Endotracheal Aspirate Specimens Research Articles

Application of a multiplex molecular pneumonia panel and real-world impact on antimicrobial stewardship among patients with hospital-acquired and ventilator-associated pneumonia in intensive care units

BackgroundThe optimal timing for applying the BioFire FilmArray Pneumonia Panel (FAPP) in intensive care unit (ICU) patients with hospital-acquired pneumonia (HAP) or ventilator-associated pneumonia (VAP) remains undefined, and there are limited data on its impact on antimicrobial stewardship. MethodsThis retrospective study was conducted at a referral hospital in Taiwan from November 2019 to October 2022. Adult ICU patients with HAP/VAP who underwent FAPP testing were enrolled. Patient data, FAPP results, conventional microbiological testing results, and the real-world impact of FAPP results on antimicrobial therapy adjustments were assessed. Logistic regression was used to determine the predictive factors for bacterial detection by FAPP. ResultsAmong 592 respiratory specimens, including 564 (95.3%) endotracheal aspirate specimens, 19 (3.2%) expectorated sputum specimens and 9 (1.5%) bronchoalveolar lavage specimens, from 467 patients with HAP/VAP, FAPP testing yielded 368 (62.2%) positive results. Independent predictors for positive bacterial detection by FAPP included prolonged hospital stay (odds ratio [OR], 3.14), recent admissions (OR, 1.59), elevated C-reactive protein levels (OR, 1.85), Acute Physiology and Chronic Health Evaluation II scores (OR, 1.58), and septic shock (OR, 1.79). Approximately 50% of antimicrobial therapy for infections caused by Gram-negative bacteria and 58.4% for Gram-positive bacteria were adjusted or confirmed after obtaining FAPP results. ConclusionsThis study identified several factors predicting bacterial detection by FAPP in critically ill patients with HAP/VAP. More than 50% real-world clinical practices were adjusted or confirmed based on the FAPP results. Clinical algorithms for the use of FAPP and antimicrobial stewardship guidelines may further enhance its benefits.

BACTERIAL ISOLATES OF THE RESPIRATORY TRACT INFECTION AND THEIR CURRENT SENSITIVITY PATTERN AMONG PATIENTS ADMITTED IN TERTIARY CARE HOSPITAL.

Background & Objectives: This study was aimed to observe the susceptibility pattern of bacterial isolates from respiratory tract infection (RTI). Respiratory tract infection is considered as one of the major public health problems and a leading cause of morbidity and mortality in many developing countries. Respiratory tract is the part of the human system that plays a vital role in breathing processes. In human, the respiratory system can be subdivided into an Upper respiratory tract and a Lower respiratory tract based on anatomical features. The respiratory tract is constantly exposed to microbes due to the extensive surface area. Methods: The present study was conducted retrospectively for a period of one year November 2021 to October 2022. All respiratory specimens included Sputum, BAL, throat swab; endotracheal aspirate specimens were collected aseptically from patients and cultured on the appropriate bacteriological media (Blood agar, MacConkey agar & Chocolate Agar). Bacterial isolates were identified by biochemical tests and antimicrobial susceptibility performed by standard methods as per CLSI 2022. Results: 152 (72.3%) of total 210 samples were positive for bacterial culture. 126 (82.8%) were gram negative bacilli (GNB) and 26 (17.1%) were gram positive cocci (GPC). The predominant pathogen isolated was K. pneumoniae 46 (30.2%) followed by Escherichia coli 28 (18.4%).The overall susceptibility of GNB was highest towards Imipenem, Meropenem followed by Piperacillin tazobactam and Amikacin. Gram positive organisms exhibited highest susceptibility towards Vancomycin and Linezolid. Conclusion: Imipenem is the most sensitive antibiotic followed by Piperacillin tazobactam and Amikacin which can be used for empirical therapy for respiratory tract infections (RTI). The antibiotic therapy should be modified as per the culture and sensitivity report. Regular determinations of the type of bacterial pathogens and updation of antibiogram must be followed in every institution to aid in better patient management by helping the clinician in the judicious use of antibiotics.

