Effect of pooled tracheal sample testing on the probability of Mycoplasma hyopneumoniae detection

Tracheal pooling for Mycoplasma hyopneumoniae (M. hyopneumoniae) DNA detection allows for decreased diagnostic cost, one of the main constraints in surveillance programs. The objectives of this study were to estimate the sensitivity of pooled-sample testing for the detection of M. hyopneumoniae in tracheal samples and to develop probability of M. hyopneumoniae detection estimates for tracheal samples pooled by 3, 5, and 10. A total of 48 M. hyopneumoniae PCR-positive field samples were pooled 3-, 5-, and 10-times using field M. hyopneumoniae DNA-negative samples and tested in triplicate. The sensitivity was estimated at 0.96 (95% credible interval [Cred. Int.]: 0.93, 0.98) for pools of 3, 0.95 (95% Cred. Int: 0.92, 0.98) for pools of 5, and 0.93 (95% Cred. Int.: 0.89, 0.96) for pools of 10. All pool sizes resulted in PCR-positive if the individual tracheal sample Ct value was < 33. Additionally, there was no significant decrease in the probability of detecting at least one M. hyopneumoniae-infected pig given any pool size (3, 5, or 10) of tracheal swabs. Furthermore, this manuscript applies the probability of detection estimates to various real-life diagnostic testing scenarios. Combining increased total animals sampled with pooling can be a cost-effective tool to maximize the performance of M. hyopneumoniae surveillance programs.

Detection of fungi in the airways of horses according to the sample site: a methodological study

Fungal detection in equine airways may be performed on either tracheal wash (TW) or bronchoalveolar lavage fluid (BALF) by either cytology or culture. However, method comparisons are sparse. Our objective was to determine the prevalence of fungi in airways of horses according to the sample site and laboratory methodology. Sixty-two adult horses, investigated in the field or referred for respiratory disease, were included. Tracheal wash, and BALF collected separately from both lungs, were collected using a videoendoscope. Fungi were detected in cytologic samples examined by light microscopy, and by fungal culture. Hay was sampled in the field. Prevalence of fungi was of 91.9% in TW and 37.1% in BALF. Fungi were cultured from 82.3% of TW and 20.9% of BALF. Fungal elements were observed cytologically in 69.4% of TW and 22.6% of BALF. In 50% of horses, the same fungi were detected in both TW and hay, but fungi detected in BALF and hay differed in all horses. Poor agreement was found for the detection of fungi between TW and BALF and between fungal culture and cytologic examination (Cohen's kappa coefficient (κ) < 0.20). Moderate agreement was found between cytologic examination of left and right lungs (κ = 0.47). The prevalence of fungi detected cytologically on pooled BALF was significantly different (p = 0.023) than on combined left and right BALF. Fungi were more prevalent in the TW than BALF, and results suggest that hay might not be the primary source of fungi of the lower respiratory tract of horses.

Inflammatory responses and barrier disruption in the trachea of chicks following Mycoplasma gallisepticum infection: a focus on the TNF-α-NF-κB/MLCK pathway

Mycoplasma gallisepticum (MG) can induce persistent inflammatory damage to the tracheal mucosa of poultry and cause chronic respiratory diseases in chickens. To further investigate the mechanism of MG-induced injury to the tracheal mucosa, we used chick embryo tracheal organ culture (TOC) as a model to study the invasion and reproduction of MG, the effect of MG on tracheal morphology, and the potential factors that promote MG tissue invasion. The results showed that MG infection significantly damaged the tracheal epithelial structure and weakened tracheal epithelial barrier function; MG also increased the occurrence of bacterial displacement, with a significant (p < 0.05) increase in the bacterial load of the infected TOCs at 5 and 7 days post-infection. In addition, MG significantly (p < 0.05) increased the expression levels of inflammatory cytokines, such as TNF-α, interleukin-1β (IL-1β), and IL-6, and activated the NF-κB signalling pathway, leading to increased nuclear translocation of NF-κB p65. Simultaneously, the map kinase pathway (MAPK) was activated. This activation might be associated with increased myosin light chain (MLC) phosphorylation, which could lead to actin-myosin contraction and disruption of tight junction (TJ) protein function, potentially compromising epithelial barrier integrity and further catalysing MG migration into tissues. Overall, our results contribute to a better understanding of the interaction between MG and the host, provide insight into the mechanisms of damage to the tracheal mucosa induced by MG infection, and provide new insights into the possible pathways involved in Mycoplasma gallisepticum infection in vivo.

A real-time PCR assay for the quantification of Mycoplasma equirhinis in tracheal wash samples from Thoroughbred horses

Mycoplasma equirhinis is the predominant equine Mycoplasma sp. isolated from clinically normal horses and is suspected to be associated with inflammatory airway disease in which cough is the primary sign. Quantitative evaluation of bacterial counts is useful in assessing the association between the bacteria in samples and observed clinical signs, but this evaluation has been difficult with conventional culture methods of M. equirhinis given the need for pre-enrichment using liquid cultures. We established a quantitative real-time PCR (qPCR) assay for the quantification of M. equirhinis, targeting the hypothetical protein FJM08_00025. We confirmed its high species-specificity for M. equirhinis and a limit of detection of 2.9 copies/reaction. We quantified M. equirhinis in tracheal wash samples from 20 clinically normal horses and 22 coughing horses. The copy numbers detected by qPCR in 18 of the 22 samples from clinically affected horses were within the range detected in the 20 clinically normal horses (0-84 copies/reaction). The remaining 4 samples had considerably higher copy numbers (734-1,620,000 copies/reaction), suggesting the likely involvement of M. equirhinis infection. Quantitative evaluation of M. equirhinis over time using our qPCR assay may allow a more accurate assessment of M. equirhinis infection in coughing horses compared to culture methods.

Preoperative oral hygiene treatment reduces bacterial transport and colonization during intubation for orthopedic surgery

PURPOSE

The process of infection by bacteria and viruses involves invasion, establishment, growth, and parasitization. Poor oral hygiene and dysbiosis are significant risk factors for pneumonia. The aim of this study was to evaluate bacterial transport into the trachea during intubation for orthopedic surgery and the impact of oral hygiene treatment.

METHODS

The study cohort included 53 patients with fracture who underwent surgical procedures under general anesthesia and were divided into two groups: an oral hygiene treatment (OHT) group (n = 27) and a control group (n = 26). Before intubation, the OHT group underwent preoperative oral hygiene treatment. Microbiological culture was used for detection and counting of bacteria from the oropharynx, trachea, and tip of the endotracheal tube (ETT).

RESULTS

Patients in the OHT group had a lower pathogen detection rate and lower degree of bacterial colonization in the oropharynx, trachea, and ETT tip.

CONCLUSION

Preoperative oral hygiene treatment is able to reduce bacterial transport and colonization during orthopedic surgery, thus providing an important adjunct to pre-anesthesia care.

Lower airway ultrasonographic, endoscopic, and cytological changes in horses undergoing inhalation anesthesia with controlled ventilation for minor elective surgeries

Effects of general anesthesia with controlled ventilation on the respiratory system have had limited evaluation in horses. A prospective observational study was performed with eleven client-owned horses undergoing elective surgery. Physical examination, auscultation with a rebreathing bag, complete blood cell count, lung ultrasound imaging, tracheal endoscopy imaging and transendoscopic tracheal wash were conducted before and 24 hours after anesthesia. Lung ultrasound imaging was also repeated just after recovery. A significant increase in blood neutrophil count between pre- and post-anesthesia (P=0.004) was observed. There was an increase in ultrasonographic score of the lungs at recovery (left P=0.007, right P=0.017). The score of the dependent lung was higher than the independent lung at recovery time (P=0.026) but no difference was observed 24 hours after anesthesia. The tracheal mucus score was higher after anesthesia (P=0.001); severe local inflammation was present in several horses at the site of endotracheal tube cuff. Neutrophil count was significantly higher on tracheal wash fluid cytology after anesthesia (P=0.016), without any significant changes on bacterial load. Increased tracheal mucus score and neutrophil count in tracheal wash samples were observed after general anesthesia in healthy horses without clinical evidence of pneumonia (fever, cough). Tracheal inflammation secondary to endotracheal intubation and cuff inflation was, therefore, suspected. Elective surgery without complications can induce inflammation of the trachea and changes in ultrasound images of the lungs in healthy horses and should be considered when evaluating respiratory system after a general anesthesia.

