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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

ABSTRACT: Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors.

SUBMITTER: Cuthbertson L

PROVIDER: S-EPMC4820042 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

Cuthbertson Leah L Rogers Geraint B GB Walker Alan W AW Oliver Anna A Green Laura E LE Daniels Thomas W V TW Carroll Mary P MP Parkhill Julian J Bruce Kenneth D KD van der Gast Christopher J CJ

The ISME journal 20151110 5

Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs t ...[more]

PMID: 26555248

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Project description:IntroductionThis study assessed the risk of first treatment for bovine respiratory disease (BRD) given detection of nasopharyngeal bacteria (Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) and corresponding likelihood of antimicrobial susceptibility (C/S) at two time points during the early feeding period. Relationships between C/S results and later treatment for BRD were evaluated at both the calf-level and pen-level. The association between calf-level and pen-level C/S findings during the early feeding period and subsequent C/S results at BRD treatment were also reported.MethodsAuction-sourced, recently-weaned beef calves (n = 1,599 steers) were placed in adjacent feedlot pens (8 × 100 calves) in two subsequent years. Deep nasopharyngeal (DNP) swabs were collected from all calves at time of arrival processing (1DOF) and before metaphylaxis administration with either tulathromycin or oxytetracycline, 12 days later (13DOF), and at the time of first treatment for BRD. All samples were tested for C/S.ResultsSeveral pen-level and individual calf-level C/S measures of interest were associated with future treatment for BRD and C/S at the time of treatment. The median DOF for first BRD treatment was 24 days following tulathromycin metaphylaxis and 11 days following oxytetracycline. Overall, sampling at 13DOF resulted in the best fit for more models of subsequent treatment for BRD and C/S results at BRD treatment than for sampling at arrival. In individual calves, recovery of M. haemolytica, P. multocida, or H. somni at 13DOF was associated with subsequent treatment for BRD within 45DOF. Pen-level prevalence of Pasteurellacea bacteria with tetracycline or macrolide resistance at arrival and 13DOF were associated with detection of bacteria with antimicrobial resistance (AMR) at BRD treatment, as were individual calf results at 13DOF.DiscussionThese findings suggest that the bacteria and AMR outcomes recovered from cattle near two weeks on feed can inform the prediction of future BRD risk and concurrent antimicrobial susceptibility results at time of first BRD treatment. Notably, the associations between pen-level C/S results from previous testing and corresponding findings in calves with BRD from the same pen suggested potential testing strategies to inform antimicrobial use protocols for feedlot cattle.

Project description:BackgroundRespiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence of antimicrobial resistance has led to an urgent and critical situation in developing countries, including Vietnam. This study aimed to investigate the distribution and antimicrobial resistance of bacteria in patients with AE-COPD using both conventional culture and multiplex real-time PCR. Additionally, associations between clinical characteristics and indicators of pneumonia in these patients were examined.MethodsThis cross-sectional prospective study included 92 AE-COPD patients with pneumonia and 46 without pneumonia. Sputum specimens were cultured and examined for bacterial identification, and antimicrobial susceptibility was determined for each isolate. Multiplex real-time PCR was also performed to detect ten bacteria and seven viruses.ResultsThe detection rates of pathogens in AE-COPD patients with pneumonia were 92.39%, compared to 86.96% in those without pneumonia. A total of 26 pathogenic species were identified, showing no significant difference in distribution between the two groups. The predominant bacteria included Klebsiella pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, followed by Acinetobacter baumannii and Streptococcus mitis. There was a slight difference in antibiotic resistance between bacteria isolated from two groups. The frequency of H. influenzae was notably greater in AE-COPD patients who experienced respiratory failure (21.92%) than in those who did not (9.23%). S. pneumoniae was more common in patients with stage I (44.44%) or IV (36.36%) COPD than in patients with stage II (17.39%) or III (9.72%) disease. ROC curve analysis revealed that C-reactive protein (CRP) levels could distinguish patients with AE-COPD with and without pneumonia (AUC = 0.78).ConclusionGram-negative bacteria still play a key role in the etiology of AE-COPD patients, regardless of the presence of pneumonia. This study provides updated evidence for the epidemiology of AE-COPD pathogens and the appropriate selection of antimicrobial agents in Vietnam.

