Bacterial Culture Underestimates Lung Pathogen Detection and Infection Status in Cystic Fibrosis

Flexible PDMS-SERS platform for culture-free diagnosis of bacterial infections in clinical wound care

The early and accurate detection of pathogenic bacteria in infected wounds is crucial for preventing severe complications such as sepsis and multiple organ failure. This study presents a new surface-enhanced Raman scattering (SERS) platform based on polydimethylsiloxane (PDMS) flexible substrates and SERS probes for culture-free detection of Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa). The PDMS flexible substrates, functionalized with gold nanoparticles (Au NPs) and specific antibodies, facilitate the efficient capture of bacteria and enhance the SERS signals through electromagnetic field coupling. The SERS probes, composed of Au@Ag core-shell nanoparticles with double-layer Raman reporter molecules, provide high sensitivity and specificity in bacterial detection. In the presence of target bacteria, the immunocomplex of PDMS flexible substrates, bacteria, and SERS probes forms, generating strong SERS signals and enabling sensitive bacterial detection. The SERS platform demonstrated limits of detection as low as 2.79 CFU/mL for E. coli, 3.42 CFU/mL for S. aureus, and 4.52 CFU/mL for P. aeruginosa. Additionally, the platform successfully monitored bacterial count changes in infected wound models and detected bacteria in clinical samples. These results indicate that the proposed SERS platform is a powerful tool for the rapid and sensitive detection of multiple bacteria in infected wounds, offering significant potential for clinical applications in infection management and advancing the field of bacterial diagnostics.

Bacterial interactions underpin worsening lung function in cystic fibrosis-associated infections

Chronic lung infections are the primary cause of morbidity and early mortality in cystic fibrosis (CF) and, as such, have been the subject of a great deal of research. Subsequently, they have become one of the key paradigms for polymicrobial infections. The literature, however, has traditionally focused on the presence of pathogens in isolation or univariate measures like number of species to predict decline of lung function and ignores large swathes of data. Here, we suggest that looking at the interactions between species identified by 16S rRNA gene sequencing, rather than at species singularly, could elucidate hitherto unknown properties of these complicated infections. To confirm this, pooled samples from studies conducted by our laboratory, sequenced using the same pipeline, were used to assess microbiome-wide associations to lung function. We found pathogenic interactions between species were limited to the most abundant species, which were composed of canonical CF pathogens (including Pseudomonas, Staphylococcus, Stenotrophomonas, and Achromobacter) and commensals. This observation is crucial for better understanding of polymicrobial infections and treatment of these conditions while providing a simple framework for expanding this research into other disease states. The adoption of ecological principles into infection science can provide better understanding and options to those suffering from chronic conditions. The statistical ecology approach presented here enables clear hypotheses from observational data that can be ratified through subsequent manipulative experimental studies. Moreover, it can also be used to support the design and construction of clinically relevant in vitro models of polymicrobial infections.

IMPORTANCE

Research studies have repeatedly demonstrated that chronic lung infection in cystic fibrosis is polymicrobial and consequently does not adhere to the single microbe-based Koch's postulates. Despite the plethora of evidence, the role of the constituent taxa present is largely unknown. Here we demonstrate how an ecological modeling perspective on lung infection microbiota can tease out potential interactions that alter progression of disease. Using techniques akin to genome-wide association studies, we show and validate 22 taxa, present in the chronic respiratory disease associated with cystic fibrosis, which have significant interactions that are negatively associated with patient lung function, the majority of which are "non-pathogenic" organisms. This work highlights the need to understand the interactive landscapes of the microbiomes to fully appreciate the complexity and treat chronic lung infections. Furthermore, this presents testable hypotheses for manipulative experiments in model systems to elucidate key mechanisms to driving disease progression.

Role of viable but non culturable cells in patients with cystic fibrosis in the era of highly effective modulator therapy

BACKGROUND

Lung infections antibiotic treatment in Cystic Fibrosis patients (pwCF) is often complicated by bacterial persisters, including the so-called Viable but Non Culturable (VBNC) forms, live cells undetected by the routine cultural microbiological methods. This study investigated the occurrence of VBNC cells of five CF bacterial pathogens in 94 pwCF over one year and the possible associations with the patients' clinical features.

METHODS

Sputum samples, recovered at routine visits and during exacerbation episodes, were analyzed for the presence of the five pathogens by both routine culture-based assays and species-specific qPCR. VBNC cells were estimated as the difference between molecular and cultural counts and their presence was matched with the clinical data in particular the therapeutic regimens.