Epidemiology and pathogenicity of M. equirhinis in equine respiratory disorders

Mycoplasmas are pathogens involved in respiratory disorders of various animal hosts. In horses, Mycoplasma (M.) equirhinis is the species most frequently detected in clinical respiratory specimens, with a prevalence of 12-16%, but its clinical implication in equine respiratory disorders remains unclear. Here we screened 1948 clinical specimens for the presence of M. equirhinis. The samples were both tracheal washes (TW) and bronchoalveolar lavages (BAL) collected by veterinarians in France in day-to-day work between 2020 and 2022. The samples were associated with a standardized form that served to collect key general and clinical information, such as horse age, breed, and living environment. M. equirhinis was detected using a combination of culture and post-enrichment PCR. Other diagnostic data included virology and bacteriology as well as neutrophil counts, when available. Prevalence of M. equirhinis was examined as a function of a clinical score based on four significant clinical signs (nasal discharge, cough, dyspnoea, and hyperthermia). Multivariate logistic regression analysis was run to identify risk factors for the presence of M. equirhinis, and comparative prevalence analysis was used to test for association with other bacteria and viruses. TW and BAL were analysed independently, as we found that TW samples were associated with a higher prevalence of M. equirhinis. As prevalence remained steady whatever the clinical score, M. equirhinis cannot be considered a primary pathogen. M. equirhinis was more frequently isolated in thoroughbreds and trotters and in horses living exclusively stabled compared to other horses or other living environments. M. equirhinis was never detected in BAL specimens with a 'normal' neutrophil count, i.e. 5%, suggesting it could be associated with an inflammatory response, similar to that observed in equine asthma. Prevalence of M. equirhinis was shown to increase in the presence of other bacteria such as Streptococcus equi subsp. zooepidemicus (S. zoo) or viruses, and S. zoo load was higher in M. equirhinis-positive samples, suggesting a potential increase of clinical signs in the event of co-infection.

Detection of Mycoplasma spp. in horses with respiratory disorders

BACKGROUND

Bacteria belonging to the genus Mycoplasma are small-sized, have no cell walls and small genomes. They commonly cause respiratory disorders in their animal hosts. Three species have been found in the respiratory tract of horses worldwide, that is., Mycoplasma (M.) equirhinis, M. pulmonis and M. felis, but their role in clinical cases remains unclear.

OBJECTIVES

The aim of this study was to i) develop and validate tools to detect, isolate and identify different Mycoplasma spp. strains in clinical equine respiratory-tract specimens and ii) subsequently define the prevalence of the three species in France depending on sample types and horse characteristics (age, breed, sex).

STUDY DESIGN

Validation of a workflow for mycoplasma diagnosis and subsequent prevalence study.

METHODS

Mycoplasma-free tracheal wash samples spiked with numerated strains and DNA dilutions were used to validate the culture methods and real-time PCR (rt-PCR) assay. Isolated strains were identified by 16S rRNA gene sequencing. Prevalences were determined on a population of 616 horses with respiratory disorders, sampled in France in 2020.

RESULTS

In total, 104 horses (16.9%) were found to be positive for Mycoplasma spp. by at least one method. M. equirhinis was the predominant circulating species, accounting for 85% of the rt-PCR-positive samples and 98% of the 40 cultured strains.

MAIN LIMITATION

The proposed pre-enrichment procedure improves the sensitivity of detection but hinders the quantification of the initial mycoplasma load in the clinical specimens.

CONCLUSIONS

Prevalence of mycoplasma varied with age, breed, and type of sample.

Airway microbiome dynamics and relationship to ventilator-associated infection in intubated pediatric patients

BACKGROUND

Little is known about the airway microbiome in intubated mechanically ventilated children. We sought to characterize the airway microbiome longitudinally and in association with clinical variables and possible ventilator-associated infection (VAI).

METHODS

Serial tracheal aspirate samples were prospectively obtained from mechanically ventilated subjects under 3 years old from eight pediatric intensive care units in the United States from June 2017 to July 2018. Changes in the tracheal microbiome were analyzed by sequencing bacterial 16S ribosomal RNA gene relative to subject demographics, diagnoses, clinical parameters, outcomes, antibiotic treatment, and the Ventilator-Associated InfectioN (VAIN) score.

RESULTS

A total of 221 samples from 58 patients were processed and 197 samples met the >1000 reads criteria (89%), with an average of 43,000 reads per sample. The median number of samples per subject was 3 (interquartile range [IQR]: 2-5), with a median VAIN score of 2 (IQR: 1-3). Proteobacteria was the highest observed phyla throughout the intubation period, followed by Firmicutes and Actinobacteria. Alpha diversity was negatively associated with days of intubation (p = .032) and VAIN score (p = .016). High VAIN scores were associated with a decrease of Mycobacterium obuense, and an increase of Streptococcus peroris, Porphyromonadaceae family (unclassified species), Veillonella atypica, and several other taxa. No specific pattern of microbiome composition related to clinically diagnosed VAIs was observed.

CONCLUSIONS

Our data demonstrate decreasing alpha diversity with increasing VAIN score and days of intubation. No specific microbiome pattern was associated with clinically diagnosed VAI.

Association of Endotracheal Aspirate Culture Variability and Antibiotic Use in Mechanically Ventilated Pediatric Patients

IMPORTANCE

Endotracheal aspirate cultures are commonly collected from patients with mechanical ventilation to evaluate for ventilator-associated pneumonia or tracheitis. However, the respiratory tract is not sterile, making differentiating between colonization from bacterial infection challenging, and results may be unreliable owing to variable specimen quality and sample processing across laboratories. Despite these limitations, clinicians routinely interpret bacterial growth in endotracheal aspirate cultures as evidence of infection, sometimes regardless of organism significance, prompting antibiotic treatment.

OBJECTIVE

To assess the variability in endotracheal aspirate culture rates and the association between culture rates and antibiotic prescribing among patients with mechanical ventilation across children's hospitals in the US.

DESIGN, SETTING, AND PARTICIPANTS

Cross-sectional retrospective analysis of data obtained from the Children's Hospital Association Pediatric Health Information System database between January 1, 2016, through December 31, 2019. Participants were all patients hospitalized with mechanical ventilation aged less than 18 years.

EXPOSURES

A charge for an endotracheal aspirate culture on a ventilated day.

MAIN OUTCOMES AND MEASURES

Endotracheal aspirate culture rate and antibiotic days of therapy per ventilated days. For mechanical ventilation, clinical transaction classification codes for mechanical ventilation other unspecified ventilator assistance were used. To identify respiratory cultures, the laboratory test code for aerobic culture was used and relevant keywords (ie, respiratory tract, sputum) were used to identify sources in the hospital charge description master.

RESULTS

A total of 152 132 patients were identified among 31 hospitals. Among these patients, 79 691 endotracheal aspirate cultures were collected on a ventilator-day (patients aged less than 1 year, 44%; 1-4 years, 27%, 5-11 years. 16%, and 12-18 years, 13%; 3% were Asian; 17% Hispanic; 21% non-Hispanic Black; 45% Non-Hispanic White patients; 14% were other; 56% of patients were male, 44% were female). The overall median rate of culture use was 46 per 1000 ventilator-days (IQR, 32-73 cultures per 1000 ventilator-days). The endotracheal aspirate culture rate was positively correlated with the hospital's antibiotic days of therapy rate (R = 0.46; P = .009). In a multivariable model adjusting for patient-level and hospital-level characteristics and among patients with mechanical ventilation, each additional endotracheal aspirate culture was associated with 2.87 (95% CI, 2.74-3.01) higher odds of receiving additional days of therapy compared with patients who did not receive and endotracheal aspirate culture.

CONCLUSIONS AND RELEVANCE

In this study, notable variability was found in endotracheal aspirate culture rates across US pediatric hospitals and pediatric intensive care units, and endotracheal aspirate culture use was associated with increased antibiotic use. These findings suggest an opportunity for diagnostic and antibiotic stewardship to standardize testing and treatment of suspected ventilator-associated infections in pediatric patients with mechanical ventilation pediatric patients.

Exclusively Tracheobronchial Paracoccidioidomycosis: A Rare Presentation

Paracoccidioidomycosis (PCM), or blastomycosis in South America, is a systemic granulomatous mycosis related to activities associated with soil management, especially agriculture. PCM restricted to tracheobronchial tree region has not yet been reported.

Endobronchial lipoma with tracheobronchial aspergillosis: A case report

INTRODUCTION

Benign neoplasm of the endobronchial tree is quite rare, while endobronchial lipoma is extremely rare. Tracheobronchial aspergillosis is a relatively uncommon but severe form of invasive aspergillosis involving the tracheobronchial tree.

PATIENT CONCERNS

A 54-year-old male presented to our hospital for investigation and treatment of a cough and hemoptysis.

DIAGNOSIS

The diagnosis was confirmed as endobronchial lipoma with tracheobronchial aspergillosis.

INTERVENTIONS

The patient received pneumonectomy and voriconazole treatment.

OUTCOMES

The patient's postoperative course was uneventful, and he was discharged 10 days after surgery. The patient had no evidence of the fungal infection and recurrence during 1 year of follow-up.

CONCLUSION

Endobronchial lipoma is a rare benign lung tumor, and this is the first report of endobronchial lipoma with tracheobronchial aspergillosis. In patients with suspected endobronchial lipoma, especially those who present with hemoptysis as the initial symptom, it is advisable to exclude coexistent aspergillosis.

