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1.
J Med Microbiol ; 70(4)2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33909552

RESUMO

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.


Assuntos
Amicacina/farmacologia , Antibacterianos/farmacologia , Fibrose Cística/complicações , Macrolídeos/farmacologia , Infecções por Mycobacterium não Tuberculosas/microbiologia , Mycobacterium abscessus/efeitos dos fármacos , Fibrose Cística/microbiologia , Farmacorresistência Bacteriana , Microbiologia Ambiental , Humanos , Infecções por Mycobacterium não Tuberculosas/complicações , Sistema Respiratório/microbiologia
2.
Sci Rep ; 11(1): 6433, 2021 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-33742096

RESUMO

In response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.


Assuntos
/microbiologia , Interações Microbianas , Microbiota , Sistema Respiratório/microbiologia , /fisiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Humanos , Pulmão/microbiologia
3.
J Allergy Clin Immunol ; 147(4): 1226-1233.e2, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33577896

RESUMO

BACKGROUND: Little is known about the relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the respiratory virus responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic, and the upper respiratory tract (URT) microbiome. OBJECTIVE: We sought to compare the URT microbiome between SARS-CoV-2-infected and -uninfected adults and to examine the association of SARS-CoV-2 viral load with the URT microbiome during COVID-19. METHODS: We characterized the URT microbiome using 16S ribosomal RNA sequencing in 59 adults (38 with confirmed, symptomatic, mild to moderate COVID-19 and 21 asymptomatic, uninfected controls). In those with COVID-19, we measured SARS-CoV-2 viral load using quantitative reverse transcription PCR. We then examined the association of SARS-CoV-2 infection status and its viral load with the ⍺-diversity, ß-diversity, and abundance of bacterial taxa of the URT microbiome. Our main models were all adjusted for age and sex. RESULTS: The observed species index was significantly higher in SARS-CoV-2-infected than in -uninfected adults (ß linear regression coefficient = 7.53; 95% CI, 0.17-14.89; P = .045). In differential abundance testing, 9 amplicon sequence variants were significantly different in both of our comparisons, with Peptoniphilus lacrimalis, Campylobacter hominis, Prevotella 9 copri, and an Anaerococcus unclassified amplicon sequence variant being more abundant in those with SARS-CoV-2 infection and in those with high viral load during COVID-19, whereas Corynebacterium unclassified, Staphylococcus haemolyticus, Prevotella disiens, and 2 Corynebacterium_1 unclassified amplicon sequence variants were more abundant in those without SARS-CoV-2 infection and in those with low viral load during COVID-19. CONCLUSIONS: Our findings suggest complex associations between SARS-CoV-2 and the URT microbiome in adults. Future studies are needed to examine how these viral-bacterial interactions can impact the clinical progression, severity, and recovery of COVID-19.


Assuntos
/microbiologia , Microbiota , Sistema Respiratório/microbiologia , Carga Viral , Adulto , Biodiversidade , Estudos de Casos e Controles , Feminino , Interações entre Hospedeiro e Microrganismos , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , Pandemias , RNA Ribossômico 16S/genética , Especificidade da Espécie
4.
Ecotoxicol Environ Saf ; 212: 112006, 2021 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-33556810

RESUMO

Particulate matter (PM) is a carrier of many substances. Microorganisms are vital constituents contained in PM, and their varieties and concentrations are closely connected to human health and animal production. This study aimed to investigate the distribution characteristics of bioaerosols inside a pig house and in the respiratory tract of pigs. Environmental indices inside a nursery pig house were monitored in winter, including temperature, relative humidity, total suspended particulate (TSP), PM10, PM2.5, NH3, CO2, CO and NO. The concentrations of airborne culturable bacteria, fungi and Escherichia coli were detected. Then, 16S rRNA sequencing technology was applied to identify different-sized bioaerosols and bacteria in the respiratory tract of piglets. The results showed that the concentration of airborne culturable bacteria inside the pig house was significantly higher than that outside, and no significant difference was found among culturable fungi and Escherichia coli. The 16S rRNA results showed that the bacterial aerosols presented high similarity to the bacteria in the respiratory tract of piglets. The airborne bacterial aerosols within the size range of 1.1-3.3 µm showed high similarity to the bacteria in the lower respiratory tract (bronchus and lung) of piglets. In addition, four potential pathogenic bacterial genera (Escherichia-Shigella, Streptococcus, Acinetobacter, Pseudomonas) were identified both in the bacterial aerosols and the respiratory tract of piglets. These results will provide a significant scientific basis for exploring the potential risk of aerosols from animal houses to human and animal health.