Evaluation of the BioFire FilmArray Pneumonia Panel for the Detection of Bacterial Respiratory Pathogens and Antimicrobial Resistance Genes in Endotracheal Aspirate Specimens

Evaluation of the BioFire FilmArray Pneumonia Panel for the Detection of Bacterial Respiratory Pathogens and Antimicrobial Resistance Genes in Endotracheal Aspirate Specimens

A 48-Year-Old Previously Healthy Man Presenting with Acute Respiratory Distress Syndrome (ARDS), Negative Tests for SARS-CoV-2, and Positive Serology for Parainfluenza Virus Type 3 (PIV-3)

Patient: Male, 48-year-old Final Diagnosis: Acute respiratory distress syndrome (ARDS) • parainfluenza virus infection Symptoms: Dyspnea Medication: — Clinical Procedure: — Specialty: Infectious Diseases • Pulmonology Objective: Rare disease Background:Human parainfluenza viruses (PIVs) belong to the Paramyxoviridae family. PIVs cause lower respiratory tract infections in children and the elderly. In addition, severe pneumonia due to PIVs has been reported in immunocompromised adults. However, no reports have described PIV infections leading to acute respiratory distress syndrome (ARDS) in immunocompetent hosts.Case Report:A 48-year-old otherwise healthy man was transported to our hospital due to worsening dyspnea. On arrival, strong effortful breathing was observed and results of arterial blood gas analysis revealed severe hypoxia. On the basis of the clinical presentation, we intubated the patient for mechanical ventilation. However, mechanical ventilation provided inadequate oxygenation. Finally, veno-venous extracorporeal membrane oxygenation was initiated. Pneumonia was considered to be a cause of the ARDS, based on the patient’s history and blood examination. Repeated reverse transcription-polymerase chain reaction tests for the novel coronavirus were performed, and endotracheal aspirate specimens were cultured for bacteria and fungus; however, the results were all negative. On day 2, the PIV-3-specific antibody titer was elevated. Two weeks later, the PIV-3-specific antibody titer had increased 4-fold. On the basis of these results, we diagnosed pneumonia induced by PIV-3 infection.Conclusions:ARDS can occur because of severe pneumonia induced by PIV-3. In cases of unexplained severe pneumonia or ARDS, PIV infection should be included in the differential diagnosis.

Time to Result for Pathogen Identification and Antimicrobial Susceptibility Testing of Bronchoalveolar Lavage and Endotracheal Aspirate Specimens in U.S. Acute Care Hospitals.

Identification (ID) and antimicrobial susceptibility testing (AST) of respiratory pathogens are critical to the management of patients with pneumonia to facilitate optimal antibiotic therapy selection. Few studies have examined the time to results (TTR) for this critical specimen, and such data can be valuable for benchmarking the current paradigm of diagnostic approaches. TTR for bronchoalveolar lavage (BAL) and endotracheal aspirate (ETA) specimens from hospitalized patients was evaluated using the Premier Healthcare Database, a comprehensive database of 194 U.S. hospitals. Times from specimen collection to reporting of organism ID/AST were evaluated and compared by specimen types and characteristics. A total of 79,662 (43,129 BAL; 36,533 ETA) specimens were included, of which 19.3% harbored no growth, 47.1% contained normal respiratory flora alone (including yeast), and 0.6% contained mycobacteria/molds. Potential bacterial pathogens (PBP) were recovered from 33.0%. ETA specimens had a higher proportion of specimens with isolation of PBP (39.2% versus 27.7%) and with normal respiratory flora (52.0% versus 43.0%) and were less likely to be negative (8.2% versus 28.6%) than BAL specimens (all P < 0.0001). Staphylococcus aureus and Pseudomonas aeruginosa were isolated in 10.5 and 6.4% of the specimens, respectively, and were the most common organisms identified. Median (interquartile range) TTR were 37.0 h (21.8 to 51.7 h) and 60.5 h (46.6 to 72.4 h) for ID and AST, respectively. Median TTR for major respiratory pathogens by organism ranged from 29.2 to 43.9 h for ID and from 47.9 to 73.9 h for AST. Organism type, specimen collection time, and hospital teaching status influenced TTR. Mechanically vented patients and ETA specimens were more likely to recover PBP.

Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens

ObjectivesThe performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. MethodsThirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. ResultsOverall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3–99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥106 copies/ml also gave culture-positive results with significant amounts of bacteria. ConclusionsFA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.

