Endotracheal tube biofilm inoculation of oral flora and subsequent colonization of opportunistic pathogens

A Scoping Review of the Oral Microbiome in Preterm Infants

The purpose of this scoping review was to examine the oral microbiome composition in preterm infants, sampling and collection methods, as well as exposures associated with oral microbiome composition and health implications. We conducted a scoping review of the literature using the Arskey and O'Malley framework. We identified a total of 13 articles which met our inclusion criteria and purpose of this scoping review. Articles included in this review compared the oral microbiome in preterm infants to term infants, examined alterations to the oral microbiome over time, compared the oral microbiome to different body site microbiomes, and explored associations with clinically relevant covariates and outcomes. Exposures associated with the diversity and composition of the oral microbiome in preterm infants included delivery mode, oral feeding, oropharyngeal care, skin-to-skin care, and antibiotics. Day of life and birth weight were also associated with oral microbiome composition. The oral microbiome may be associated with the composition of the tracheal and gut microbiomes, likely due to their proximity. Alpha and beta diversity findings varied across studies as well as the relative abundance of taxa. This is likely due to the different sampling techniques and timing of collection, as well as the wide range of infant clinical characteristics. Multiple factors may influence the composition of the oral microbiome in preterm infants. However, given the heterogeneity of sampling techniques and results within this review, the evidence is not conclusive on the development as well as short- and long-term implications of the oral microbiome in preterm infants and needs to be explored in future research studies. KEY POINTS: · Day of life is a critical factor in oral microbiome development in preterm infants.. · The oral microbiome may be associated with tracheal and gut microbiome colonization.. · Future research should examine sampling methodology for examining the oral microbiome.. · Future research should explore associations with the oral microbiome and adverse health outcomes..

A review on antimicrobial strategies in mitigating biofilm-associated infections on medical implants

Biomedical implants are crucial in providing support and functionality to patients with missing or defective body parts. However, implants carry an inherent risk of bacterial infections that are biofilm-associated and lead to significant complications. These infections often result in implant failure, requiring replacement by surgical restoration. Given these complications, it is crucial to study the biofilm formation mechanism on various biomedical implants that will help prevent implant failures. Therefore, this comprehensive review explores various types of implants (e.g., dental implant, orthopedic implant, tracheal stent, breast implant, central venous catheter, cochlear implant, urinary catheter, intraocular lens, and heart valve) and medical devices (hemodialyzer and pacemaker) in use. In addition, the mechanism of biofilm formation on those implants, and their pathogenesis were discussed. Furthermore, this article critically reviews various approaches in combating implant-associated infections, with a special emphasis on novel non-antibiotic alternatives to mitigate biofilm infections.

Antimicrobial materials for endotracheal tubes: A review on the last two decades of technological progress

Ventilator-associated pneumonia (VAP) is an unresolved problem in nosocomial settings, remaining consistently associated with a lack of treatment, high mortality, and prolonged hospital stay. The endotracheal tube (ETT) is the major culprit for VAP development owing to its early surface microbial colonization and biofilm formation by multiple pathogens, both critical events for VAP pathogenesis and relapses. To combat this matter, gradual research on antimicrobial ETT surface coating/modification approaches has been made. This review provides an overview of the relevance and implications of the ETT bioburden for VAP pathogenesis and how technological research on antimicrobial materials for ETTs has evolved. Firstly, certain main VAP attributes (definition/categorization; outcomes; economic impact) were outlined, highlighting the issues in defining/diagnosing VAP that often difficult VAP early- and late-onset differentiation, and that generate misinterpretations in VAP surveillance and discrepant outcomes. The central role of the ETT microbial colonization and subsequent biofilm formation as fundamental contributors to VAP pathogenesis was then underscored, in parallel with the uncovering of the polymicrobial ecosystem of VAP-related infections. Secondly, the latest technological developments (reported since 2002) on materials able to endow the ETT surface with active antimicrobial and/or passive antifouling properties were annotated, being further subject to critical scrutiny concerning their potentialities and/or constraints in reducing ETT bioburden and the risk of VAP while retaining/improving the safety of use. Taking those gaps/challenges into consideration, we discussed potential avenues that may assist upcoming advances in the field to tackle VAP rampant rates and improve patient care. STATEMENT OF SIGNIFICANCE: The use of the endotracheal tube (ETT) in patients requiring mechanical ventilation is associated with the development of ventilator-associated pneumonia (VAP). Its rapid surface colonization and biofilm formation are critical events for VAP pathogenesis and relapses. This review provides a comprehensive overview on the relevance/implications of the ETT biofilm in VAP, and on how research on antimicrobial ETT surface coating/modification technology has evolved over the last two decades. Despite significant technological advances, the limited number of gathered reports (46), highlights difficulty in overcoming certain hurdles associated with VAP (e.g., persistent colonization/biofilm formation; mechanical ventilation duration; hospital length of stay; VAP occurrence), which makes this an evolving, complex, and challenging matter. Challenges and opportunities in the field are discussed.

Airway and Respiratory Devices in the Prevention of Ventilator-Associated Pneumonia

Ventilator-associated pneumonia (VAP) is the most common ICU-acquired infection among patients under mechanical ventilation (MV). It may occur in up to 50% of mechanically ventilated patients and is associated with an increased duration of MV, antibiotic consumption, increased morbidity, and mortality. VAP prevention is a multifaceted priority of the intensive care team. The use of specialized artificial airways and other devices can have an impact on the prevention of VAP. However, these devices can also have adverse effects, and aspects of their efficacy in the prevention of VAP are still a matter of debate. This article provides a narrative review of how different airway and respiratory devices may help to reduce the incidence of VAP.

Microbial diversity and antimicrobial susceptibility in endotracheal tube biofilms recovered from mechanically ventilated COVID-19 patients

In patients with acute respiratory failure, mechanical ventilation through an endotracheal tube (ET) may be required to correct hypoxemia and hypercarbia. However, biofilm formation on these ETs is a risk factor for infections in intubated patients, as the ET can act as a reservoir of microorganisms that can cause infections in the lungs. As severely ill COVID-19 patients often need to be intubated, a better knowledge of the composition of ET biofilms in this population is important. In Spring 2020, during the first wave of the COVID-19 pandemic in Europe, 31 ETs were obtained from COVID-19 patients at Ghent University Hospital (Ghent, Belgium). Biofilms were collected from the ET and the biofilm composition was determined using culture-dependent (MALDI-TOF mass spectrometry and biochemical tests) and culture-independent (16S and ITS1 rRNA amplicon sequencing) approaches. In addition, antimicrobial resistance was assessed for isolates collected via the culture-dependent approach using disc diffusion for 11 antimicrobials commonly used to treat lower respiratory tract infections. The most common microorganisms identified by the culture-dependent approach were those typically found during lung infections and included both presumed commensal and potentially pathogenic microorganisms like Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa and Candida albicans. More unusual organisms, such as Paracoccus yeei, were also identified, but each only in a few patients. The culture-independent approach revealed a wide variety of microbes present in the ET biofilms and showed large variation in biofilm composition between patients. Some biofilms contained a diverse set of bacteria of which many are generally considered as non-pathogenic commensals, whereas others were dominated by a single or a few pathogens. Antimicrobial resistance was widespread in the isolates, e.g. 68% and 53% of all isolates tested were resistant against meropenem and gentamicin, respectively. Different isolates from the same species recovered from the same ET biofilm often showed differences in antibiotic susceptibility. Our data suggest that ET biofilms are a potential risk factor for secondary infections in intubated COVID-19 patients, as is the case in mechanically-ventilated non-COVID-19 patients.