Assuntos
Microbiologia do Ar/normas , Poluentes Atmosféricos/análise , Bactérias/isolamento & purificação , Monitoramento Ambiental/métodos , Material Particulado/análise , Sistema Respiratório/microbiologia , Aerossóis , Animais , China , Poeira , Humanos , RNA Ribossômico 16S , Estações do Ano , Suínos , Temperatura
5.
Commun Biol ; 4(1): 240, 2021 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-33603076

RESUMO

SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.


Assuntos
/microbiologia , Microbioma Gastrointestinal , Microbiota , Sistema Respiratório/microbiologia , Adolescente , Adulto , Idoso , Feminino , Microbioma Gastrointestinal/genética , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Adulto Jovem
6.
PLoS One ; 16(1): e0241732, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33406075

RESUMO

Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant bacterial taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. However, a few differentially abundant shared taxa were observed at family and genus levels. Furthermore, between-kit differences in alpha and beta diversity metrics at the amplicon sequence variant level were statistically indistinguishable. Therefore, both kits perform similarly in terms of 16S rRNA gene-based poultry microbiome analysis for the sample types analyzed in this study.


Assuntos
Galinhas/microbiologia , DNA Bacteriano , DNA Ribossômico , Microbiota , RNA Ribossômico 16S , Kit de Reagentes para Diagnóstico , Sistema Respiratório/microbiologia , Animais , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , DNA Ribossômico/genética , DNA Ribossômico/isolamento & purificação , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação
7.
Artigo em Inglês | MEDLINE | ID: mdl-33470926

RESUMO

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia. As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena. Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena. Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.


Assuntos
Bovinos/microbiologia , Mannheimia/classificação , Filogenia , Sistema Respiratório/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Mannheimia/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suíça , Ubiquinona/química
8.
Toxicol Lett ; 334: 14-20, 2020 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-32949622

RESUMO

Air pollution is known to trigger and exacerbate many respiratory diseases. The interaction between respiratory microbiome and host plays a significant role in maintaining airway immune homeostasis and health. Emerging evidence has revealed the associations of disturbances in the airway microbiome with air pollution and respiratory disease. However, respiratory microbiome has been an undervalued player in progressions of respiratory disease caused by air pollution. In this review, we summarize the current research advances with respect to the effects of air pollution on respiratory microbiome, then discuss the underlying mechanisms of air pollution induction of dysbiosis in respiratory microbiota and its links to respiratory diseases. This work may be helpful to deepening understanding the relationships between exposure, microbiome and airway disease and discovering new preventive and therapeutic strategies for air pollution-mediated respiratory disease.


Assuntos
Poluentes Atmosféricos/toxicidade , Poluição do Ar/efeitos adversos , Microbiota/efeitos dos fármacos , Material Particulado/toxicidade , Sistema Respiratório/efeitos dos fármacos , Doenças Respiratórias/induzido quimicamente , Humanos , Exposição por Inalação/efeitos adversos , Sistema Respiratório/microbiologia , Doenças Respiratórias/microbiologia
9.
BMC Infect Dis ; 20(1): 646, 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873235