Gram-Negative Bacteria and Antibiotic Resistances Isolated from Endotracheal Aspirate Samples of Patients Hospitalized in the Intensive Care Unit: 3-Years Retrospective Analysis

Intensive care units (ICUs) are the most frequent department where hospital-acquired infections caused by multi-resistant microorganisms. Ventilator-associated pneumonia (VAP) is one of the most common serious infections in intensive care units with high mortality rate. In this study, it was aimed to determine the microorganisms and their antibiotic resistance rates of endotracheal aspirate (ETA) samples taken from patients who applied mechanical ventilation in our hospital's ICU. Gram negative microorganisms isolated from ETA samples sent from patients hospitalized at ICU between January 2016 and December 2018 were included in this study. For identification of the growing strains, matrix-mediated laser desorption ionization-flight time mass spectrometry (MALDI-TOF) (VITEK-MS, bioMérieux, France), VITEK 2 automated system (bioMérieux, France) were used to determine antibiotic susceptibility. The antibiotic susceptibility of the strains was evaluated according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. A total of 385 Gram negative microorganisms were isolated from ETA specimens with significant growth over the three-year period. When analyzing the distribution of microorganisms, A. baumannii (34.2%) was in the first place, followed by P. aeruginosa and K. pneumoniae. There was no significant difference in bacterial distribution in the three-year period. A. baumannii strains showed high levels of carbapenem resistance (94%), while the most effective antibiotics were colistin and tigecycline. Carbapenem and colistin resistance in P. aeruginosa strains were determined as 27% and 6.5%, respectively. Tigecycline was found to be the most effective antibiotic with 8% resistance rate in K. pneumoniae isolates. The high carbapenem resistance seen in A. baumannii strains isolated in our study is remarkable. Increased colistin resistance in K. pneumoniae shows that the last line drugs are also in danger. It is thought that following the antimicrobial resistance patterns of the ICU regularly, updating the treatment protocols in this direction and applying the infection control measures carefully will contribute to both the success of the treatment and the reduction of the resistance rates. Keywords: Endotracheal aspirate, intensive care units, antibiotic resistance. Special Issue of Health Sciences DOI: 10.7176/JSTR/6-03-31

Microbiological profile of ventilator-associated pneumonia among intensive care unit patients in tertiary Egyptian hospitals.

Ventilator-associated pneumonia (VAP) is one of the common serious infectious diseases encountered in the intensive care unit (ICU), which highly affects the healthcare cost and patient prognosis. VAP is caused by various antimicrobial-resistant aetiological agents and the clinical manifestations lack sensitivity and specificity, making the prompt treatment is a challenge. This study aimed to investigate the microbial profile of VAP causing microorganisms among ICU patients in Egypt, antimicrobial susceptibility patterns and the genetic diversity among the frequently isolated organisms. Throughout the period from August 2016 to August 2017, endotracheal aspirate (ETA) specimens were collected from ICU patients with clinically suspected VAP in two tertiary hospitals in Cairo. ETA specimens were investigated for the microbial content. The antimicrobial susceptibility was determined by the Kirby-Bauer method. ERIC-PCR was performed for genotyping. Fifty microbiologically confirmed VAP cases were identified. The most frequently isolated microorganisms were Klebsiella spp., followed by Pseudomonas aeruginosa, Acinetobacter baumannii. Candida spp. was the most isolated fungi. A single isolate of each Cupriavidus pauculus and Aeromonas salmonicida was isolated. Antimicrobial susceptibility profiles indicated 40% of isolates were multidrug-resistant (MDR). ERIC-PCR revealed no genetic relatedness among K. pneumoniae isolates, the most frequently isolated microorganism. Gram-negative bacteria are the main causative agents of VAP cases, which mostly are MDR. Microorganisms like C. pauculus and A. salmonicida should be taken into consideration as VAP causative agents. There was no common source of infection suggesting likely endogenous sources of K. pneumoniae, the main causative agent of VAP in this study.

245. Plasma and Respiratory Specimen Metagenomic Sequencing for the Diagnosis of Severe Pneumonia in Mechanically-Ventilated Patients