The alterations of tracheal microbiota and inflammation caused by different levels of ammonia exposure in broiler chickens

Ammonia (NH3) is a known harmful gas and exists in haze, forming secondary organic aerosols. Exposure to ambient ammonia correlates with the respiratory tract infection, and microbiota in the upper respiratory tract is an emerging crucial player in the homeostatic regulation of respiratory tract infection, and microbiota perturbation is usually accompanied by the inflammatory reactions; however, the effects of different levels of ammonia exposure on tracheal microbiota and inflammation are unclear. A total of 288 22-day-old male Arbor Acres broilers were chosen and divided into 4 groups with 6 replicates of 12 chickens, and respectively exposed to ammonia at 0, 15, 25, and 35 ppm for 21-d trial period. Cytokines (interleukin (IL)-1β, IL-6, and IL-10) in the trachea were measured at the 21 d of exposure to NH3. Tracheal microbiota at the 21 d was analyzed by the 16S rRNA gene analysis. The results showed that an increase in ammonia levels, even in 15 ppm, significantly decreased the alpha diversity and changed the bacterial community structure. Six genera (Faecalibacterium, Ruminococcus]_torques_group, unclassified_f__Lachnospiraceae, Ruminococcaceae_UCG-014, Streptococcus, Blautia) significantly increased, whereas Lactobacillus significantly decreased under different levels of ammonia exposure. We also observed positive associations of Faecalibacterium, Blautia, g__Ruminococcaceae_UCG-014, unclassified_f__Lachnospiraceae and Ruminococcus]_torques_group abundances with tracheal IL-1β concentration. Moreover, an increase in ammonia levels, even in 15 ppm, caused respiratory tract inflammatory injury. The results indicated that 15 ppm ammonia exposure changed the composition of tracheal microbiota that caused the tracheal injury possibly through increasing the IL-1β, which might make the broiler more sensitive to the changes of environment and pathogenic micro-organisms in the poultry house, and may be also a critical value that needs high alertness. Herein, the present experiment also suggested that the standard limit of ammonia concentration in adult poultry house is 15 ppm. This research provides an insight into the relationship between the upper respiratory tract microbiota and inflammation under ammonia exposure.

Proteolytic cleavage of HLA class II by human neutrophil elastase in pneumococcal pneumonia

Bacterial and viral respiratory infections can initiate acute lung injury and acute respiratory distress syndrome. Neutrophils and their granule enzymes, including neutrophil elastase, are key mediators of the pathophysiology of acute respiratory failure. Although intracellular neutrophil elastase functions as a host defensive factor against pathogens, its leakage into airway spaces induces degradation of host connective tissue components. This leakage disrupts host innate immune responses via proteolytic cleavage of Toll-like receptors and cytokines. Here, we investigated whether neutrophils possess proteases that cleave adaptive immune molecules. We found that expression of the human leukocyte antigen (HLA) class II molecule HLA-DP β1 was decreased in THP-1-derived macrophages treated with supernatants from dead neutrophils. This decreased HLA-DP β1 expression was counteracted by treatment with neutrophil elastase inhibitor, suggesting proteolytic cleavage of HLA-DP β1 by neutrophil elastase. SDS-PAGE showed that neutrophil elastase cleaved recombinant HLA-DP α1, -DP β1, -DQ α1, -DQ β1, -DR α, and -DR β1. Neutrophil elastase also cleaved HLA-DP β1 on extracellular vesicles isolated from macrophages without triggering morphological changes. Thus, leakage of neutrophil elastase may disrupt innate immune responses, antigen presentation, and T cell activation. Additionally, inhibition of neutrophil elastase is a potential therapeutic option for treating bacterial and viral pneumonia.

The influence of host tissue on M. gallisepticum vlhA gene expression

Mycoplasma gallisepticum, a significant poultry pathogen, has evolved rapidly in its new passerine host since its first reported isolation from house finches in the US in 1994. In poultry, M. gallisepticum infects the upper respiratory tract, causing tracheal mucosal thickening and inflammation, in addition to inflammation of the reproductive tract. However, in house finches M. gallisepticum primarily causes inflammation of the conjunctiva. Given that different tissues are primarily affected by the same pathogen in different hosts, we have compared the early changes in gene expression of the phase-variable lipoproteins (vlhA) gene family of M. gallisepticum collected directly from target tissues in both hosts. Previous data have demonstrated that vlhA genes may be related to virulence, exhibiting changes in expression in a non-stochastic, temporal progression and we hypothesize that this may be influenced by differences in the target host tissue. If this is true, we would expect M. gallisepticum to display a different vlhA gene expression pattern in the chicken trachea compared to its expression pattern in house finch conjunctiva. Here we report significant differences in vlhA gene expression patterns between M. gallisepticum collected from chicken tracheas compared to those collected from house finch conjunctiva. While many of the predominant vlhA genes expressed in the input population showed an increase in expression in the chicken trachea at day one postinfection, those same vlhA genes decreased in expression in the house finch. These data suggest that discrete suites of vlhA genes may be involved in M. gallisepticum pathogenesis and tropism for unique tissues in two disparate avian hosts.

Progression of nasopharyngeal and tracheal bacterial microbiotas of feedlot cattle during development of bovine respiratory disease

It is generally accepted that as bovine respiratory disease (BRD) develops, bacterial pathogens first proliferate in the nasopharynx and then colonize the lungs, leading to bronchopneumonia. However, such temporal changes have never been definitively demonstrated. Therefore, the objective was to describe the progression of the nasopharyngeal and tracheal bacterial microbiotas of feedlot cattle during development of BRD. Nasopharyngeal swabs and tracheal wash samples were collected from 24 heifers over 20 d after arrival at a feedlot. Heifers were assessed daily and sampled based on reticulo-rumen/rectal temperatures and development of clinical signs of BRD. The study end point for each heifer was either at BRD treatment (BRD group; n = 15) or day 20 if the heifer remained healthy or did not meet BRD treatment criteria (TOL group; n = 9). Total DNA was extracted from each sample and the 16S rRNA gene (V3-V4) sequenced. Alpha and beta diversity were compared between BRD-TOL groups and sampling locations over time. There were no common patterns of change over time in composition or diversity of either the nasopharyngeal or tracheal bacterial microbiotas of cattle that developed BRD. Health status affected bacterial composition (R² = 0.043; < 0.001), though this effect was low compared to variation among individual animals (R² = 0.335; < 0.001) and effects of days on feed (R² = 0.082; < 0.001). Specific bacterial taxa (Moraxella and Mycoplasma dispar) nevertheless appeared to have a potential role in respiratory health.

Randomised study of the immunomodulatory effects of azithromycin in severely asthmatic horses

Neutrophilic inflammation is believed to contribute to the airway obstruction and remodelling in equine asthma. Azithromycin, an antibiotic with immunomodulatory properties, reduces pulmonary neutrophilia and hyper-responsiveness in human asthmatics and decreases airway remodelling in rodent models of asthma. It was therefore hypothesised that azithromycin would improve lung function, mucus accumulation and central airway remodelling by decreasing luminal neutrophilia in severe equine asthma. The effects of a 10-day treatment with either azithromycin or ceftiofur, an antimicrobial without immune-modulating activity, were assessed using a blind, randomised, crossover design with six severe asthmatic horses in clinical exacerbation. Lung function, tracheal mucus accumulation, tracheal wash bacteriology, bronchial remodelling, airway neutrophilia and mRNA expression of proinflammatory cytokines (interleukin (IL)-8, IL-17A, IL-1β, tumour necrosis factor-α) in bronchoalveolar lavage fluid were evaluated. Azithromycin decreased the expression of IL-8 (P=0.03, one-tailed) and IL-1β (P=0.047, one-tailed) but failed to improve the other variables evaluated. Ceftiofur had no effect on any parameter. The reduction of neutrophilic chemoattractants (IL-8, IL-1β) justifies further efforts to investigate the effects of a prolonged treatment with macrolides on airway neutrophilia and remodelling. The lack of efficacy of ceftiofur suggests that severe equine asthma should not be treated with antibiotics at first-line therapy.

Economic evaluation alongside the Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial (E-PROSPECT): study protocol

INTRODUCTION

Ventilator-associated pneumonia (VAP) is a common healthcare-associated infection in the intensive care unit (ICU). Probiotics are defined as live microorganisms that may confer health benefits when ingested. Prior randomised trials suggest that probiotics may prevent infections such as VAP and Clostridioides difficile-associated diarrhoea (CDAD). PROSPECT (Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial) is a multicentre, double-blinded, randomised controlled trial comparing the efficacy of the probiotic Lactobacillus rhamnosus GG with usual care versus usual care without probiotics in preventing VAP and other clinically important outcomes in critically ill patients admitted to the ICU.