RESUMO

BACKGROUND: COVID-19 is known as a new viral infection. Viral-bacterial co-infections are one of the biggest medical concerns, resulting in increased mortality rates. To date, few studies have investigated bacterial superinfections in COVID-19 patients. Hence, we designed the current study on COVID-19 patients admitted to ICUs. METHODS: Nineteen patients admitted to our ICUs were enrolled in this study. To detect COVID-19, reverse transcription real-time polymerase chain reaction was performed. Endotracheal aspirate samples were also collected and cultured on different media to support the growth of the bacteria. After incubation, formed colonies on the media were identified using Gram staining and other biochemical tests. Antimicrobial susceptibility testing was carried out based on the CLSI recommendations. RESULTS: Of nineteen COVID-19 patients, 11 (58%) patients were male and 8 (42%) were female, with a mean age of ~ 67 years old. The average ICU length of stay was ~ 15 days and at the end of the study, 18 cases (95%) expired and only was 1 case (5%) discharged. In total, all patients were found positive for bacterial infections, including seventeen Acinetobacter baumannii (90%) and two Staphylococcus aureus (10%) strains. There was no difference in the bacteria species detected in any of the sampling points. Seventeen of 17 strains of Acinetobacter baumannii were resistant to the evaluated antibiotics. No metallo-beta-lactamases -producing Acinetobacter baumannii strain was found. One of the Staphylococcus aureus isolates was detected as methicillin-resistant Staphylococcus aureus and isolated from the patient who died, while another Staphylococcus aureus strain was susceptible to tested drugs and identified as methicillin-sensitive Staphylococcus aureus. CONCLUSIONS: Our findings emphasize the concern of superinfection in COVID-19 patients due to Acinetobacter baumannii and Staphylococcus aureus. Consequently, it is important to pay attention to bacterial co-infections in critical patients positive for COVID-19.


Assuntos
Infecções por Acinetobacter/complicações , Acinetobacter baumannii/isolamento & purificação , Betacoronavirus/fisiologia , Coinfecção/epidemiologia , Infecções por Coronavirus/complicações , Pneumonia Viral/complicações , Infecções Estafilocócicas/complicações , Staphylococcus aureus/isolamento & purificação , Infecções por Acinetobacter/epidemiologia , Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/efeitos dos fármacos , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Complicações do Diabetes/epidemiologia , Feminino , Cardiopatias/complicações , Humanos , Hipertensão/complicações , Unidades de Terapia Intensiva , Masculino , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Sistema Respiratório/microbiologia , Infecções Estafilocócicas/epidemiologia , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/efeitos dos fármacos
10.
BMC Infect Dis ; 20(1): 697, 2020 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-32962658

RESUMO

BACKGROUND: The microbiota of the respiratory tract has an important role in maintaining respiratory health. However, little is known on the respiratory microbiota in asthmatic patients among Middle Eastern populations. This study investigated the respiratory microbiota composition and functionality associated with asthma in Emirati subjects. METHODS: We performed 16S rRNA and ITS2-gene based microbial profiling of 40 expectorated sputum samples from adult and pediatric Emirati individuals averaging 52 and 7 years of age, respectively with or without asthma. RESULTS: We report bacterial difference belonging to Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria phyla between asthmatic and non-asthmatic controls. Similarly, fungal difference belonging to Ascomycota, Basidiomycota phyla and other unclassified fungi. Differential abundance testing among asthmatic individuals with relation to Asthma Control Test show a significant depletion of Penicillium aethiopicum and Alternaria spp., among poorly controlled asthmatics. Moreover, data suggest a significant expansion of Malassezia spp. and other unclassified fungi in the airways of those receiving steroids and leukotriene receptor antagonists' combination therapy, in contrast to those receiving steroids alone. Functional profiling from 16S data showed marked differences between pediatric asthmatic and non-asthmatic controls, with pediatric asthmatic patients showing an increase in amino acid (p-value < 5.03 × 10- 7), carbohydrate (p-value < 4.76 × 10- 7), and fatty acid degradation (p-value < 6.65 × 10- 7) pathways, whereas non-asthmatic controls are associated with increase in amino acid (p-value < 8.34 × 10- 7), carbohydrate (p-value < 3.65 × 10- 7), and fatty acid (p-value < 2.18 × 10- 6) biosynthesis pathways in concordance with enterotype composition. CONCLUSIONS: These differences provide an insight into respiratory microbiota composition in Emirati population and its possible role in the development of asthma early in life. This study provides important information that may eventually lead to the development of screening biomarkers to predict early asthma development and novel therapeutic approaches.