Oral health and the presence of infectious microorganisms in hospitalized patients: a preliminary observational study

OBJECTIVE

Characterise oral health, and the presence in the oral cavity of pathogenic non-oral microorganisms potentially associated with nosocomial infections and antimicrobial resistance in non-intubated patients admitted to a Brazilian university hospital.

MATERIALS AND METHODS

An intraoral examination and oral swab were performed on hospitalized individuals at three different times, T1 (within 48 h of hospitalization), T2 (48 h after T1) and T3 (7 days after hospitalization). The oral health status was defined by the Oral Health Assessment Tool (OHAT) and Tongue Coating Status (TCS). The swabs were processed and microorganisms potentially related to nosocomial infections were phenotypically identified through colony morphology, staining and microscopy.

RESULTS

The most prevalent microorganisms were Escherichia coli, Enterococcus spp., Enterobacter spp., Pseudomonas spp., Candida albicans and Staphylococcus aureus. The oral health status was considered median, and the tongue coating index was considered high throughout the study period. The prevalence of potentially pathogenic non-oral microorganisms was high and constant from the first 48 h to the seventh day of hospitalization.

CONCLUSIONS

The results point out that the mouth can act as a reservoir of epidemiologically important pathogens within hospital settings, even in patients without mechanical ventilation, thus increasing the risk of nosocomial infections in susceptible individuals. KEY MESSAGESThe present study investigated the oral health status and the presence of pathogenic non-oral microorganisms in the oral cavity of patients hospitalized in the ward, non-intubated and mostly independent of self-care.The presence in the mouth of microorganisms related to the epidemiology of nosocomial infections and resistance to antimicrobials was high and constant from the first 48 h to the 7th day of hospitalization.The results of this study point out that the mouth can act as a reservoir of epidemiologically important pathogens within hospital settings even in patients without mechanical ventilation, increasing the risk of nosocomial infections in susceptible individuals.

The biofilm formation and antibiotic resistance of bacterial profile from endotracheal tube of patients admitted to intensive care unit in southwest of Iran

Ventilator-associated pneumonia (VAP) is a prevalent nosocomial illness in mechanically ventilated patients. Hence, the aim of this study was to investigate the pattern of antibiotic resistance and biofilm formation of bacterial profiles from Endotracheal Tubes of patients hospitalized in an intensive care unit in southwest Iran. According to the standard operating method, the microbiological laboratory conducts bacteria culture and susceptibility testing on endotracheal Tube samples suspected of carrying a bacterial infection. The Clinical and laboratory standards institute (CLSI) techniques are used to determine the Antimicrobial resistance (AMR) of bacterial isolates to antibiotics using the disk diffusion method. The crystal violet staining method was used to assess the biofilm-forming potential of isolates in a 96-well microtiter plate. In total, (51%) GPBs were included in this study. The isolated GPB were coagulase-negative Staphylococcus (16%), S. aureus (14%). In total, (40%) of GNB were included in this study. The isolated GNB were Klebsiella spp. (36%), A. baumannii (22%), P. aeruginosa (35%). (32%) bacterial strains were MDR and (29%) strains were XDR. The results of biofilm formation showed (72%) were biofilm producers. VAP is a common and severe nosocomial infection in mechanically ventilated patients. Controlling biofilm formation, whether on the ET or in the oropharyngeal cavity, is thus an important technique for treating VAP. Colistin and linezolid are antibiotics that are effective against practically all resistant GNB and GPB isolates.

Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment

Background

Studies of the respiratory tract microbiome primarily focus on airway and lung microbial diversity, but it is still unclear how these microbial communities may be affected by intubation and long periods in intensive care units (ICU), an aspect that today could aid in the understanding of COVID19 progression and disease severity. This study aimed to explore and characterize the endotracheal tube (ETT) microbiome by analyzing ETT-associated microbial communities.

Methods

This descriptive study was carried out on adult patients subjected to invasive mechanical ventilation from 2 to 21 days. ETT samples were obtained from 115 patients from ICU units in two hospitals. Bacteria isolated from endotracheal tubes belonging to the ESKAPE group were analyzed for biofilm formation using crystal violet quantification. Microbial profiles were obtained using Illumina sequencing of 16S rRNA gene.

Results

The ETT microbiome was mainly composed by the phyla Proteobacteria, Firmicutes and Bacteroidetes. Microbiome composition correlated with the ICU in which patients were hospitalized, while intubation time and diagnosis of ventilator-associated pneumonia (VAP) did not show any significant association.

Conclusion

These results suggest that the ICU environment, or medical practices, could be a key to microbial colonization and have a direct influence on the ETT microbiomes of patients that require mechanical ventilation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02086-7.

Candida Spp. in Lower Respiratory Tract Secretions - A Ten Years Retrospective Study

Introduction

Lower respiratory tract secretions (LRTS) like sputum and tracheal aspirates are frequently sent to the microbiology laboratory from patients with various respiratory pathologies. Improper collection techniques can lead to false-positive results, resulting in improper therapy.

Aim of the study

To determine the percentage of contaminated samples sent to the microbiology laboratory, to establish the prevalence of Candida spp. in non-contaminated samples and therefore, the presence of Candida spp. originating in lower respiratory tract infections. Material and

Methods

A 10-year data survey was conducted to assess the differences in Candida prevalence from contaminated versus non-contaminated samples, assessed and categorised by Bartlett grading system, and to emphasise the importance of quality control for potentially contaminated samples. The data were analysed according to gender, age, referring departments, and the species of Candida. For the statistical analysis, Kruskal-Wallis and Fisher tests were used, and the alpha value was set for 0.5.

Results

The prevalence of Candida spp. in all analysed samples was 31.60%. After excluding the contaminated samples, the actual prevalence was 27.66%. Of all sputum samples, 31.6% were contaminated. Patients aged more than 40 years old were more prone to provide contaminated sputum samples. C. albicans is more prevalent in non-contaminated sputum samples. In both sputum and tracheal aspirates, the chances of identifying a single species are higher than the chances of identifying multiple species.

Conclusions

The study emphasises the importance of assessing the quality of sputum samples because of the high number of improperly collected samples sent to the microbiology laboratory.

Drug-Eluting Endotracheal Tubes for Preventing Bacterial Inflammation in Subglottic Stenosis

OBJECTIVES/HYPOTHESIS

Subglottic stenosis (SGS) results from dysregulated extracellular matrix deposition by laryngotracheal fibroblasts causing scar tissue formation following intubation. Recent work has highlighted a relationship between this inflammatory state and imbalances in the upper airway microbiome. Herein, we engineer novel drug-eluting endotracheal (ET) tubes to deliver a model antimicrobial peptide Lasioglossin-III (Lasio) for the local modulation of the microbiome during intubation.