METHODS AND ANALYSIS

The objective of E-PROSPECT is to determine the incremental cost-effectiveness of L. rhamnosus GG plus usual care versus usual care without probiotics in critically ill patients. E-PROSPECT will be performed from the public healthcare payer's perspective over a time horizon from ICU admission to hospital discharge.We will determine probabilities of in-ICU and in-hospital events from all patients alongside PROSPECT. We will retrieve unit costs for each resource use item using jurisdiction-specific public databases, supplemented by individual site unit costs if such databases are unavailable. Direct costs will include medications, personnel costs, radiology/laboratory testing, operative/non-operative procedures and per-day hospital 'hoteling' costs not otherwise encompassed. The primary outcome is the incremental cost per VAP prevented between the two treatment groups. Other clinical events such as CDAD, antibiotic-associated diarrhoea and in-hospital mortality will be included as secondary outcomes. We will perform pre-specified subgroup analyses (medical/surgical/trauma; age; frailty status; antibiotic use; prevalent vs no prevalent pneumonia) and probabilistic sensitivity analyses for VAP, then generate confidence intervals using the non-parametric bootstrapping approach.

ETHICS AND DISSEMINATION

Study approval for E-PROSPECT was granted by the Hamilton Integrated Research Ethics Board of McMaster University on 29 July 2019. Informed consent was obtained from the patient or substitute decision-maker in PROSPECT. The findings of this study will be published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER

NCT01782755; Pre-results.

Bovine Respiratory Syncytial Virus Decreased Pasteurella multocida Adherence by Downregulating the Expression of Intercellular Adhesion Molecule-1 on the Surface of Upper Respiratory Epithelial Cells

The synergistic infection of bovine respiratory syncytial virus (BRSV) and Pasteurella multocida (PM) may predispose cattle to develop severe pneumonia. Previously, we reported that BRSV infection significantly decreased PM adherence to the upper respiratory epithelial cells. It may allow bacteria to invade into the lower respiratory tract and lead to severe pneumonia. To investigate whether BRSV infection regulates the cell surface adherence receptor on bovine trachea epithelial cells (bTECs), we performed proteomic and functional analyses. BRSV infection decreased the expression of intercellular adhesion molecule-1 (ICAM1) on bTECs. Inhibition and knockdown experiments using anti-ICAM1 antibody and siRNAs targeting ICAM1 indicated that PM adherence to bTECs was dependent on ICAM1 expression. These data suggest that under normal conditions bTECs may capture PM in the upper respiratory tract, while BRSV infection reverses this mechanism. The proposed gateway function of bTECs is disrupted by BRSV infection that may facilitate bacterial invasion into the lower respiratory tract and lead to secondary or more severe respiratory infection.

The association between the microbes in the tracheobronchial aspirate fluid and bronchopulmonary dysplasia in preterm infants

OBJECTIVE

The study aimed to evaluate the association between microbes in the lower respiratory tract (LRT) and the srisk for severe bronchopulmonary dysplasia (sBPD) in premature infants.

METHODS

We conducted a retrospective, single-center study of preterm infants who were admitted to the neonatal intensive care unit (NICU) of Southern Medical University Affiliated Maternal & Child Health Hospital of Foshan, China, between January 2015 and December 2017. The microbes in the LRT were screened by using tracheobronchial aspirate fluid (TAF) culture.

RESULTS

One hundred and fifty-five infants were included in the analysis. Among 155 infants, 41 were diagnosed with sBPD, and 114 were diagnosed without sBPD. There were significant differences between infants with and without sBPD in regard to birth weight (BW), gestational age (GA), the duration of endotracheal ventilation and supplemental oxygen. The incidence of retinopathy (ROP) and sepsis was higher in the sBPD infants than in the infants without sBPD. There was a difference in the detection rate of Gram-negative bacteria (GNB) between the two groups. Stenotrophomonas maltophilia and Klebsiella pneumoniae were mainly detected in TAF.

CONCLUSIONS

The LRT microbes were different between infants with and without sBPD, and GNB is more frequently detected in sBPD infants.

Differential Response of the Chicken Trachea to Chronic Infection with Virulent Mycoplasma gallisepticum Strain Ap3AS and Vaxsafe MG (Strain ts-304): a Transcriptional Profile

Mycoplasma gallisepticum is the primary etiological agent of chronic respiratory disease in chickens. Live attenuated vaccines are most commonly used in the field to control the disease, but current vaccines have some limitations. Vaxsafe MG (strain ts-304) is a new vaccine candidate that is efficacious at a lower dose than the current commercial vaccine strain ts-11, from which it is derived. In this study, the transcriptional profiles of the trachea of unvaccinated chickens and chickens vaccinated with strain ts-304 were compared 2 weeks after challenge with M. gallisepticum strain Ap3AS during the chronic stage of infection. After challenge, genes, gene ontologies, pathways, and protein classes involved in inflammation, cytokine production and signaling, and cell proliferation were upregulated, while those involved in formation and motor movement of cilia, formation of intercellular junctional complexes, and formation of the cytoskeleton were downregulated in the unvaccinated birds compared to the vaccinated birds, reflecting immune dysregulation and the pathological changes induced in the trachea by infection with M. gallisepticum Vaccination appears to protect the structural and functional integrity of the tracheal mucosa 2 weeks after infection with M. gallisepticum.

Integrative study of the upper and lower airway microbiome and transcriptome in asthma

Relatively little is known about interactions between the airway microbiome and airway host transcriptome in asthma. Since asthma affects and is affected by the entire airway, studying the upper (e.g., nasal) and lower (e.g., bronchial) airways together represents a powerful approach to understanding asthma. Here, we performed a systematic, integrative study of the nasal and bronchial microbiomes and nasal and bronchial host transcriptomes of children with severe persistent asthma and healthy controls. We found that (a) the microbiomes and host transcriptomes of asthmatic children are each distinct by site (nasal versus bronchial); (b) among asthmatic children, Moraxella and Alloiococcus are hub genera in the nasal microbiome, while there are no hubs among bronchial genera; (c) bronchial Actinomyces is negatively associated with bronchial genes for inflammation, suggesting Actinomyces may be protective; (d) compared with healthy children, asthmatic children express more nasal genes for ciliary function and harbor more nasal Streptococcus; and (e) nasal genera such as Corynebacterium are negatively associated with significantly more nasal genes for inflammation in healthy versus asthmatic children, suggesting a potentially stronger protective role for such nasal genera in healthy versus asthmatic children. Our systematic, integrative study provides a window into host-microbiome associations in asthma.

A Novel AAV-mediated Gene Delivery System Corrects CFTR Function in Pigs

Cystic fibrosis is an autosomal-recessive disease that is caused by a mutant CFTR (cystic fibrosis transmembrane conductance regulator) gene and is characterized by chronic bacterial lung infections and inflammation. Complementation with functional CFTR normalizes anion transport across the airway surface. Adeno-associated virus (AAV) is a useful vector for gene therapy because of its low immunogenicity and ability to persist for months to years. However, because its episomal expression may decrease after cell division, readministration of the AAV vector may be required. To overcome this, we designed an integrating AAV-based CFTR-expressing vector, termed piggyBac (PB)/AAV, carrying CFTR flanked by the terminal repeats of the piggyBac transposon. With codelivery of the piggyBac transposase, PB/AAV can integrate into the host genome. Because of the packaging constraints of AAV, careful consideration was required to ensure that the vector would package and express its CFTR cDNA cargo. In this short-term study, PB/AAV-CFTR was aerosolized to the airways of CF pigs in the absence of the transposase. Two weeks later, transepithelial Cl- current was restored in freshly excised tracheal and bronchial tissue. Additionally, we observed an increase in tracheal airway surface liquid pH and bacterial killing in comparison with untreated CF pigs. Airway surface liquid from primary airway cells cultured from treated CF pigs exhibited increased pH correlating with decreased viscosity. Together, these results show that complementing CFTR in CF pigs with PB/AAV rescues the anion transport defect in a large-animal CF model. Delivery of this integrating viral vector system to airway progenitor cells could lead to persistent, life-long expression in vivo.

The microbiome of the upper respiratory tract in health and disease

The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.