Assuntos
Asma/microbiologia , Bactérias , Fungos , Microbiota/fisiologia , Sistema Respiratório/microbiologia , Adolescente , Adulto , Aminoácidos/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Metabolismo dos Carboidratos , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Escarro/microbiologia , Emirados Árabes Unidos , Adulto Jovem
12.
PLoS One ; 15(7): e0235537, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32614926

RESUMO

Recent studies describe the use of UAVs in collecting blow samples from large whales to analyze the microbial and viral community in exhaled air. Unfortunately, attempts to collect blow from small cetaceans have not been successful due to their swimming and diving behavior. In order to overcome these limitations, in this study we investigated the application of a specific sampling tool attached to a UAV to analyze the blow from small cetaceans and their respiratory microbiome. Preliminary trials to set up the sampling tool were conducted on a group of 6 bottlenose dolphins (Tursiops truncatus) under human care, housed at Acquario di Genova, with approximately 1 meter distance between the blowing animal and the tool to obtain suitable samples. The same sampling kit, suspended via a 2 meter rope assembled on a waterproof UAV, flying 3 meters above the animals, was used to sample the blows of 5 wild bottlenose dolphins in the Gulf of Ambracia (Greece) and a sperm whale (Physeter macrocephalus) in the southern Tyrrhenian Sea (Italy), to investigate whether this experimental assembly also works for large whale sampling. In order to distinguish between blow-associated microbes and seawater microbes, we pooled 5 seawater samples from the same area where blow samples' collection were carried out. The the respiratory microbiota was assessed by using the V3-V4 region of the 16S rRNA gene via Illumina Amplicon Sequencing. The pooled water samples contained more bacterial taxa than the blow samples of both wild animals and the sequenced dolphin maintained under human care. The composition of the bacterial community differed between the water samples and between the blow samples of wild cetaceans and that under human care, but these differences may have been mediated by different microbial communities between seawater and aquarium water. The sperm whale's respiratory microbiome was more similar to the results obtained from wild bottlenose dolphins. Although the number of samples used in this study was limited and sampling and analyses were impaired by several limitations, the results are rather encouraging, as shown by the evident microbial differences between seawater and blow samples, confirmed also by the meta-analysis carried out comparing our results with those obtained in previous studies. Collecting exhaled air from small cetaceans using drones is a challenging process, both logistically and technically. The success in obtaining samples from small cetacean blow in this study in comparison to previous studies is likely due to the distance the sampling kit is suspended from the drone, which reduced the likelihood that the turbulence of the drone propeller interfered with successfully sampling blow, suggested as a factor leading to poor success in previous studies.


Assuntos
Cetáceos/microbiologia , Microbiota , Sistema Respiratório/microbiologia , Aeronaves , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Golfinho Nariz-de-Garrafa/microbiologia , Análise por Conglomerados , Análise de Componente Principal , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Robótica , Baleias/microbiologia
13.
J Med Microbiol ; 69(8): 1124-1131, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32597749

RESUMO

Introduction. Acute otitis media (AOM) is the most common bacterial infection in early childhood, but the underlying mechanisms making some children more susceptible are poorly understood.Aim. To examine the associations between bacterial airway colonization in early life and the risk of AOM and tympanostomy tube insertion (TTI), and whether such associations are modulated by an insufficient local immune mediator response to bacterial colonization.Methodology. Bacterial cultures from hypopharyngeal samples were obtained at 1 week, 1 month and 3 months of age in the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort comprising 700 children. Twenty immune mediators were quantified from airway mucosal lining fluid sampled at 1 month. AOM symptoms were registered in a daily diary until 3 years. Information on TTI in the first 3 years was obtained from national registers.Results. Children colonized with Streptococcus pneumoniae at 1 month of age had increased incidence of AOM [aIRR 2.43 (1.14-5.21)] and children colonized with Moraxella catarrhalis at 1 month or Haemophilus influenzae at 3 months had an increased risk of TTI [aHR 1.45 (1.00-2.10) and 1.73 (1.10-2.71)]. There were no associations between the local immune mediator response to colonization and risk of AOM or TTI.Conclusion. Pathogenic bacterial airway colonization in early life was found to be associated with an increased risk of otitis media, albeit not consistently. These associations were independent of the local immune response to colonization.