STUDY DESIGN

Controlled in vitro study.

METHODS

ET tubes were coated with a water-in-oil (w/o) emulsion of Lasio in poly(d,l-lactide-co-glycolide) (PLGA) by dipping thrice. Peptide release was quantified over 2 weeks via fluorometric peptide assays. The antibacterial activity was tested against airway microbes (Staphylococcus epidermidis, Streptococcus pneumoniae, and pooled human microbiome samples) by placing Lasio/PLGA-coated tubes and appropriate controls in 48 well plates with diluted bacteria. Bacterial inhibition and tube adhesion were tested by measuring optical density and colony formation after tube culture, respectively. Biocompatibility was tested against laryngotracheal fibroblasts and lung epithelial cells.

RESULTS

We achieved a homogeneous coating of ET tubes with Lasio in a PLGA matrix that yields a prolonged, linear release over 1 week (typical timeframe before the ET tube is changed). We observed significant antibacterial activity against S. epidermidis, S. pneumoniae, and human microbiome samples, and prevention of bacterial adherence to the tube. Additionally, the released Lasio did not cause any cytotoxicity toward laryngotracheal fibroblasts or lung epithelial cells in vitro.

CONCLUSION

Overall, we demonstrate the design of an effective-eluting ET tube to modulate upper-airway bacterial infections during intubation which could be deployed to help prevent SGS.

LEVEL OF EVIDENCE

N/A Laryngoscope, 2021.

A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature

Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and the intestinal microbiota that has rarely been described in human infections. Besides its role in halitosis and oral infections, S. moorei is considered to be an opportunistic pathogen causing mainly bloodstream and surgical wound infections. We performed a retrospective study of 27 cases of infections involving S. moorei in two French university hospitals between 2006 and 2021 with the aim of increasing our knowledge of this unrecognized opportunistic pathogen. We also reviewed all the data available in the literature and in genetic and metagenomic sequence databases. In addition to previously reported infections, S. moorei had been isolated from various sites and involved in intra-abdominal, osteoarticular, and cerebral infections more rarely or not previously reported. Although mostly involved in polymicrobial infections, in seven cases, it was the only pathogen recovered. Not included in all mass spectrometry databases, its identification can require 16S rRNA gene sequencing. High susceptibility to antibiotics (apart from rifampicin, moxifloxacin, and clindamycin; 91.3%, 11.8%, and 4.3% of resistant strains, respectively) has been noted. Our global search strategy revealed S. moorei to be human-associated, widely distributed in the human microbiota, including the vaginal and skin microbiota, which may be other sources for infection in addition to the oral and gut microbiota.

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

BACKGROUND

The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies.

RESULTS

To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interest. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are (1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; (2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; (3) trimming the training set to match the sequenced regions, if necessary; and (4) placing species sharing closely related sequences into a training-set-specific supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio single molecule, real-time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets.

CONCLUSION

Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies. Video Abstract.

Prolonged inhibitory effects against planktonic growth, adherence, and biofilm formation of pathogens causing ventilator-associated pneumonia using a novel polyamide/silver nanoparticle composite-coated endotracheal tube

Microbial cells can rapidly form biofilm on endotracheal tubes (ETT) causing ventilator-associated pneumonia, a serious complication in patients receiving mechanical ventilation. A novel polyamide with a good balance of hydrophilic/hydrophobic moieties was used for the embedment of green-reduction silver nanoparticles (AgNPs) for the composite-coated ETT. The films were conformal with a thickness of ∼ 17 ± 3 µm accommodating high loading of 60 ± 35 nm spherical-shaped AgNPs. The coated ETT resulted in a significant difference in reducing both planktonic growth and microbial adhesion of single and mixed-species cultures, compared with uncoated ETT (p < 0.05). A time-kill assay demonstrated rapid bactericidal effects of the coating on bacterial growth and cell adhesion to ETT surface. Biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus, commonly encountered pathogens, was inhibited by > 96% after incubation for 72 h. Polyamide/AgNP composite-coated ETT provided a broad-spectrum activity against both Gram-positive and Gram-negative bacteria as well as Candida albicans and prolonged antimicrobial activity.

Recent progress in experimental and human disease-associated multi-species biofilms

Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown about the spatial organizations and interspecies interactions of individual species within the human microbiota. Bacterial cells tend to form surface-attached biofilms in many natural environments, which enable intercellular communications and interactions in a microbial ecosystem. In this review, we summarize the recent progresses on the experimental and human disease-associated multi-species biofilm studies. We hypothesize that engineering biofilm structures and interspecies interactions might provide a tool for manipulating the composition and function of human microbiota.

Antimicrobial polymer modifications to reduce microbial bioburden on endotracheal tubes and ventilator associated pneumonia

Hospital associated infections (HAIs), infections acquired by patients during care in a hospital, remain a prevalent issue in the healthcare field. These infections often occur with the use of indwelling medical devices, such as endotracheal tubes (ETTs), that can result in ventilator-associated pneumonia (VAP). When examining the various routes of infection, VAP is associated with the highest incidence, rate of morbidity, and economic burden. Although ETTs are essential for the survival of patients requiring mechanical ventilation, their use comes with complications. The presence of an ETT in the airway impairs physiological host defense mechanisms for clearance of pathogens and provides a platform for oropharynx microorganism transport to the sterile tracheobronchial network. Antibiotics are administered to treat lower respiratory infections; however, they are not always effective and consequently can result in increased antibiotic resistance. Prophylactic approaches by altering the surface of ETTs to prevent the establishment and growth of bacteria have exhibited promising results. In addition, passive surface modifications that prevent bacterial establishment and growth, or active coatings that possess a bactericidal effect have also proven effective. In this review we aim to highlight the importance of preventing biofilm establishment on indwelling medical devices, focusing on ETTs. We will investigate successful antimicrobial modifications to ETTs and the future avenues that will ultimately decrease HAIs and improve patient care. STATEMENT OF SIGNIFICANCE: Infections that occur with indwelling medicals devices remain a constant concern in the medical field and can result in hospital-acquired infections. Specifically, ventilator associated pneumonia (VAP) occurs with the use of an endotracheal tube (ETT). Infections often require use of antibiotics and can result in patient mortality. Our review includes a summary of the recent collective work of antimicrobial ETT modifications and potential avenues for further investigations in an effort to reduce VAP associated with ETTs. Polymer modifications with antibacterial nature have been developed and tested; however, a focus on ETTs is lacking and clinical availability of new antimicrobial ETT devices is limited. Our collective work shows the successful and prospective applications to the surfaces of ETTs that can support researchers and physicians to create safer medical devices.

Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity

Multidrug-resistant bacterial pathogens are becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. Bacterial central metabolism is crucial for catabolic processes and provides precursors for anabolic pathways, such as the biosynthesis of essential biomolecules like amino acids or vitamins. However, most essential pathways are not regarded as good targets for antibiotic therapy since their products might be acquired from the environment. This issue raises doubts about the essentiality of such targets during infection. A putative target in bacterial anabolism is the methionine biosynthesis pathway. In contrast to humans, almost all bacteria carry methionine biosynthesis pathways which have often been suggested as putative targets for novel anti-infectives. While the growth of methionine auxotrophic strains can be stimulated by exogenous methionine, the extracellular concentrations required by most bacterial species are unknown. Furthermore, several phenotypic characteristics of methionine auxotrophs are only partly reversed by exogenous methionine. We investigated methionine auxotrophic mutants of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli (all differing in methionine biosynthesis enzymes) and found that each needed concentrations of exogenous methionine far exceeding that reported for human serum (∼30 µM). Accordingly, these methionine auxotrophs showed a reduced ability to proliferate in human serum. Additionally, S. aureus and P. aeruginosa methionine auxotrophs were significantly impaired in their ability to form and maintain biofilms. Altogether, our data show intrinsic defects of methionine auxotrophs. This result suggests that the pathway should be considered for further studies validating the therapeutic potential of inhibitors.IMPORTANCE New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated the nutritional needs of methionine auxotrophs of the pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli We found that each auxotrophic strain retained a growth disadvantage at methionine concentrations mimicking those available in vivo and showed that biofilm biomass was strongly influenced by endogenous methionine biosynthesis. Our experiments suggest that inhibition of the methionine biosynthesis pathway has deleterious effects even in the presence of external methionine. Therefore, additional efforts to validate the effects of methionine biosynthesis inhibitors in vivo are warranted.

Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries

Introduction: The human oral microbiota continues to change phenotype by many factors (environment, diet, genetics, stress, etc.), throughout life with a major impact on human physiology, psychology, metabolism and immune system. Amongst one such factor with unique and extreme environmental conditions is Antarctica. The sea voyage to Antarctica has many risks than at station for expedition members. In this study, we investigated the influence of Antarctic sea voyage and stay at the Indian Antarctic station Maitri, on the health of Indian expedition members by using a metagenomic approach to explore oral biodiversity. Methods: Saliva samples were collected from 12 expedition members, at 3 different time points viz. before the start of the ship voyage, after the completion of the voyage and at the end of the stay at Antarctica. Samples were analyzed for whole genome and 16S rRNA sequencing. Result: The oral microbial diversity of the expedition members was significantly changed, during the days of sailing and after the stay at Antarctica. The oral microbiota comprised mainly of the phyla Firmicutes (46%, 29% & 36%); Proteobacteria (40%, 48%, & 44%), Bacteroidetes (10%, 22%, &14%), Fusobacterium and Actinobacteria (5%-1%) and Unclassified (17%, 25% & 23%), at three time points, respectively. Further, the differential analysis of microbes across all the phyla revealed 89, 157 and 157 OTUs genera. The altered microbiota indicated changes in amino acid, lipid and carbohydrate metabolism. Conclusion: Study suggests that understanding the compositional and functional differences in the oral microbiota of Antarctic expedition members, can lay the foundation to relate these differences to their health status. It will further demonstrate the need for providing improved management during ship voyage and stay in Antarctica.

Ex Vivo Evaluation of Secretion-Clearing Device in Reducing Airway Resistance within Endotracheal Tubes

Background

Secretions accumulate in endotracheal tubes' (ETT) lumens upon their placement in patients. The secretions impact airway resistance and pressure. Secretions potentiate prolonged mechanical ventilation and ventilator-associated pneumonia. Our primary objective in this study was to evaluate an ETT-clearing device (ETT-CD) in its ability to remove secretions from ex vivo ETT lumens.

Methods

Forty ETTs, obtained from intensive care patients at extubation, were individually placed into a ventilator field performance testing simulator at 37°C. The pressure drop through the ETTs was measured at a flow rate of 60 L/min before and after cleaning with the ETT-CD and compared with unused, similarly sized controls tubes. The ETT-CD was inserted into an ETT until the tip reached Murphy's eye (hole in the side) of the ETT. The wiper, set back from the tip, was expanded by ETT-CD handle activation. As the ETT-CD was removed, the distal wiper extracted secretions from the ETT lumen.

Results

Forty ETTs were tested with nonparametric Wilcoxon signed-rank tests. Before being cleared with the ETT-CD, the median pressure drop in the extubated 7.5 mm ETTs was 17.8 cm H₂O; after ETT-CD use, it was 12.3. The cleared ETTs were significantly improved over the ETTs before being cleared (p < 0.001); however, there remained a significant difference between the cleared ETTs and the control tubes (p=0.005), indicating the clearing was not to the level of an unused ETT. Similar results were determined for the 8.0 mm ETTs.

Conclusions

For the 7.5 mm and the 8.0 mm EETs, the ETT-CD improved effective patency of the ETTs over the uncleared ETTs, independent of occlusion location, tube size, or length of tube. However, there remained a significant difference between the cleared tubes and controls.

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

Assessment of in vivo versus in vitro biofilm formation of clinical methicillin-resistant Staphylococcus aureus isolates from endotracheal tubes

Our aim was to demonstrate that biofilm formation in a clinical strain of methicillin-resistant Staphylococcus aureus (MRSA) can be enhanced by environment exposure in an endotracheal tube (ETT) and to determine how it is affected by systemic treatment and atmospheric conditions. Second, we aimed to assess biofilm production dynamics after extubation. We prospectively analyzed 70 ETT samples obtained from pigs randomized to be untreated (controls, n = 20), or treated with vancomycin (n = 32) or linezolid (n = 18). A clinical MRSA strain (MRSA-in) was inoculated in pigs to create a pneumonia model, before treating with antibiotics. Tracheally intubated pigs with MRSA severe pneumonia, were mechanically ventilated for 69 ± 16 hours. All MRSA isolates retrieved from ETTs (ETT-MRSA) were tested for their in vitro biofilm production by microtiter plate assay. In vitro biofilm production of MRSA isolates was sequentially studied over the next 8 days post-extubation to assess biofilm capability dynamics over time. All experiments were performed under ambient air (O₂) or ambient air supplemented with 5% CO₂. We collected 52 ETT-MRSA isolates (placebo N = 19, linezolid N = 11, and vancomycin N = 22) that were clonally identical to the MRSA-in. Among the ETT-MRSA isolates, biofilm production more than doubled after extubation in 40% and 50% under 5% CO₂ and O₂, respectively. Systemic antibiotic treatment during intubation did not affect this outcome. Under both atmospheric conditions, biofilm production for MRSA-in was at least doubled for 9 ETT-MRSA isolates, and assessment of these showed that biofilm production decreased progressively over a 4-day period after extubation. In conclusion, a weak biofilm producer MRSA strain significantly enhances its biofilm production within an ETT, but it is influenced by the ETT environment rather than by the systemic treatment used during intubation or by the atmospheric conditions used for bacterial growth.

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24–48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.