BackgroundMetagenomic sequencing of respiratory microbial communities may overcome the limitations of culture-based pneumonia diagnostics. Nonetheless, respiratory metagenomics requires high-quality specimens, may miss deep-seated infections and cannot distinguish colonization from infection. Plasma microbial cell-free DNA (mcfDNA) sequencing may offer a noninvasive alternative for culture-independent diagnosis and help refine interpretations of respiratory metagenomics.MethodsWe obtained concurrent plasma and endo-tracheal aspirate (ETA) samples from 29 mechanically-ventilated patients (15 culture-positive, 11 culture-negative pneumonia, 3 uninfected control patients). We performed plasma mcfDNA sequencing (Karius®Test, Redwood City, CA) and ETA metagenomics (MiNION, Oxford Nanopore Technologies). We compared sequencing results with clinical microbiologic cultures for identified DNA pathogens.ResultsUninfected control patients had a negative signal for mcfDNA in plasma and oral bacteria in ETA specimens. In culture-positive pneumonia samples, Karius testing identified a median of 2 pathogens per sample (range 0–10), which were concordant with clinical isolates in 11/15 (73%) cases (figure). In 5/11 (45%) of concordant cases, Karius and MiNION suggested polymicrobial infections with additional pathogens not identified by cultures. In culture-negative cases, Karius detected potential pathogens in 8/11 (73% cases), which matched the species identified in ETA specimens by MiNION. In cases of clinical aspiration, Karius detected more organisms (median 8, range 0–14) per sample mainly consisting of oral origin bacteria compared with cases without history of aspiration (median 1, range 0–6, P = 0.04).ConclusionMetagenomic sequencing in plasma and ETA samples showed good concordance between the blood and lung compartments as well as with culture results in pneumonia patients. Metagenomics revealed potential pathogens missed by cultures in ~75% of culture-negative pneumonias and suggested polymicrobial infections especially in cases with aspiration. Further research is needed to evaluate the clinical utility of real-time metagenomics for pneumonia diagnosis in mechanically ventilated patients. Disclosures All authors: No reported disclosures.

Microbiological analysis of endotracheal aspirate and endotracheal tube cultures in mechanically ventilated patients

BackgroundTo compare the microbiological culture within endotracheal aspirate specimens (ETAs) and endotracheal tube specimens (ETTs) in patients undergoing mechanical ventilation (MV) by statistical tools.MethodETAs and ETTs from a total number of 81 patients, who were undergoing MV at the intensive care unit (ICU) of Jiading Central Hospital Affiliated Shanghai University of Medicine & Health Sciences from September 1st, 2017 to August 31st, 2018, were collected for microbiological culture analysis. Correlation of ETAs and ETTs cultures were obtained by Spear-men correlation analysis, while the consistency of the two specimens was determined by Kappa analysis and principal component analysis (PCA).ResultsMicrobiological culture from both ETAs and ETTs showed that Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae were the main pathogens, with Spear-man correlation coefficients of 0.676, 0.951, 0.730 and 0.687 respectively (all P < 0.01), and the overall Spear-man correlation coefficient is 0.757 (P < 0.01). This result shows that two samples were positively correlated. Kappa analysis also revealed high consistency of the microbial culture results from the ETAs and the ETTs (overall κ = 0.751, P < 0.01). The κ values for the four bacteria detected were 0.670, 0.949, 0.723, and 0.687, respectively (all P < 0.001). PCA also revealed high similarity.ConclusionCombining microbiological culture and statistical analysis of samples collected from 81 patients who were undergoing MV in ICU, we showed that microbe found in the ETAs had high similarity with that found in the ETTs which collected at the end of the catheters. In clinical practice, ETAs analysis is easily accessible meanwhile provides a valuable information for MV patients.

Clinical, virological and immunological features from patients infected with re-emergent avian-origin human H7N9 influenza disease of varying severity in Guangdong province.

BackgroundThe second wave of avian influenza H7N9 virus outbreak in humans spread to the Guangdong province of China by August of 2013 and this virus is now endemic in poultry in this region.MethodsFive patients with H7N9 virus infection admitted to our hospital during August 2013 to February 2014 were intensively investigated. Viral load in the respiratory tract was determined by quantitative polymerase chain reaction (Q-PCR) and cytokine levels were measured by bead-based flow cytometery.ResultsFour patients survived and one died. Viral load in different clinical specimens was correlated with cytokine levels in plasma and broncho-alveolar fluid (BALF), therapeutic modalities used and clinical outcome. Intravenous zanamivir appeared to be better than peramivir as salvage therapy in patients who failed to respond to oseltamivir. Higher and more prolonged viral load was found in the sputum or endotracheal aspirates compared to throat swabs. Upregulation of proinflammatory cytokines IP-10, MCP-1, MIG, MIP-1α/β, IL-1β and IL-8 was found in the plasma and BALF samples. The levels of cytokines in the plasma and viral load were correlated with disease severity. Reactivation of herpes simplex virus type 1(HSV-1) was found in three out of five patients (60%).ConclusionExpectorated sputum or endotracheal aspirate specimens are preferable to throat swabs for detecting and monitoring H7N9 virus. Severity of the disease was correlated to the viral load in the respiratory tract as well as the extents of cytokinemia. Reactivation of HSV-1 may contribute to clinical outcome.