Assuntos
Otite Média/epidemiologia , Sistema Respiratório/imunologia , Sistema Respiratório/microbiologia , Análise de Variância , Distribuição de Qui-Quadrado , Pré-Escolar , Humanos , Lactente , Recém-Nascido , Modelos Lineares , Otite Média/imunologia , Otite Média/microbiologia , Distribuição de Poisson , Análise de Componente Principal , Modelos de Riscos Proporcionais , Fatores de Risco , Estatísticas não Paramétricas
14.
PLoS One ; 15(6): e0234558, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32584852

RESUMO

Recently, our understanding of the elusive bacterial communities in the lower respiratory tract and their role in chronic lung disease has increased significantly. However, little is known about the respiratory microorganisms in patients with endobronchial tuberculosis (EBTB), which is a chronic inflammatory disease characterized by destruction of the tracheobronchial tree due to Mycobacterium tuberculosis (MTB) infection. We retrospectively reviewed data for histopathologically and microbiologically confirmed EBTB patients diagnosed at a tertiary referral hospital in South Korea between January 2013 and January 2019. Bacterial cultures were performed on bronchial washing from these patients at the time of EBTB diagnosis. A total of 216 patients with EBTB were included in the study. The median age was 73 years and 142 (65.7%) patients were female. Bacteria were detected in 42 (19.4%) patients. Additionally, bacterial co-infection was present in 6 (2.8%) patients. Apart from MTB, the most common microorganisms identified were Staphylococcus aureus (n = 14, 33.3%) followed by Klebsiella species (n = 12, 28.6%; 10 Klebsiella pneumoniae, 2 Klebsiella oxytoca), Streptococcus species (n = 5, 11.9%), Enterobacter species (n = 4, 9.5%), and Pseudomonas aeruginosa (n = 3, 7.1%). A variety of microorganisms were isolated from the bronchial washing indicating that changes in microorganism composition occur in the airways of patients with EBTB. Further studies are needed to investigate the clinical significance of this finding.


Assuntos
Sistema Respiratório/microbiologia , Tuberculose Pulmonar/microbiologia , Idoso , Broncoscopia , Enterobacter/isolamento & purificação , Feminino , Humanos , Klebsiella/isolamento & purificação , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/isolamento & purificação , Pseudomonas aeruginosa/isolamento & purificação , República da Coreia , Estudos Retrospectivos , Staphylococcus/isolamento & purificação
16.
FEBS Lett ; 594(11): 1651-1660, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32449939

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major global challenge. The virus infects host cells using its spike glycoprotein (S-protein) and has significantly higher infectivity and mortality rates among the aged population. Here, based on bioinformatic analysis, I provide evidence that some members of the upper respiratory tract (URT) commensal bacteria express viral S-protein -binding proteins. Based on this analysis and available data showing a decline in the population of these bacteria in the elderly, I propose that some URT commensal bacteria hamper SARS-CoV-2 infectivity and that a decline in the population of these bacteria contributes to the severity of infection. Further studies should provide a better understanding of the interaction of URT bacteria and SARS-CoV-2, which may lead to new therapeutic approaches.


Assuntos
Proteínas de Bactérias/metabolismo , Interações Microbianas , Sistema Respiratório/microbiologia , Glicoproteína da Espícula de Coronavírus/metabolismo , Envelhecimento , Betacoronavirus , Proteínas de Transporte/metabolismo , Biologia Computacional , Infecções por Coronavirus , Humanos , Modelos Moleculares , Orthomyxoviridae , Pandemias , Pneumonia Viral , Estrutura Secundária de Proteína , Proteobactérias/metabolismo
17.
Vet Clin North Am Food Anim Pract ; 36(2): 297-320, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32451027

RESUMO

The respiratory tract of cattle is colonized by complex bacterial ecosystems also known as bacterial microbiotas. These microbiotas evolve over time and are shaped by numerous factors, including maternal vaginal microbiota, environment, age, diet, parenteral antimicrobials, and stressful events. The resulting microbiota can be diverse and enriched with known beneficial bacteria that can provide colonization resistance against bacterial pathogens or, on the contrary, with opportunistic pathogens that can predispose cattle to respiratory disease. The respiratory microbiota can be modulated by nonantimicrobial approaches to promote health, creating new potential strategies for prevention and treatment of bovine respiratory disease.