Comparison of the sensitivity of laryngeal swabs and deep tracheal catheters for detection of Mycoplasma hyopneumoniae in experimentally and naturally infected pigs early and late after infection

Detection of Mycoplasma hyopneumoniae infection in live pigs is a critical component to measure the success of disease control or elimination strategies. However, in vivo diagnosis of M. hyopneumoniae is difficult and the imperfect sensitivity of diagnostic tools has been deemed as one of the main challenges. Here, the sensitivity of laryngeal swabs and deep tracheal catheters for detection of M. hyopneumoniae early and late after infection was determined using inoculation status as a gold standard in experimentally infected pigs and a Bayesian approach in naturally infected pigs. Three-hundred and twenty 8-week old seeder pigs were intra-tracheally inoculated with M. hyopneumoniae strain 232 and immediately placed with 1920 contact pigs to achieve a 1:6 seeder-to-contact ratio. A subset of seeders and contacts were longitudinally sampled at 7, 28, 97, and 113 days post-inoculation (dpi) and at 28, 56, 84, and 113 days post-exposure (dpe), respectively, using laryngeal swabs and deep tracheal catheters. Samples were tested for M. hyopneumoniae by a species-specific real-time PCR. The sensitivity of deep tracheal catheters was higher than the one obtained in laryngeal swabs at all samplings (seeders: 36% higher than laryngeal swabs at 7 dpi, 29% higher at 97 dpi, and 44% higher at 113 dpi; contacts: 51% higher at 56 dpe, 42% higher at 84 dpe, and 32% higher at 113 dpe). Our study indicates that deep tracheal catheters were a more sensitive sample than laryngeal swabs. The sensitivity of both sample types varied over time and by exposure method, and these factors should be considered when designing diagnostic strategies.

In vitro activity of ceftolozane-tazobactam and ceftazidime-avibactam against clinical isolates of meropenem-non-susceptible Pseudomonas aeruginosa: A two-centre study

OBJECTIVES

This study aimed to compare the activity of ceftazidime-avibactam (C/A), ceftolozane-tazobactam (C/T) and three anti-pseudomonal β-lactams (piperacillin-tazobactam, ceftazidime and cefepime) against a collection of meropenem-non-susceptible Pseudomonas aeruginosa (P. aeruginosa) clinical isolates recovered from two centres in Turkey.

METHODS

A total of 102 unique patient isolates of meropenem-non-susceptible P. aeruginosa were included in the study. MICs of antimicrobials were determined by the gradient diffusion method.

RESULTS

Overall susceptibility rates for C/A and C/T were 83.3% and 82.4%, respectively. Both C/A and C/T had better activity than any one of the three anti-pseudomonal β-lactams. According to the MIC₅₀ values, C/T was the most potent agent against isolates. Although the susceptibility rates of isolates to C/T and C/A were similar, C/T (MIC₅₀, 1 μg/mL) was four-fold more potent than C/A (MIC₅₀, 4 μg/mL). The MIC₅₀ values of C/A and C/T for the isolates that were non-susceptible to three β-lactams were significantly higher than those for isolates that were non-susceptible to zero, one or two β-lactams. Also, the C/A MIC₅₀ value for the isolates that were non-susceptible to two β-lactams was higher than that for isolates which were non-susceptible to one β-lactam.

CONCLUSIONS

C/A and C/T showed good activity against meropenem-non-susceptible P. aeruginosa isolates. However, resistance to these agents was not uncommon among these isolates. The overall β-lactam susceptibility profile of isolates seems to have an effect on the probability of susceptibility to C/A and C/T. Antimicrobial susceptibility testing should be performed for C/A and C/T if these agents are considered for treatment of infections caused by meropenem-non-susceptible P. aeruginosa.

Intranasal Inoculation of Cryptococcus neoformans in Mice Produces Nasal Infection with Rapid Brain Dissemination

Cryptococcus neoformans is an important fungal pathogen, causing life-threatening pneumonia and meningoencephalitis. Brain dissemination of C. neoformans is thought to be a consequence of an active infection in the lung which then extravasates to other sites. Brain invasion results from dissemination via either transport by free yeast cells in the bloodstream or Trojan horse transport within mononuclear phagocytes. We assessed brain dissemination in three mouse models of infection: intravenous, intratracheal, and intranasal models. All three modes of infection resulted in dissemination of C. neoformans to the brain in less than 3 h. Further, C. neoformans was detected in the entirety of the upper respiratory tract and the ear canals of mice. In recent years, intranasal infection has become a popular mechanism to induce pulmonary infection because it avoids surgery, but our findings show that instillation of C. neoformans produces cryptococcal nasal infection. These findings imply that immunological studies using intranasal infection should assume that the initial sites of infection of infection are brain, lung, and upper respiratory tract, including the nasal airways.IMPORTANCECryptococcus neoformans causes an estimated 181, 000 deaths each year, mostly associated with untreated HIV/AIDS. C. neoformans has a ubiquitous worldwide distribution. Humans become infected from exposure to environmental sources, after which the fungus lays dormant within the human body. Upon AIDS-induced immunosuppression or therapy-induced immunosuppression (required for organ transplant recipients or those suffering from autoimmune disorders), cryptococcal disease reactivates and causes life-threatening meningitis and pneumonia. This study showed that upon contact with the host, C. neoformans can quickly (a few hours) reach the host brain and also colonizes the nose of infected animals. Therefore, this work paves the way to better knowledge of how C. neoformans travels through the host body. Understanding how C. neoformans infects, disseminates, and survives within the host is critically required so that we can prevent infections and the disease caused by this deadly fungus.

Increased Serum Sedimentation and Positive Tuberculosis Antibody Combined Left Lung Consolidation in Chest CT Scan in an Adult Patient Firstly Misdiagnosed as Tuberculosis Proved as Foreign Body Aspiration in the Left Main Stem Bronchus by Bronchoscopy: a Case Report and Literature Review

BACKGROUND

Foreign body aspiration is a rare entity in adults. We presented an adult case with recurrent pulmonary infection firstly misdiagnosed as tuberculosis, which proved as foreign body aspiration in the left main stem bronchus by bronchoscopy.

METHODS

Appropriate laboratory tests are carried out. The chest CT scan and bronchoscopy were performed for diagnosis.

RESULTS

Serum sedimentation was increased and tuberculosis antibody was positive. The chest CT scan showed left lung consolidation and small pleural exudate on the left side. Significant calcification can be seen near the left main bronchus. The bronchoscopy demonstrated plenty of yellow sputum in left main bronchus and a peanut shell completely obstructed the left main bronchus and peripheral granulation tissue hyperplasia. The peanut shell was removed and the left main trachea was unobstructed.

CONCLUSIONS

When a patient has recurrent pulmonary infection, especially at the same site, physicians should pay attention to airway obstruction caused by foreign body, cancer and other causes of airway stenosis. Bronchoscopy is crucial for the ultimate diagnosis.

Identification of respiratory microbiota markers in ventilator-associated pneumonia

PURPOSE

To compare bacteria recovered by standard cultures and metataxonomics, particularly with regard to ventilator-associated pneumonia (VAP) pathogens, and to determine if the presence of particular bacteria or microbiota in tracheal and oropharyngeal secretions during the course of intubation was associated with the development of VAP.

METHODS

In this case-control study, oropharyngeal secretions and endotracheal aspirate were collected daily in mechanically ventilated patients. Culture and metataxonomics (16S rRNA gene-based taxonomic profiling of bacterial communities) were performed on serial upper respiratory samples from patients with late-onset definite VAP and their respective controls.

RESULTS

Metataxonomic analyses showed that a low relative abundance of Bacilli at the time of intubation in the oropharyngeal secretions was strongly associated with the subsequent development of VAP. On the day of VAP, the quantity of human and bacterial DNA in both tracheal and oropharyngeal secretions was significantly higher in patients with VAP than in matched controls with similar ventilation times. Molecular techniques identified the pathogen(s) of VAP found by culture, but also many more bacteria, classically difficult to culture, such as Mycoplasma spp. and anaerobes.

CONCLUSIONS

Molecular analyses of respiratory specimens identified markers associated with the development of VAP, as well as important differences in the taxa abundance between VAP and controls. Further prospective trials are needed to test the predictive value of these markers, as well as the relevance of uncultured bacteria in the pathogenesis of VAP.

Co-infection of epithelial cells established from the upper and lower bovine respiratory tract with bovine respiratory syncytial virus and bacteria

Bovine respiratory disease complex is a major disease affecting the global cattle industry. Multiple infections by viruses and bacteria increase disease severity. Previously, we reported that bovine respiratory syncytial virus (BRSV) infection increases adherence of Pasteurella multocida to human respiratory and bovine kidney epithelial cells. To examine the interaction between the virus and bacteria in bovine respiratory cells, we generated respiratory epithelial cell lines from bovine trachea (bTEC), bronchus (bBEC), and lung (bLEC). Although all established cell lines were infected by BRSV and P. multocida susceptibility differed according to site of origin. The cells derived from the lower respiratory tract (bBEC and bLEC) were significantly more susceptible to BRSV than those derived from the upper respiratory tract (bTEC). Pre-infection of bBEC and bLEC with BRSV increased adherence of P. multocida; this was not the case for bTEC. These results indicate that BRSV may reproduce better in the lower respiratory tract and encourage adherence of bacteria. Thus, we identify one possible mechanism underlying severe pneumonia.

Prenatal complications are associated with the postnatal airway host response and microbiota in intubated preterm infants

PURPOSE

To prospectively examine the relationship between prenatal events, postnatal airway host response and microbiota, and clinical outcomes.

