two(67.6%), with a median age of one year. HMPV can independently cause acute lower respiratory tract infection in young children, while all patients showed mild clinical symptoms. Of all the co-infected patients, HMPV was most commonly detected with enterovirus(EV) or rhinovirus(RhV)(38.0%),followed by respiratory syncytial virus(RSV)(32.0%). The highest detection rate occurred from March to May in both northern and southern China. Out of 145 HMPV positive samples, 48 were successfully typed, of which 36strains were subgrouped into subtypes A2c(75%), eight strains were included in subtype B1(16.7%), and four strains were included in subtype B2(8.3%). Moreover, 16 A2c strains contained 111-nucleotide duplications in the G gene. Twenty-seven complete HMPV genomes were successfully obtained, and 25(92.6%) strains belonged to subtype A2c, whereas one strain was included in subgroup B1 and another was included in subgroup B2. A total of 277 mutations were observed in the complete genomes of 25 A2c strains. All results presented here improve our understanding of clinical characteristics and molecular epidemiology of HMPV infection in children.

A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019

Human respiratory syncytial virus(RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015–2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A(RSV-A) was the predominant subgroup during this research period except in2016. Totally, 535 sequences of the second hypervariable region(HVR-2) of the G gene were obtained. Combined with182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1(512),NA1(6) and GA5(3), respectively;while 196 RSV-B sequences fell in BA9(193) and SAB4(3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258 Q and H266 L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than10%, while the sequences with T290 I and T312 I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites(296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015–2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.