Assuntos
Doenças dos Bovinos/microbiologia , Microbiota/fisiologia , Sistema Respiratório/microbiologia , Doenças Respiratórias/veterinária , Animais , Bactérias/genética , Bovinos , Doenças Respiratórias/microbiologia
18.
PLoS One ; 15(5): e0228606, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32392246

RESUMO

Bordetella pertussis, the causative agent of whopping cough, produces an adenylate cyclase toxin (CyaA) that plays a key role in the host colonization by targeting innate immune cells which express CD11b/CD18, the cellular receptor of CyaA. CyaA is also able to invade non-phagocytic cells, via a unique entry pathway consisting in a direct translocation of its catalytic domain across the cytoplasmic membrane of the cells. Within the cells, CyaA is activated by calmodulin to produce high levels of cyclic adenosine monophosphate (cAMP) and alter cellular physiology. In this study, we explored the effects of CyaA toxin on the cellular and molecular structure remodeling of A549 alveolar epithelial cells. Using classical imaging techniques, biochemical and functional tests, as well as advanced cell mechanics method, we quantify the structural and functional consequences of the massive increase of intracellular cyclic AMP induced by the toxin: cell shape rounding associated to adhesion weakening process, actin structure remodeling for the cortical and dense components, increase in cytoskeleton stiffness, and inhibition of migration and repair. We also show that, at low concentrations (0.5 nM), CyaA could significantly impair the migration and wound healing capacities of the intoxicated alveolar epithelial cells. As such concentrations might be reached locally during B. pertussis infection, our results suggest that the CyaA, beyond its major role in disabling innate immune cells, might also contribute to the local alteration of the epithelial barrier of the respiratory tract, a hallmark of pertussis.


Assuntos
Toxina Adenilato Ciclase/genética , Bordetella pertussis/enzimologia , Imunidade Inata/genética , Coqueluche/genética , Toxina Adenilato Ciclase/metabolismo , Bordetella pertussis/patogenicidade , Calmodulina/metabolismo , Membrana Celular/metabolismo , AMP Cíclico/genética , Células Epiteliais/microbiologia , Humanos , Sistema Respiratório/metabolismo , Sistema Respiratório/microbiologia , Sistema Respiratório/patologia , Coqueluche/microbiologia , Coqueluche/patologia
19.
PLoS One ; 15(4): e0232215, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32343737

RESUMO

BACKGROUND: High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota. METHODS: Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results. RESULTS: AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3-11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa. CONCLUSION: Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.


Assuntos
Bactérias/genética , DNA Bacteriano/isolamento & purificação , DNA Fúngico/isolamento & purificação , Fungos/genética , Sistema Respiratório/microbiologia , Bactérias/classificação , Bactérias/isolamento & purificação , Biodiversidade , DNA Bacteriano/genética , DNA Fúngico/genética , França , Fungos/classificação , Fungos/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Metagenômica/métodos , Microbiota/genética , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA/métodos , Escarro/microbiologia
20.
New Microbiol ; 43(2): 70-77, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32310299

RESUMO

The aim of this study was to test the detection performance of the cpsA, lytA and ply genes through qPCR in the identification of Streptococcus pneumoniae in respiratory tract samples. Specificity was tested on a panel of 128 streptococci and other bacteria DNA samples. The qPCR assay was tested on a total of 51 respiratory tract samples from patients with community-acquired pneumonia (CAP). The specificity of the cpsA, lytA and ply genes was 100%, 100%, and 86%, respectively. The quantitative assessment, based on lytA, determined a cutoff value of ~2x104, 4x102 and 4x102 DNA copies per 1 mL of valid sputum, tracheal aspirate and bronchial aspirate samples, respectively. The results from the present study suggest that qPCR detection of all three genes would be optimal in the accurate detection of Streptococcus pneumoniae.


Assuntos
Infecções Comunitárias Adquiridas , Pneumonia Pneumocócica , Reação em Cadeia da Polimerase em Tempo Real , Infecções Comunitárias Adquiridas/diagnóstico , Infecções Comunitárias Adquiridas/microbiologia , DNA Bacteriano/genética , Humanos , Pneumonia Pneumocócica/diagnóstico , Pneumonia Pneumocócica/microbiologia , Sistema Respiratório/microbiologia , Sensibilidade e Especificidade , Streptococcus pneumoniae/genética
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