MATERIALS AND METHODS

Tracheal aspirates collected at seven days of age from 71 mechanically ventilated infants (median gestational age (GA), 25 weeks [range 23-28]) were simultaneously processed for a 12-plex protein assay and bacterial identification by 16S rRNA sequencing. Phenotypes were determined by unsupervised clustering of the protein analytes. Subject characteristics, microbial communities and clinical factors and outcomes were compared across the phenotype groups.

RESULTS

Three clusters were identified: 1 (high protein levels), 2 (high proinflammatory proteins and low anti-inflammatory proteins), and 3 (low protein levels), respectively. Antenatal hemorrhage was most common in cluster 1, while chorioamnionitis characterized cluster 2 and preeclampsia was most prevalent in cluster 3, which was characterized by a predominance of Staphylococcus and relative absence of Ureaplasma. There were higher rates of adverse clinical outcomes in cluster 1.

CONCLUSIONS

Airway protein profiles in seven days old mechanically ventilated preterm infants are associated with important antenatal events and unique airway microbial communities. These relationships may reveal new mechanisms by which antenatal events impact the course and outcomes of preterm infants.

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis

Laryngotracheal stenosis is an obstructive respiratory disease that leads to voicing difficulties and dyspnea with potential life-threatening consequences. The majority of incidences are due to iatrogenic etiology from endotracheal tube intubation; however, airway scarring also has idiopathic causes. While recent evidence suggests a microbial contribution to mucosal inflammation, the microbiota associated with different types of stenosis has not been characterized. High-throughput sequencing of the V4 region of the16S rRNA gene was performed to characterize the microbial communities of 61 swab samples from 17 iatrogenic and 10 adult idiopathic stenosis patients. Nonscar swabs from stenosis patients were internal controls, and eight swabs from four patients without stenosis represented external controls. Significant differences in diversity were observed between scar and nonscar samples and among sample sites, with decreased diversity detected in scar samples and the glottis region. Permutational analysis of variance (PERMANOVA) results revealed significant differences in community composition for scar versus nonscar samples, etiology type, sample site, groups (iatrogenic, idiopathic, and internal and external controls), and individual patients. Pairwise Spearman's correlation revealed a strong inverse correlation between Prevotella and Streptococcus among all samples. Finally, bacteria in the family Moraxellaceae were found to be distinctly associated with idiopathic stenosis samples in comparison with external controls. Our findings suggest that specific microbiota and community shifts are present with laryngotracheal stenosis in adults, with members of the family Moraxellaceae, including the known pathogens Moraxella and Acinetobacter, identified in idiopathic scar. Further work is warranted to elucidate the contributing role of bacteria on the pathogenesis of laryngotracheal stenosis.IMPORTANCE The laryngotracheal region resides at the intersection between the heavily studied nasal cavity and lungs; however, examination of the microbiome in chronic inflammatory conditions of the subglottis and trachea remains scarce. To date, studies have focused on the microbiota of the vocal folds, or the glottis, for laryngeal carcinoma, as well as healthy larynges, benign vocal fold lesions, and larynges exposed to smoking and refluxate. In this study, we seek to examine the structure and composition of the microbial community in adult laryngotracheal stenosis of various etiologies. Due to the heterogeneity among the underlying pathogenesis mechanisms and clinical outcomes seen in laryngotracheal stenosis disease, we hypothesized that different microbial profiles will be detected among various stenosis etiology types. Understanding differences in the microbiota for subglottic stenosis subtypes may shed light upon etiology-specific biomarker identification and offer novel insights into management approaches for this debilitating disease.

Characterization of an intratracheal aerosol challenge model of Brucella melitensis in guinea pigs

B. melitensis is considered the most virulent of the Brucella species, and a need exists for an improved laboratory animal model of infection that mimics natural transmission and disease. Guinea pigs are highly susceptible to infection with Brucella spp. and develop a disease syndrome that mimics natural disease after aerosol inoculation. Intratracheal inoculation is a targeted means of generating aerosols that offer advantages over aerosol chamber delivery. To establish this delivery method, female, Hartley guinea pigs were infected via intratracheal inoculation with PBS or 16M B. melitensis at low dose (101 to 103) or high dose (106 to 108) and monitored for 30 days for signs of disease. Guinea pigs in the high dose groups developed fever between 12-17 days post-inoculation. Bacteria were recovered from the spleen, liver, lymph nodes, lung, and uterus at 30-days post-inoculation and demonstrated dose dependent mean increases in colonization and pathologic changes consistent with human brucellosis. To study the kinetics of extrapulmonary dissemination, guinea pigs were inoculated with 107 CFU and euthanized at 2-hours post inoculation and at weekly intervals for 3 weeks. 5.8x105 to 4.2x106 CFU were recovered from the lung 2 hours post-inoculation indicating intratracheal inoculation is an efficient means of infecting guinea pigs. Starting at 1-week post inoculation bacteria were recovered from the aforementioned organs with time dependent mean increases in colonization. This data demonstrates that guinea pigs develop a disease syndrome that models the human manifestation of brucellosis, which makes the guinea pig a valuable model for pathogenesis studies.

Pertussis epidemiology in Tunisian infants and children and characterization of Bordetella pertussis isolates: results of a 9-year surveillance study, 2007 to 2016

PURPOSE

Pertussis remains a public health concern in most countries. Our study aimed to prospectively explore the epidemiology of pertussis in the Tunis area of Tunisia between 2007 and 2016, and to characterize the virulence-associated genes of the collected Bordetella pertussis isolates.

METHODOLOGY

Infants and children hospitalized at the Children's Hospital of Tunis, Tunisia, between 2007 and 2016 for suspicion of pertussis were enrolled in the study. Culture and real-time PCR (qPCR) assays targeting IS481, IS1001, recA, H-IS1001 and ptxP were used to confirm the pertussis diagnosis. Phenotypic and genotypic characterization of recovered isolates was performed.Results/Key findings. A total of 1844 children were included in the study. Overall, 306 children (16.6 %) with Bordetella infection were confirmed by qPCR. Among them, 265 (86.6 %) were confirmed as having B. pertussis (IS481+, ptxP+, H-IS1001-), 18 (5.9 %) as having Bordetella parapertussis (IS481-, IS1001+) and 11 (3.6 %) as having Bordetella spp. (IS481+, ptxP-, H-IS1001-). No Bordetella holmesii (IS481+, IS1001-, H-IS1001+) was identified. The estimated pertussis incidence in the Tunis area was 134/100 000 in children aged less than 5 years. Two epidemic peaks were observed in 2009 and 2014. Ten B. pertussis isolates were cultured and characterized. Deficiency in pertactin expression was not observed, and genotyping of the isolates revealed a predominant allelic profile: ptxP3-ptxA1-prn2-fim2-1-fim3-2.

CONCLUSION

This study demonstrated that pertussis is still present as a cyclical disease in Tunisia, despite high primo-vaccination coverage with a pertussis whole-cell vaccine. The predominant genotype of Tunisian B. pertussis isolates is similar to isolates circulating in countries using the acellular vaccine.

Mechanical ventilator as a major cause of infection and drug resistance in intensive care unit

Ventilator-associated pneumonia (VAP) is the most frequent infection in intensive care units (ICU). It is associated with high rates of long morbidity and mortality. Management of a case of VAP is often said to add $40,000 to hospital costs USA. All these data directed our interest to study the etiology, risk factors, and antibiotic susceptibility patterns of VAP in ICU of Tanta University Hospital. This study included 36 cases of VAP. Endotracheal aspirates were obtained from all cases and microbiologically analyzed. Samples were collected over 1 year. Forty-two strains were isolated from 28 cases, while eight cases showed no bacterial growth. The most frequent organism was Staphylococcus aureus (30.95%), followed by Acinetobacter baumannii and Pseudomonas aeruginosa (21.43% for each), and the least common was Staphylococcus epidermidis (2.38%). Multi-drug resistance was detected in (50%) of the isolated bacteria in this study. Imipenem, amikacin, linezolid, vancomycin, and levofloxacin are recommended to be the most effective drugs in management of VAP. VAP is a serious problem in ICU carrying many risks for the patient live. Regimens of empirical treatment should take in consideration the update in the bacterial etiology and antibiotic susceptibility patterns of VAP.

The Role of Presepsin Obtained from Tracheal Aspirates in the Diagnosis of Early Onset Pneumonia in Intubated Newborns

OBJECTIVES

To investigate the role of presepsin obtained from tracheal aspirate of intubated newborns in the diagnosis of early neonatal pneumonia.

METHODS

A cross-sectional observational study was performed on 60 intubated newborns during the two-year period. Tracheal aspirate for examination was taken in aseptic conditions in usual toilets, by lavage with 2 ml of 0.9% NaCl in Mucus suction set. On the same day, presepsin (blood) was measured.