Endotracheal Tube Biofilm and its Impact on the Pathogenesis of Ventilator-Associated Pneumonia

Ventilator-associated pneumonia (VAP) is a common and serious nosocomial infection in mechanically ventilated patients and results in high mortality, prolonged intensive care unit- (ICU) and hospital-length of stay and increased costs. In order to reduce its incidence, it is imperative to better understand the involved mechanisms and to identify the source of infection. The role of the endotracheal tube (ET) in VAP pathogenesis became more prominent over the last decades, along with extensive research dedicated to medical device-related infections and biofilms. ET biofilm formation is an early and constant process in intubated patients. New data regarding its temporal dynamics, composition, germ identification and consequences enhance knowledge about VAP occurrence, microbiology, treatment response and recurrence. This paper presents a structured analysis of the medical literature to date, in order to outline the role of ET biofilm in VAP pathogenesis and to review recommended methods to identify ET biofilm microorganisms and to prevent or decrease VAP incidence.

Microbial Biofilms in Pulmonary and Critical Care Diseases

Microbial biofilms can colonize medical devices and human tissues, and their role in microbial pathogenesis is now well established. Not only are biofilms ubiquitous in natural and human-made environments, but they are also estimated to be associated with approximately two-thirds of nosocomial infections. This multicellular aggregated form of microbial growth confers a remarkable resistance to killing by antimicrobials and host defenses, leading biofilms to cause a wide range of subacute or chronic infections that are difficult to eradicate. We have gained tremendous knowledge on the molecular, genetic, microbiological, and biophysical processes involved in biofilm formation. These insights now shape our understanding, diagnosis, and management of many infectious diseases and direct the development of novel antimicrobial therapies that target biofilms. Bacterial and fungal biofilms play an important role in a range of diseases in pulmonary and critical care medicine, most importantly catheter-associated infections, ventilator-associated pneumonia, chronic Pseudomonas aeruginosa infections in cystic fibrosis lung disease, and Aspergillus fumigatus pulmonary infections.

Molecular analysis of endotracheal tube biofilms and tracheal aspirates in the pediatric intensive care unit

BACKGROUND

Ventilator-associated pneumonia (VAP) is a known complication of mechanically ventilated children in the pediatric intensive care unit (PICU). Endotracheal tube (ETT) biofilms are often implicated in the development of VAP by providing a conduit for pathogens to the lower respiratory tract.

METHODS

A prospective cohort study from April 2010-March 2011 of children 4 weeks to 18 years of age ventilated for greater than 72 hours to determine the microbiota of ETT biofilms and tracheal aspirates.

RESULTS

Thirty-three patients were included with a mean age of 6.1 years (SD ± 5.1 years) and average length of intubation of 8.8 days (SD ± 5.0 days). Bacterial communities from tracheal aspirates and the proximal and distal ends of ETTs were determined using 16S rRNA gene libraries. Statistical analysis utilized two-part statistics and the Wilcoxon signed rank sum test for comparison of bacterial communities. Sequencing revealed a predominance of oropharyngeal microbiota including Prevotella and Streptococcus spp. Pathogenic bacterial genera including Staphylococcus, Burkholderia, Moraxella, and Haemophilus were also represented. Bacterial load was greatest at the proximal aspect of the ETT. Duration of intubation did not significantly impact bacterial load. Morisita Horn analysis across sites showed similar communities in 24/33 (72%) of patients.

CONCLUSIONS

ETT biofilms and tracheal aspirates of intubated patients in the PICU primarily consisted of oropharyngeal microbiota, but had a significant representation of potentially pathogenic genera. While the majority of patients had similar microbiota when comparing their ETT biofilms and tracheal aspirates, a subset of patients showed a divergence between communities that requires further investigation.

Microbial investigations in throat swab and tracheal aspirate specimens are beneficial to predict the corresponding endotracheal tube biofilm flora among intubated neonates with ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in neonatal intensive care units with high morbidity and mortality. Bacterial biofilm in the endotracheal tube (ET) provides a notable and persistent source of pathogens that may cause VAP, and thus is important for VAP detection. However, during intubation microbial investigations in ET, samples are unavailable due to the infeasibility of collecting ET samples during intubation of neonates. It is therefore of great importance to find alternative sources of samples that can help identify the ET biofilm flora. In the present study, the microbial signatures of throat swabs and tracheal aspirates were compared with ET biofilm samples from VAP neonates using 16S ribosomal RNA gene polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE), cloning and sequencing. Sequences were assigned to phylogenetic species using BLAST. Microbial diversity and richness among the three types of specimens were compared based on their DGGE fingerprints, and taxonomic characteristics based on the BLAST results. The microbial richness and diversity of ET biofilms were similar to tracheal aspirate yet significantly different from throat swab samples (P<0.05). Compared with ET biofilms, the overall constituent ratio of microflora was significantly different in throat swab and tracheal aspirate samples (P<0.05). However tracheal aspirate samples were useful for predicting Staphylococcus sp. in ET biofilms with a sensitivity of 85.7% and a specificity of 83.3%. The sensitivity for the combination of tracheal aspirate and throat swab samples to detect Staphylococcus sp. in ET biofilms was 100%. The detection of Pseudomonas sp. in throat swabs assisted its identification in ET biofilms (sensitivity 33.3% and specificity 100%). The results of the present study suggest that microbial investigations in throat swab and tracheal aspirate samples are beneficial for identifying the ET biofilm flora. There may therefore be clinical applications of using substituent samples to identify pathogens in ET biofilms for VAP surveillance among intubated neonates.

Streptococcus sp. in neonatal endotracheal tube biofilms is associated with ventilator-associated pneumonia and enhanced biofilm formation of Pseudomonas aeruginosa PAO1

Ventilator-associated pneumonia (VAP) is a serious complication of mechanical ventilation leading to high morbidity and mortality among intubated neonates in neonatal intensive care units (NICUs). Endotracheal tube (ETT) biofilm flora were considered to be responsible for the occurrence of VAP as a reservoir of pathogens. However, regarding neonates with VAP, little is known about the complex microbial signatures in ETT biofilms. In the present study, a culture-independent approach based on next generation sequencing was performed as an initial survey to investigate the microbial communities in ETT biofilms of 49 intubated neonates with and without VAP. Our results revealed a far more complex microflora in ETT biofilms from intubated neonates compared to a previous culture-based study. The abundance of Streptococci in ETT biofilms was significantly related to the onset of VAP. By isolating Streptococci in ETT biofilms, we found that Streptococci enhanced biofilm formation of the common nosocomial pathogen Pseudomonas aeruginosa PAO1 and decreased IL-8 expression of airway epithelia cells exposed to the biofilm conditioned medium of PAO1. This study provides new insight into the pathogenesis of VAP among intubated neonates. More studies focusing on intubated neonates are warranted to develop strategies to address this important nosocomial disease in NICUs.

Low Efficacy of Antibiotics Against Staphylococcus aureus Airway Colonization in Ventilated Patients

Background

Airway-colonization by Staphylococcus aureus predisposes to the development of ventilator-associated tracheobronchitis (VAT) and ventilator-associated pneumonia (VAP). Despite extensive antibiotic treatment of intensive care unit patients, limited data are available on the efficacy of antibiotics on bacterial airway colonization and/or prevention of infections. Therefore, microbiologic responses to antibiotic treatment were evaluated in ventilated patients.