RESULTS

All but ten pwCF showed the presence of VBNC cells at least once during the study. Pseudomonas aeruginosa and methicillin-susceptible Staphylococcus aureus were the species most frequently found in the VBNC state. Only the former showed a significant association between chronic infection and VBNC cells presence; VBNC-MSSA positive patients significantly increased overtime. The presence of non culturable bacteria was generally concurrent with poor lung functionality and more frequent pulmonary exacerbations. No significant association with modulator treatment was evidenced.

CONCLUSIONS

The obtained data demonstrated the overwhelming occurrence of bacterial VBNC cells in CF lung infections, warranting a constant monitoring of pwCF and underlining the need of implementing the routine culture-based assays with culture-independent techniques. This is pivotal to understand the CF bacterial population dynamics and to efficiently contrast the lung infection progression and worsening.

Ecological patterns and processes of temporal turnover within lung infection microbiota

BACKGROUND

Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical 'one microbe, one disease' concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota.

RESULTS

The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend's rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function.

CONCLUSIONS

Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases. Video Abstract.

Improving Protection to Prevent Bacterial Infections: Preliminary Applications of Reverse Vaccinology against the Main Cystic Fibrosis Pathogens

Reverse vaccinology is a powerful tool that was recently used to develop vaccines starting from a pathogen genome. Some bacterial infections have the necessity to be prevented then treated. For example, individuals with chronic pulmonary diseases, such as Cystic Fibrosis, are prone to develop infections and biofilms in the thick mucus that covers their lungs, mainly caused by Burkholderia cepacia complex, Haemophilus influenzae, Mycobacterium abscessus complex, Pseudomonas aeruginosa and Staphylococcus aureus. These infections are complicated to treat and prevention remains the best strategy. Despite the availability of vaccines against some strains of those pathogens, it is necessary to improve the immunization of people with Cystic Fibrosis against all of them. An effective approach is to develop a broad-spectrum vaccine to utilize proteins that are well conserved across different species. In this context, reverse vaccinology, a method based on computational analysis of the genome of various microorganisms, appears as one of the most promising tools for the identification of putative targets for broad-spectrum vaccine development. This review provides an overview of the vaccines that are under development by reverse vaccinology against the aforementioned pathogens, as well as the progress made so far.

Real-time PCR has advantages over culture-based methods in identifying major airway bacterial pathogens in chronic obstructive pulmonary disease: Results from three clinical studies in Europe and North America

Introduction

We compared the performance of real-time PCR with culture-based methods for identifying bacteria in sputum samples from patients with chronic obstructive pulmonary disease (COPD) in three studies.

Methods

This was an exploratory analysis of sputum samples collected during an observational study of 127 patients (AERIS; NCT01360398), phase 2 study of 145 patients (NTHI-004; NCT02075541), and phase 2b study of 606 patients (NTHI-MCAT-002; NCT03281876). Bacteria were identified by culture-based microbiological methods in local laboratories using fresh samples or by real-time PCR in a central laboratory using frozen samples. Haemophilus influenzae positivity with culture was differentiated from H. haemolyticus positivity by microarray analysis or PCR. The feasibility of bacterial detection by culture-based methods on previously frozen samples was also examined in the NTHI-004 study.

Results

Bacterial detection results from both culture-based and PCR assays were available from 2,293 samples from AERIS, 974 from the NTHI-004 study, and 1736 from the NTHI-MCAT-002 study. Quantitative real-time PCR (qPCR) showed higher positivity rates than culture for H. influenzae (percentages for each study: 43.4% versus 26.2%, 47.1% versus 23.6%, 32.7% versus 10.4%) and Moraxella catarrhalis (12.9% versus 6.3%, 19.0% versus 6.0%, 15.5% versus 4.1%). In the NTHI-004 and NTHI-MCAT-002 studies, positivity rates were higher with qPCR for Streptococcus pneumoniae (15.6% versus 6.1%, 15.5% versus 3.8%); in AERIS, a lower rate with qPCR than with culture (11.0% versus 17.4%) was explained by misidentification of S. pseudopneumoniae/mitis isolates via conventional microbiological methods. Concordance analysis showed lowest overall agreement for H. influenzae (82.0%, 75.6%, 77.6%), due mainly to culture-negative/qPCR-positive samples, indicating lower sensitivity of the culture-based methods. The lowest positive agreement (culture-positive/qPCR-positive samples) was observed for S. pneumoniae (35.1%, 71.2%, 71.2%). Bacterial load values for each species showed a proportion of culture-negative samples with a load detected by qPCR; for some samples, the loads were in line with those observed in culture-positive samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples.

Discussion

Real-time PCR on frozen sputum samples has enhanced sensitivity and specificity over culture-based methods, supporting its use for the identification of common respiratory bacterial species in patients with COPD.