RESULTS

There were 34 newborns in the examined group (with pneumonia) and 26 in the control group. Patient groups were similar regarding demographic characteristics related to gender and Apgar score. The coefficients of simple linear correlation revealed the statistically significant connection between presepsin (from tracheal aspirate) and birth body weight, presepsin (plasma), maternal infection and pneumonia. Significant differences in the values of presepsin (from tracheal aspirate) (p < 0.001) and birth body weight (p = 0.036) were found.

CONCLUSIONS

In intubated newborns, measurements of presepsin obtained from tracheal aspirate suggested that it can be used as a complementary marker in diagnosing early onset neonatal pneumonia.

Clinical features, bacteriology of endotracheal aspirates and treatment outcomes of patients with chronic obstructive pulmonary disease and community-acquired pneumonia in an intensive care unit in Taiwan with an emphasis on eosinophilia versus non-eosinophilia: a retrospective case-control study

OBJECTIVES

The clinical implications of blood eosinophil level in patients with chronic obstructive pulmonary disease (COPD) and community-acquired pneumonia (CAP) requiring invasive mechanical ventilation (IMV) and intensive care unit (ICU) admission are still unknown. Thus, this study aimed to compare the features of such patients with and without blood eosinophilia.

DESIGN

This was a retrospective case-control study.

SETTING

An ICU of a medical centre in central Taiwan.

PARTICIPANTS

A total of 262 patients with COPD and CAP requiring IMV and ICU admission.

RESULTS

Of all participants (n=262), 32 (12.2%) had an eosinophil percentage (EP) >2% and 169 (64.5%) had an absolute eosinophil count (AEC) >300 cells/µL. Regardless of whether 2% or 300 cells/µL was used as a cut-off value, the eosinophilia group were slightly older (years) (82.9±5.4 vs 78.1±9.1, p=0.000 and 79.2±8.4 vs 77.6±9.6, p=0.246, respectively), and had a higher forced expiratory volume in 1 s/forced vital capacity (%) (56.0±8.0 vs 51.3±11.6, p=0.005 and 53.1±11.2 vs 49.5±11.2, p=0.013, respectively), less severe spirometric classification (p=0.008 and p=0.001, respectively), and lower white cell count 109/L (8.8±3.2 vs 11.1±4.9, p=0.009 and 10.3±4.4 vs 11.8±5.3, p=0.017, respectively) than the non-eosinophilia group. The bacteriology of endotracheal aspirates showed that Pseudomonas aeruginosa and other gram-negative bacilli were the most common organisms in all study groups. Participants with an EP >2% had a shorter ICU length of stay (OR=12.13, p=0.001) than those with an EP ≤2%, while an AEC >300 cells/µL was not associated with any in-ICUoutcomes.

CONCLUSIONS

The results of this study have significant clinical implications and should be considered when making treatment decisions for the management of patients with COPD and CAP requiring IMV and ICU admission.

Hospital-acquired colonization and infections in a Vietnamese intensive care unit

Data concerning intensive care unit (ICU)-acquired bacterial colonization and infections are scarce from low and middle-income countries (LMICs). ICU patients in these settings are at high risk of becoming colonized and infected with antimicrobial-resistant organisms (AROs). We conducted a prospective observational study at the Ho Chi Minh City Hospital for Tropical Diseases, Vietnam from November 2014 to January 2016 to assess the ICU-acquired colonization and infections, focusing on the five major pathogens in our setting: Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), Klebsiella spp., Pseudomonas spp. and Acinetobacter spp., among adult patients with more than 48 hours of ICU stay. We found that 61.3% (223/364) of ICU patients became colonized with AROs: 44.2% (161/364) with rectal ESBL-producing E. coli and Klebsiella spp.; 30.8% (40/130) with endotracheal carbapenemase-producing Acinetobacter spp.; and 14.3% (52/364) with nasal methicillin-resistant S. aureus. The incidence rate of ICU patients becoming colonized with AROs was 9.8 (223/2,276) per 100 patient days. Significant risk factor for AROs colonization was the Charlson Comorbidity Index score. The proportion of ICU patients with HAIs was 23.4% (85/364), and the incidence rate of ICU patients contracting HAIs was 2.3 (85/3,701) per 100 patient days. The vascular catheterization (central venous, arterial and hemofiltration catheter) was significantly associated with hospital-acquired bloodstream infection. Of the 77 patients who developed ICU-acquired infections with one of the five specified bacteria, 44 (57.1%) had prior colonization with the same organism. Vietnamese ICU patients have a high colonization rate with AROs and a high risk of subsequent infections. Future research should focus on monitoring colonization and the development of preventive measures that may halt spread of AROs in ICU settings.

Does antimicrobial therapy improve outcomes in horses with severe equine asthma and a positive tracheal wash bacterial culture?

The objective of this study was to observe the outcomes of adding an antimicrobial treatment to a conventional treatment regime in horses with severe equine asthma in a clinical setting. Eleven client-owned horses with a history consistent with severe equine asthma, increased respiratory effort and nostril flaring, ≥ 20% neutrophils on bronchoalveolar lavage (BAL), and a positive tracheal wash (TW) bacterial culture were treated with environmental management, corticosteroids, and bronchodilators. Six horses were also treated with an antimicrobial (principal group), while the other 5 were administered saline as a placebo (control group). Treatment with antimicrobials significantly improved the post-treatment clinical score of the principal group compared with the pre-treatment score, whereas no significant difference occurred in the control group. The principal group also had significantly less neutrophil myeloperoxidase (MPO) activity post-treatment than pre-treatment, with a median difference of -0.39 units/[protein] in the principal group and a median difference of -0.21 units/[protein] in the controls. There was no difference in MPO activity pre- versus post-treatment in the control group. No differences were noted in the intra-group comparisons of pre- versus post-treatment BAL neutrophil counts, mucus scores, and concentrations of interleukin-8 (IL-8) or tumor necrosis factor-alpha (TNF-α) in bronchoalveolar lavage fluid (BALF) in either group. There were no differences found in the inter-group comparisons of the principal versus controls for each of the pre- and post-treatment time periods for BAL neutrophil count, mucus score, clinical scores, MPO activity, and IL-8 or TNF-α concentrations. The role of airway bacteria in horses with severe equine asthma requires further investigation as antimicrobial therapy improved post-treatment clinical scores and decreased MPO activity in the group of horses studied, but did not affect other measures of airway inflammation.

Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

Several species of the Gram-negative genus Bordetella are the cause of respiratory infections in mammals and birds, including whooping cough (pertussis) in humans. Very recently, a novel atypical species, Bordetella pseudohinzii, was isolated from laboratory mice. These mice presented no obvious clinical symptoms but elevated numbers of neutrophils in bronchoalveolar lavage fluid and inflammatory signs in histopathology. We noted that this species can occur at high prevalence in a mouse facility despite regular pathogen testing according to the FELASA-recommendations. Affected C57BL/6 J mice had, in addition to the reported pulmonary alterations, tracheal inflammation with reduced numbers of ciliated cells, slower ciliary beat frequency, and largely (>50%) compromised cilia-driven particle transport speed on the mucosal surface, a primary innate defence mechanism. In an in vitro-model, Bordetella pseudohinzii attached to respiratory kinocilia, impaired ciliary function within 4 h and caused epithelial damage within 24 h. Regular testing for this ciliotropic Bordetella species and excluding it from colonies that provide mice for lung research shall be recommended. On the other hand, controlled colonization and infection with Bordetella pseudohinzii may serve as an experimental model to investigate mechanisms of mucociliary clearance and microbial strategies to escape from this primary innate defence response.

Behaviour during transportation predicts stress response and lower airway contamination in horses

This study aimed to document the effects of an eight hour journey on behavioural, clinical, haematological, environmental and respiratory parameters, and to identify possible associations between factors. Twelve horses underwent clinical examination, respiratory endoscopy with tracheal wash (TW) aspiration, and collection of venous and arterial blood before (BJ) and after the journey (AJ). TW were submitted for conventional quantitative bacteriological evaluation and genetic microbiome analyses. Behaviour was assessed in stables prior to transportation and throughout the journey. Transportation caused mild, but significant, effects on fluid and electrolyte balance and an acute phase response, characterized by neutrophilia, hyperfibrinogenaemia and hyperglobulinaemia. The proportion of neutrophils in TW, tracheal mucus and TW bacterial concentration was increased AJ, with preferential replication of Pasteurellaceae. Horse behaviour en route predicted clinical and respiratory outcomes. The frequency of stress related behaviours was greatest in the first hour of the journey, and balance-related behaviours were most common in the final hour of the journey. Horses which lowered their heads less frequently en route and showed more stress-related behaviours had higher physiological stress (serum cortisol and heart rate on arrival), increased tracheal mucus and inflammation scores, and higher TW bacterial concentration AJ (P<0.05). Six horses with abnormal lung auscultation AJ proved to have had higher tracheal inflammation scores at preloading (P = 0.017), an overall higher concentration of bacteria in their TW (P = 0.013), and an increased percentage of neutrophils in TW at five days AJ (P = 0.003) in comparison to the other horses. While transport-related health problems are multifactorial, clinical examination, including auscultation and endoscopic inspection of the lower respiratory tract before and after journey, and behavioural observation en route may identify animals at increased risk of transport associated respiratory disease.