Methods

Results of semiquantitative analyses of S. aureus burden in serial endotracheal-aspirate (ETA) samples and VAT/VAP diagnosis were correlated to antibiotic treatment. Minimum inhibitory concentrations of relevant antibiotics using serially collected isolates were evaluated.

Results

Forty-eight mechanically ventilated patients who were S. aureus positive by ETA samples and treated with relevant antibiotics for at least 2 consecutive days were included in the study. Vancomycin failed to reduce methicillin-resistant S. aureus (MRSA) or methicillin-susceptible S. aureus (MSSA) burden in the airways. Oxacillin was ineffective for MSSA colonization in approximately 30% of the patients, and responders were typically coadministered additional antibiotics. Despite antibiotic exposure, 15 of the 39 patients (approximately 38%) colonized only by S. aureus and treated with appropriate antibiotic for at least 2 days still progressed to VAP. Importantly, no change in antibiotic susceptibility of S. aureus isolates was observed during treatment. Staphylococcus aureus colonization levels inversely correlated with the presence of normal respiratory flora.

Conclusions

Antibiotic treatment is ineffective in reducing S. aureus colonization in the lower airways and preventing VAT or VAP. Staphylococcus aureus is in competition for colonization with the normal respiratory flora. To improve patient outcomes, alternatives to antibiotics are urgently needed.

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus

In this paper, the metabolic activity in single and dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus isolates was investigated. Our results demonstrated that there was less metabolic activity in dual species biofilms compared to S. aureus biofilms. However, this was not observed if S. aureus and S. epidermidis were obtained from the same sample. The largest effect on metabolic activity was observed in biofilms of S. aureus Mu50 and S. epidermidis ET-024. A transcriptomic analysis of these dual species biofilms showed that urease genes and genes encoding proteins involved in metabolism were downregulated in comparison to monospecies biofilms. These results were subsequently confirmed by phenotypic assays. As metabolic activity is related to acid production, the pH in dual species biofilms was slightly higher compared to S. aureus Mu50 biofilms. Our results showed that S. epidermidis ET-024 in dual species biofilms inhibits metabolic activity of S. aureus Mu50, leading to less acid production. As a consequence, less urease activity is required to compensate for low pH. Importantly, this effect was biofilm-specific. Also S. aureus Mu50 genes encoding virulence-associated proteins (Spa, SplF and Dps) were upregulated in dual species biofilms compared to monospecies biofilms and using Caenorhabditis elegans infection assays, we demonstrated that more nematodes survived when co-infected with S. epidermidis ET-024 and S. aureus mutants lacking functional spa, splF or dps genes, compared to nematodes infected with S. epidermidis ET-024 and wild- type S. aureus. Finally, S. epidermidis ET-024 genes encoding resistance to oxacillin, erythromycin and tobramycin were upregulated in dual species biofilms and increased resistance was subsequently confirmed. Our data indicate that both species in dual species biofilms of S. epidermidis and S. aureus influence each other’s behavior, but additional studies are required necessary to elucidate the exact mechanism(s) involved.

Biofilms in ventilator-associated pneumonia

Biofilms develop rapidly following endotracheal intubation and represent a persistent source of unnecessary pathogens in the critically ill patient. Overall, the imbalance in the lung microbiome caused by an endotracheal tube and its role in biofilm formation and in ventilator-associated pneumonia is still unclear. Although endotracheal tube–biofilm preventive measures are being tested, no outcome impact has ever been demonstrated, and therefore no approach has been clinically recommended. Nonetheless, an accurate description of the actual biofilm morphology in vivo could be useful to implement effective preventive measures. The combined use of in vitro biofilm models, in vivo animal models and clinical research is vitally important to the attainment of a comprehensive understanding of biofilms in ventilator-associated pneumonia in the near future.

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis

Ventilator-associated pneumonia (VAP) is one of the commonest hospital-acquired infections associated with high mortality. VAP pathogenesis is closely linked to organisms colonizing the endotracheal tube (ETT) such as Staphylococcus epidermidis and Pseudomonas aeruginosa, the former a common commensal with pathogenic potential and the latter a known VAP pathogen. However, recent gut microbiome studies show that pathogens rarely function alone. Hence, we determined the ETT microbial consortium co-colonizing with S. epidermidis or P. aeruginosa to understand its importance in the development of VAP and for patient prognosis. Using bacterial 16S rRNA and fungal ITS-II sequencing on ETT biomass showing presence of P. aeruginosa and/or S. epidermidis on culture, we found that presence of P. aeruginosa correlated inversely with patient survival and with bacterial species diversity. A decision tree, using 16S rRNA and patient parameters, to predict patient survival was generated. Patients with a relative abundance of Pseudomonadaceae <4.6% and of Staphylococcaceae <70.8% had the highest chance of survival. When Pseudomonadaceae were >4.6%, age of patient <66.5 years was the most important predictor of patient survival. These data indicate that the composition of the ETT microbiome correlates with patient prognosis, and presence of P. aeruginosa is an important predictor of patient outcome.

Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation

PURPOSE

In mechanically ventilated patients, the endotracheal tube is an essential interface between the patient and ventilator, but inadvertently, it also facilitates the development of ventilator-associated pneumonia (VAP) by subverting pulmonary host defenses. A number of investigations suggest that bacteria colonizing the oral cavity may be important in the etiology of VAP. The present study evaluated microbial changes that occurred in dental plaque and lower airways of 107 critically ill mechanically ventilated patients.

MATERIALS AND METHODS

Dental plaque and lower airways fluid was collected during the course of mechanical ventilation, with additional samples of dental plaque obtained during the entirety of patients' hospital stay.

RESULTS

A "microbial shift" occurred in dental plaque, with colonization by potential VAP pathogens, namely, Staphylococcus aureus and Pseudomonas aeruginosa in 35 patients. Post-extubation analyses revealed that 70% and 55% of patients whose dental plaque included S aureus and P aeruginosa, respectively, reverted back to having a predominantly normal oral microbiota. Respiratory pathogens were also isolated from the lower airways and within the endotracheal tube biofilms.

CONCLUSIONS

To the best of our knowledge, this is the largest study to date exploring oral microbial changes during both mechanical ventilation and after recovery from critical illness. Based on these findings, it was apparent that during mechanical ventilation, dental plaque represents a source of potential VAP pathogens.

Microbial profiling of dental plaque from mechanically ventilated patients

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97 % gene similarity cut-off for bacterial species level identifications. A significant ‘microbial shift’ occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains

Pseudomonas putida strains are ubiquitous in soil and water but have also been reported as opportunistic human pathogens capable of causing nosocomial infections. In this study we describe the multilocus sequence typing of four P. putida strains (HB13667, HB8234, HB4184, and HB3267) isolated from in-patients at the Besançon Hospital (France). The four isolates (in particular HB3267) were resistant to a number of antibiotics. The pathogenicity and virulence potential of the strains was tested ex vivo and in vivo using different biological models: human tissue culture, mammalian tissues, and insect larvae. Our results showed a significant variability in the ability of the four strains to damage the host; HB13667 did not exhibit any pathogenic traits, HB4184 caused damage only ex vivo in human tissue cultures, and HB8234 had a deleterious effect in tissue culture and in vivo on rat skin, but not in insect larvae. Interestingly, strain HB3267 caused damage in all the model systems studied. The putative evolution of these strains in medical environments is discussed.