Project description:BackgroundChronic obstructive pulmonary disease (COPD) is a common respiratory disease globally, characterized by obstructive ventilatory disorder under pulmonary function tests. Recent years have witnessed a yearly increase in the prevalence of COPD.ObjectiveTo investigate the impact of respiratory virus infections on patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD), and to perform sequencing typing and mutation analysis of viruses with high detection rate.MethodsA total of 1523 inpatients with AECOPD admitted to our hospital from April 1,2020 to March 30,2022 were collected and divided into two groups: the infected group (n= 532) and the non-infected group (n= 991). The related indexes between the two groups were collected and compared (including clinical characteristics and laboratory tests that blood cell count, PCT, CRP, adenovirus, respiratory syncytial virus, rhinovirus, influenza A virus, influenza B virus, etc.).ResultsIn the infected group, the proportion of patients with palpitations (49.44% VS 8.07%, P< 0.001), lipid metabolism abnormalities (18.42% VS 39.96%, P< 0.001), heart failure (39.85% VS 29.87%, P< 0.001), disease duration (17.48 ± 7.47 VS 12.45 ± 11.43 d, P< 0.001), and poor prognosis (69.55% VS 17.15%, P< 0.001) were higher than those in the non-infected group; Adenovirus (ADV) accounted for 75.94% (404/532) of all infected viruses. 31 virus strains could be categorized into 16 ADV-C1, one ADV-C5, two ADV-B3, three ADV-B7, two ADV-D17, two ADV-D19, and five ADV-D27, which were similar to the serotypes reported in severe pneumonia. Furthermore, three strains of C1 adenovirus were found to be highly homologous to the original strain AF534906 by sequencing, and the phylogenetic trees of the three main structural genes were all on the same branch as the original strain. Base mutations and amino acid variants were found in each structural gene segment. In clinical data, it's found that patients with mutations are worse than those without mutations.ConclusionRespiratory viruses are common in patients with poor prognosis of AECOPD, especially adenovirus, respiratory syncytial virus. Respiratory virus infections will lead to the deterioration of patients with AECOPD, accompanied by longer treatment cycles and poor prognosis.

Project description:Understanding mechanisms governing the resistance and resilience of microbial communities is essential for predicting their ecological responses to environmental disturbances. Although we have a good understanding of such issues for soil and lake ecosystems, how ecological resistance and resilience regulate the microbiota in the fish gut ecosystem remains unclear. Using the zebrafish model, we clarified the potential mechanisms governing the gut microbiota after exposure to silver nanoparticles (AgNPs). Here, we explored the ecological resistance and resilience of gut microbiota in zebrafish exposed to different concentrations of AgNPs (i.e., 10, 33 and 100 μg/liter) for 15, 45, 75 days. The high-throughput sequencing analysis of the 16S rRNA gene showed that AgNP exposure significantly reduced the α-diversity of gut microbiota and resulted in obvious dynamics of community composition and structure. However, the rebound of zebrafish gut microbiota was pushed toward an alternative state after 15 days of AgNP exposure. We found that homogeneous selection was a more prevalent contributor in driving gut community recovery after AgNP exposure. The resilience and resistance of gut microbiota responses to AgNP disturbance might be mainly determined by the predominant keystone taxa such as Acinetobacter and Gemmata. This study not only expanded our understanding of fish gut microbiota's responses to pollutants but also provided new insights into maintaining host-microbiome stability during environmental perturbations. IMPORTANCE Understanding the ecological mechanisms governing the resistance and resilience of microbial communities is a key issue to predict their responses to environmental disturbances. Using the zebrafish model, we wanted to clarify the potential mechanisms governing the resistance and resilience of gut microbiota after exposure to silver nanoparticles (AgNPs). We found that AgNP contamination significantly reduced the α-diversity of gut microbiota and resulted in obvious changes in community composition. The resilience and resistance of gut microbiota to AgNPs might be associated with the predominant keystone taxa (e.g., Acinetobacter and Gemmata). This study greatly expanded our understanding of how fish gut microbiota responds to environmental perturbations and maintains stability.

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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

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