Aerobic bacteriological studies on the respiratory tracts of apparently healthy and pneumonic camels (Camelus dromedaries) in selected districts of Afar Region, Ethiopia

A cross-sectional study was conducted to isolate and identify bacterial species from the respiratory tract of apparently healthy and pneumonic camels in Asayita and Dubti woredas in the Afar Region, Ethiopia. From a total of 74 lung tissue and 74 tracheal swab samples Staphylococcus aureus, 16.3%, Streptococcus equi subsp. equi, 13.0%, and Pasteurella multocida, 10.9%, were dominant isolates from pneumonic lungs; Escherichia coli, 12.7%, Proteus species, 10.9%, and Klebsiella pneumoniae, 9.1%, were the majority in the normal lungs. The majority of the isolates colonized both anatomical sites investigated. There was a statistically significant association between the health status of the camels as well as the anatomical site studied with the isolation rates of the major respiratory pathogens (p < 0.05). Furthermore, the isolates were susceptible to norfloxacin, streptomycin, and gentamicin but resistant to ampicillin and tetracycline on in vitro test. Further studies on the pathogenicity of the major isolates are recommended.

Characterization of pathogens involved in ventilator associated pneumonia in surgical and medical intensive care units - A single center experience

In the present study 60 samples were collected from lower respiratory tract of patients suffering from Ventilator Associated Pneumonia (VAP) admitted in surgical and medical Intensive Care Units (ICUs) of Khyber Teaching Hospital, Peshawar, Pakistan. Recovered pathogens were characterized and their susceptibility pattern against commonly used antibacterial agents investigated. Most frequent bacterial pathogen found was methicillin- resistant Staphylococcus aureus (MRSA) (40%) followed by members of Enterobacteriaceae (22%; of which Escherichia coli (50%), Klebsiella pneumonia (30%), Enterobacter cloacae (10%) and Citrobacter freundii (10%), Pseudomonas aeruginosa 20% and Acinetobacter baumannii 18%. Majority of the specimens yielded polymicrobial growth (85.75% polymicrobial growth compared to 14.25% specimens yielding monomicrobial growth). The susceptibility pattern showed that A. baumannii was the most resistant bacterial pathogen. Based on the results of susceptibility pattern obtained in the present study, combination of linezolid with meropenem and colistin has been found to be the best combination option for empirical therapy for VAP pathogens in this region.

Proteomic variation and diversity in clinical Streptococcus pneumoniae isolates from invasive and non-invasive sites

Streptococcus pneumoniae is responsible for a variety of invasive and non-invasive human infections. There are over 90 serotypes of S. pneumoniae differing in their ability to adapt to the different niches within the host. Two-dimensional gel electrophoresis was used to discriminate clinical S. pneumoniae isolates recovered from either blood cultures (invasive site isolates) or other sites, including sputum, tracheal aspirate, ear, eye and skin swabs (non-invasive site isolates). Global protein expression profiles for five invasive site and six non-invasive site isolates representing five different serotypes (serotypes 4, 6, 9, 14 and 23) were obtained for each isolate and combined into a single data set using Progenesis SameSpots^™ software. One-hundred and eighty six protein spots (39% of the protein spots in the dataset) differed significantly (ANOVA, p<0.05) in abundance between the invasive site (101 upregulated protein spots) and non-invasive site (85 upregulated protein spots) isolates. Correlations between the bacterial proteomes and their sites of isolation were determined by Principal Component Analysis (PCA) using the significantly different protein spots. Out of the 186 variable protein spots, 105 exhibited a serotype-associated pattern of variability. The expression of the remaining 81 protein spots was concluded to be uniquely linked to the site of bacterial isolation. Mass spectrometry was used to identify selected protein spots that showed either constant or differential abundance levels. The identified proteins had a diverse range of functions including, capsule biogenesis, DNA repair, protein deglycation, translation, stress response and virulence as well as amino acid, carbohydrate, lipid and nucleotide metabolism. These findings provide insight on the proteins that contribute towards the adaptation of the bacteria to different sites within the host.

Suspicion of respiratory tract infection with multidrug-resistant Enterobacteriaceae: epidemiology and risk factors from a Paediatric Intensive Care Unit

BACKGROUND

Multidrug-resistant (MDR) infections are a serious concern for children admitted to the Paediatric Intensive Care Unit (PICU). Tracheal colonization with MDR Enterobacteriaceae predisposes to respiratory infection, but underlying risk factors are poorly understood. This study aims to determine the incidence of children with suspected infection during mechanical ventilation and analyses risk factors for the finding of MDR Enterobacteriaceae in tracheal aspirates.

METHODS

A retrospective single-centre analysis of Enterobacteriaceae isolates from the lower respiratory tract of ventilated PICU patients from 2005 to 2014 was performed. Resistance status was determined and clinical records were reviewed for potential risk factors. A classification and regression tree (CRT) to predict risk factors for infection with MDR Enterobacteriaceae was employed. The model was validated by simple and multivariable logistic regression.

RESULTS

One hundred sixty-seven Enterobacteriaceae isolates in 123 children were identified. The most frequent isolates were Enterobacter spp., Klebsiella spp. and E.coli. Among these, 116 (69%) isolates were susceptible and 51 (31%) were MDR. In the CRT analysis, antibiotic exposure for ≥ 7 days and presence of gastrointestinal comorbidity were the most relevant predictors for an MDR isolate. Antibiotic exposure for ≥ 7 days was confirmed as a significant risk factor for infection with MDR Enterobacteriaceae by a multivariable logistic regression model.

CONCLUSIONS

This study shows that critically-ill children with tracheal Enterobacteriaceae infection are at risk of carrying MDR isolates. Prior use of antibiotics for ≥ 7 days significantly increased the risk of finding MDR organisms in ventilated PICU patients with suspected infection. Our results imply that early identification of patients at risk, rapid microbiological diagnostics and tailored antibiotic therapy are essential to improve management of critically ill children infected with Enterobacteriaceae.

Airway Microbial Community Turnover Differs by BPD Severity in Ventilated Preterm Infants

Preterm birth exposes the developing lung to an environment with direct exposure to bacteria, often facilitated by endotracheal intubation. Despite evidence linking bacterial infections to the pathogenesis of bronchopulmonary dysplasia (BPD), systematic studies of airway microbiota are limited. The objective was to identify specific patterns of the early respiratory tract microbiome from tracheal aspirates of mechanically ventilated preterm infants that are associated with the development and severity of BPD. Infants with gestational age ≤34 weeks, and birth weight 500-1250g were prospectively enrolled. Mechanically ventilated infants had tracheal aspirate samples collected at enrollment, 7, 14, and 21 days of age. BPD was determined by modified NIH criteria with oxygen reduction tests; infants without BPD were excluded due to low numbers. Aspirates were processed for bacterial identification by 16S rRNA sequencing, and bacterial load by qPCR. Cross-sectional analysis was performed using 7 day samples and longitudinal analysis was performed from subjects with at least 2 aspirates. Microbiome analysis was performed on tracheal aspirates from 152 infants (51, 49, and 52 with mild, moderate, and severe BPD, respectively). Seventy-nine of the infants were included in the cross-sectional analysis and 94 in the longitudinal. Shannon Diversity, bacterial load, and relative abundance of individual taxa were not strongly associated with BPD status. Longitudinal analysis revealed that preterm infants who eventually developed severe BPD exhibited greater bacterial community turnover with age, acquired less Staphylococcus in the first days after birth, and had higher initial relative abundance of Ureaplasma. In conclusion, longitudinal changes in the airway microbial communities of mechanically ventilated preterm infants may be associated with BPD severity, whereas cross-sectional analysis of airway ecology at 7 days of age did not reveal an association with BPD severity. Further evaluation is necessary to determine whether the observed longitudinal changes are causal or in response to clinical management or other factors that lead to BPD.

Disseminated Cryptococcosis with Rapidly Growing Lung Nodules in an End-stage Renal Disease Patient

A 73-year-old man with type 2 diabetes mellitus and end-stage renal disease was diagnosed with acute myocardial infarction. He required continuous dialysis after percutaneous coronary intervention. Subsequently, multiple nodules were discovered in both lungs for the first time, and Cryptococcus neoformans was isolated from the patient's sputum, blood, bilateral pleural fluid, and cerebrospinal fluid cultures, resulting in a diagnosis of disseminated cryptococcosis. This case represents an invaluable example of disseminated cryptococcosis with rapidly growing lung nodules in a dialysis patient, and illustrates that dialysis causes innate immune disorder and the reactivation of cryptococcosis.