Microbial composition and antibiotic resistance of biofilms recovered from endotracheal tubes of mechanically ventilated patients

In critically ill patients, breathing is impaired and mechanical ventilation, using an endotracheal tube (ET) connected to a ventilator, is necessary. Although mechanical ventilation is a life-saving procedure, it is not without risk. Because of several reasons, a biofilm often forms at the distal end of the ET and this biofilm is a persistent source of bacteria which can infect the lungs, causing ventilator-associated pneumonia (VAP). There is a link between the microbial flora of ET biofilms and the microorganisms involved in the onset of VAP. Culture dependent and independent techniques were already used to identify the microbial flora of ET biofilms and also, the antibiotic resistance of microorganisms obtained from ET biofilms was determined. The ESKAPE pathogens play a dominant role in the onset of VAP and these organisms were frequently identified in ET biofilms. Also, antibiotic resistant microorganisms were frequently present in ET biofilms. Members of the normal oral flora were also identified in ET biofilms but it is thought that these organisms initiate ET biofilm formation and are not directly involved in the development of VAP.

The role of filamentous hemagglutinin adhesin in adherence and biofilm formation in Acinetobacter baumannii ATCC19606(T)

Filamentous hemagglutinin adhesins (FHA) are key factors for bacterial attachment and subsequent cell accumulation on substrates. Here an FHA-like Outer membrane (OM) adhesin of Acinetobacter baumannii ATCC19606(T) was displayed on Escherichia coli. The candidate autotransporter (AT) genes were identified in A. baumannii ATCC19606(T) genome. The exoprotein (FhaB1) and transporter (FhaC1) were produced independently within the same cell (FhaB1C1). The fhaC1 was mutated. In vitro adherence to epithelial cells of the recombinant FhaB1C1 and the mutant strains were compared with A. baumanni ATCC19606(T). A bivalent chimeric protein (K) composed of immunologically important portions of fhaB1 (B) and fhaC1 (C) was constructed. The mice vaccinated with chimeric protein were challenged with A. baumannii ATCC19606(T) and FhaB1C1 producing recombinant E. coli. Mutations in the fhaC1 resulted in the absence of FhaB1 in the OM. Expression of FhaB1C1 enhanced the adherence of recombinant bacteria to A546 bronchial cell line. The results revealed association of FhaB1 with bacterial adhesion and biofilm formation. Immunization with a combination of recombinant B and K proteins proved protective against A. baumanni ATCC19606(T). The findings may be applied in active and passive immunization strategies against A. baumannii.

Risk factors for tracheobronchial acquisition of resistant Gram-negative bacterial pathogens in mechanically ventilated ICU patients

The aim of this study was to identify risk factors for tracheobronchial acquisition with the most common resistant Gram-negative bacteria in the intensive care unit (ICU) during the first week after intubation and mechanical ventilation. Tracheobronchial and oropharyngeal cultures were obtained at admission, after 48 hours, and after 7 days of mechanical ventilation. Patient characteristics, interventions, and antibiotic usage were recorded. Among 71 eligible patients with two negative bronchial cultures for resistant Gram-negative bacteria (at admission and within 48 hours), 41 (58%) acquired bronchial resistant Gram-negative bacteria by day 7. Acquisition strongly correlated with presence of the same pathogens in the oropharynx: Acinetobacter baumannii [odds ratio (OR) = 20·2, 95% confidence interval (CI): 5·5-73·6], Klebsiella pneumoniae (OR = 8·0, 95% CI: 1·9-33·6), and Pseudomonas aeruginosa (OR = 27, 95%: CI 2·7-273). Bronchial acquisition with resistant K. pneumoniae also was associated with chronic liver disease (OR = 3·9, 95% CI: 1·0-15·3), treatment with aminoglycosides (OR = 4·9, 95% CI: 1·4-18·2), tigecycline (OR = 4·9, 95% CI: 1·4-18·2), and linezolid (OR = 3·9, 95% CI: 1·1-15·0). In multivariate analysis, treatment with tigecycline and chronic liver disease were independently associated with bronchial resistant K. pneumoniae acquisition. Our results show a high incidence of tracheobronchial acquisition with resistant Gram-negative microorganisms in the bronchial tree of newly intubated patients. Oropharynx colonization with the same pathogens and specific antibiotics use were independent risk factors.

Upper aero-digestive contamination by Pseudomonas aeruginosa and implications in Cystic Fibrosis

BACKGROUND

Cystic Fibrosis (CF) is a severe genetic disorder that is common among the Caucasian population. Bacterial respiratory infections are the main cause of morbidity and mortality in CF patients. Pseudomonas aeruginosa is the main pathogen of lower airways (LAW) decline.

METHOD

To understand chronic broncho-pulmonary colonization, a systematic review is conducted. The aim of our article is to identify the pathways of contamination in the upper aero-digestive tract.

RESULTS

A large number of articles report that P. aeruginosa is established first at nasopharyngeal sites. The vast majority of authors agree that the upper aero-digestive tract is the first location of colonization by P. aeruginosa and its presence appears to be predictive of subsequent broncho-pulmonary colonization.

CONCLUSION

This review supports the possible involvement of the nasal and paranasal sinuses and oral cavity as means of contamination.

Fructooligosacharides reduce Pseudomonas aeruginosa PAO1 pathogenicity through distinct mechanisms

Pseudomonas aeruginosa is ubiquitously present in the environment and acts as an opportunistic pathogen on humans, animals and plants. We report here the effects of the prebiotic polysaccharide inulin and its hydrolysed form FOS on this bacterium. FOS was found to inhibit bacterial growth of strain PAO1, while inulin did not affect growth rate or yield in a significant manner. Inulin stimulated biofilm formation, whereas a dramatic reduction of the biofilm formation was observed in the presence of FOS. Similar opposing effects were observed for bacterial motility, where FOS inhibited the swarming and twitching behaviour whereas inulin caused its stimulation. In co-cultures with eukaryotic cells (macrophages) FOS and, to a lesser extent, inulin reduced the secretion of the inflammatory cytokines IL-6, IL-10 and TNF-α. Western blot experiments indicated that the effects mediated by FOS in macrophages are associated with a decreased activation of the NF-κB pathway. Since FOS and inulin stimulate pathway activation in the absence of bacteria, the FOS mediated effect is likely to be of indirect nature, such as via a reduction of bacterial virulence. Further, this modulatory effect is observed also with the highly virulent ptxS mutated strain. Co-culture experiments of P. aeruginosa with IEC18 eukaryotic cells showed that FOS reduces the concentration of the major virulence factor, exotoxin A, suggesting that this is a possible mechanism for the reduction of pathogenicity. The potential of these compounds as components of antibacterial and anti-inflammatory cocktails is discussed.

Silver nanoparticles enhance Pseudomonas aeruginosa PAO1 biofilm detachment

OBJECTIVES

Silver nanoparticles (AgNPs) with a size ranging from 7 to 70 nm were synthesized using the ascorbic acid-citrate seed-mediated growth approach at room temperature.

METHODS

The 8 nm silver particles were prepared using gallic acid in alkaline conditions and used as seed to prepare AgNPs.

RESULTS

The presence of ascorbic acid and citrate allows the regulation of size and size distribution of the nanoparticles. The increase in free silver ion-to-seed ratio (Ag(+)/Ag(0)) resulted in changes of particle shape from spherical to pseudo-spherical and minor cylindrical shape. Further, a repetitive seeding approach resulted in the formation of pseudo-spherical particles with higher polydispersity index and minor distributions of tetrahedral particles. Citrate-capped AgNPs were stable and did not agglomerate upon centrifugation. The effect of AgNPs on biofilm reduction was evaluated using static culture on 96-well microtiter plates. Results showed that AgNPs with the smallest average diameter were most effective in the reduction of Pseudomonas aeruginosa biofilm colonies, which accounted for 90% of removal.

CONCLUSION

The biofilm removal activities of the nanoparticles were found to be concentration-independent particularly for the concentration within the range of 80-200 µg/mL.

Assessment of microbial diversity in biofilms recovered from endotracheal tubes using culture dependent and independent approaches

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e.g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm.

Tracheal colonization in preterm infants supported with nasal continuous positive airway pressure

BACKGROUND

The aim of this study was to examine endotracheal bacteriological status in premature infants who are supported by nasal continuous positive airway pressure (CPAP) without any history of tracheal intubation.

METHODS

In this prospective study, we enrolled 60 premature infants with respiratory distress; of these, 30 were supported by CPAP without tracheal intubation, and 30 were intubated and mechanically ventilated. Infants were enrolled at a postnatal age of < 24 h. Endotracheal (ET) cultures were taken at 24 h and at the 5th day of life. In the CPAP group, a suction catheter was sterilely inserted into the trachea while directly visualizing the vocal cords using a laryngoscope.

RESULTS

ET cultures taken on the 1st day of life showed colonization in 7/30 (23%) in the CPAP group versus 19/30 (63%) in the mechanically ventilated group (P= 0.002). Tracheal cultures on day 5 were positive in 5/30 (17%) and 11/30 (37%), respectively (P= 0.093). Klebsiella ssp. represented the most frequently isolated organism in both groups. A positive tracheal culture at 5 days was associated with a longer duration of respiratory support in the CPAP group (P= 0.05) but not in the ventilation group. Endotracheal culture at 5 days was associated with mortality in the ventilation group (8/11 vs 5/19, P= 0.02), but not in the CPAP group (1/5 vs 2/25, P= 0.45). Early endotracheal cultures did not relate with mortality in either of the groups.

CONCLUSION

The trachea of premature infants supported with CPAP is at risk for bacterial colonization. Predisposing factors, mechanisms and clinical implications of these novel findings need to be studied.

The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management

Background

Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways.

Methodology and Principal Findings

Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus.

Conclusions

In light of the recent concept of CF lung microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving survival in CF.

Effects of systematic oral care in critically ill patients: a multicenter study

BACKGROUND

No standard oral assessment tools are available for determining frequency of oral care in critical care patients, and the method of providing oral care is controversial.

OBJECTIVES

To examine the effects of a systematic program of oral care on oral assessment scores in critically ill intubated and nonintubated, patients.

METHODS

Clinical data were collected 3 times during critical care admissions before and after institution of a systematic program of oral care in 3 different medical centers. The oral care education program consisted of instruction from a dentist or dental hygienist and a clear procedure outlining systematic oral care. The Beck Oral Assessment Scale and the mucosal-plaque score were used to assess the oral cavity. Data were analyzed by using linear mixed modeling with controls for severity of illness.

RESULTS

Scores on the Beck Scale differed significantly (F = 4.79, P = .01) in the pattern of scores across the 3 days and between the control group (before oral education) and the systematic oral care group. Unlike the control group, the treatment group had decreasing scores on the Beck Scale from day 1 to day 5. The mucosal-plaque score and the Beck Scale scores had strong correlations throughout the study; the highest correlation was on day 5 (r = 0.798, P < .001, n = 43).

CONCLUSIONS

Oral assessment scores improved after nurses implemented a protocol for systematic oral care. Use of the Beck Scale and the mucosal-plaque score could standardize oral assessment and guide nurses in providing oral interventions.

The oral health of critically ill children: an observational cohort study

AIMS AND OBJECTIVES

This study will describe the oral health status of critically ill children over time spent in the paediatric intensive care unit, examine influences on the development of poor oral health and explore the relationship between dysfunctional oral health and healthcare-associated infections.

BACKGROUND

The treatment modalities used to support children experiencing critical illness and the progression of critical illness may result in dysfunction in the oral cavity. In adults, oral health has been shown to worsen during critical illness as well as influence systemic health.

DESIGN

A prospective observational cohort design was used.

METHOD

The study was undertaken at a single tertiary-referral Paediatric Intensive Care Unit. Oral health status was measured using the Oral Assessment Scale and culturing oropharyngeal flora. Information was also collected surrounding the use of supportive therapies, clinical characteristics of the children and the occurrence of healthcare-associated infections.

RESULTS

Of the 46 participants, 63% (n = 32) had oral dysfunction and 41% (n = 19) demonstrated pathogenic oropharyngeal colonisation during their critical illness. The potential systemic pathogens isolated from the oropharynx and included Candida sp., Staphylococcus aureus, Haemophilus influenzae, Enterococcus sp. and Pseudomonas aeruginosa. The severity of critical illness had a significant positive relationship (p < 0·05) with pathogenic and absent colonisation of the oropharynx. Sixty-three percent of healthcare-associated infections involved the preceding or simultaneous colonisation of the oropharynx by the causative pathogen.

CONCLUSIONS

This study suggests paediatric oral health to be frequently dysfunctional and the oropharynx to repeatedly harbour potential systemic pathogens during childhood critical illness.

RELEVANCE TO CLINICAL PRACTICE

Given the frequency of poor oral health during childhood critical illness in this study and the subsequent potential systemic consequences, evidence based oral hygiene practices should be developed and validated to guide clinicians when nursing critically ill children.

Strategies in the prevention of ventilator-associated pneumonia

Ventilator-associated pneumonia (VAP) remains a significant problem in the hospital setting, with very high morbidity, mortality, and cost. We performed an evidence-based review of the literature focusing on clinically relevant pharmacological and nonpharmacological interventions to prevent VAP. Owing to the importance of this condition the implementation of preventive measures is paramount in the care of mechanically ventilated patients. There is evidence that these measures decrease the incidence of VAP and improve outcomes in the intensive care unit. A multidisciplinary approach, continued education, and ventilator protocols ensure the implementation of these measures. Future research will continue to investigate cost/benefit relationships, antibiotic resistance, as well as newer technologies to prevent contamination and aspiration in mechanically ventilated patients.