An outbreak of methicillin resistant Staphylococcus epidermidis among neonates in a hospital in Saudi Arabia

Staphylococcus epidermidis is a pathogen associated with nosocomial infection in neonatal intensive care units (NICU). This study investigates an outbreak of methicillin resistant S. epidermidis in an NICU in a hospital in Saudi Arabia. A total of 41 isolates identified as Gram-positive cocci were obtained from blood culture, umbilical wound swabs and endotracheal aspirate specimens of neonates, of which 29 were identified as S. epidermidis. Bacterial identification at the species level and determination of antibiotic resistance were performed by MicroScan (Dade Behring, USA). Genotyping was completed using randomly amplified polymorphic DNA (RAPD) and the mecA gene was detected by PCR. All 29 S. epidermidis isolates were found to be resistant to oxacillin and were positive for the mecA gene. The isolates showed several multidrug-resistance patterns; the resistance rates to gentamicin, erythromycin, clindamycin, and trimethoprim/sulfamethoxazole were 89.7%, 86.2%, 75.9% and 72.4%, respectively. All isolates were susceptible to vancomycin, teicoplanin, rifampin, synercid, and ciprofloxacin. Several genotypic and phenotypic patterns were detected among the S. epidermidis isolates: antibiogram typing showed seven different patterns, one of which was shared by 65% of the isolates, whereas the most prevalent RAPD genotype was shared by only five S. epidermidis isolates, and did not correlate with antibiotic resistance phenotype. The diverse clonal origin of tested isolates indicates the presence of multiple S. epidermidis strains among neonates in the NICU setting.

Ventilator‐Associated Tracheobronchitis and Pneumonia: Thinking Outside the Box

Lower respiratory tract infections in intubated patients include ventilator-associated tracheobronchitis (VAT) and ventilator-associated pneumonia (VAP). These infections are increasingly caused by multidrug-resistant bacteria, which colonize the patient's oropharynx and enter the lower respiratory tract around the endotracheal tube cuff or through the lumen. Progression of colonization to VAT and, in some patients, to VAP is related to the quantity, types, and virulence of invading bacteria versus containment by host defenses. Diagnostic criteria for VAT and VAP overlap in terms of clinical signs and symptoms, and they share similar microbiologic criteria when endotracheal sputum aspirate samples are used. In addition, the diagnosis of VAP requires a new and persistent infiltrate on a chest radiograph, which may be difficult to assess in critically ill patients, and a significant bacterial culture of a endtotracheal aspirate or bronchoalveolar lavage specimen. Current guidelines for the management of VAP strongly recommend the use of early, appropriate empirical antibiotic therapy based on patient risk factors for multidrug-resistant pathogens. An alternative model focused on VAT, using serial surveillance of endotracheal aspirate specimens to identify multidrug-resistant pathogens and their antibiotic susceptibilities, would allow earlier, targeted antibiotic treatment that could improve outcomes in patients, prevent VAP, and provide an attractive model for clinical research trials.

Multi-drug resistant Acinetobacter ventilator-associated pneumonia

Background:Ventilator-associated pneumonia (VAP) due to a multi-drug resistant (MDR) Acinetobacter is one of the most dreadful complications, which occurs in the critical care setting.Aims and objectives:To find out the incidence of Acinetobacter infection in VAP cases, to determine various risk factors responsible for acquisition of Acinetobacter infection and to determine the antimicrobial susceptibility pattern of Acinetobacter.Materials and Methods:A total of 60 endotracheal aspirate specimens from intubated patients diagnosed clinically and microscopically as VAP were studied bacteriologically. All clinical details and prior exposure to antibiotics were recorded.Results:An incidence of 11.6% of Acinetobacter VAP cases was recorded. Various underlying conditions like head injury, cerebral hemorrhage and chronic obstructive pulmonary disease (COPD) were found to be associated with Acinetobacter VAP. Acinetobacter strains exhibited MDR pattern.Conclusion:Strict infection control measures, judicious prescribing of antibiotics, antibiotic resistance surveillance programs and antibiotic cycling should be adopted to control infections due to these bacteria in patients admitted to intensive care units.

INCIDENCE OF CARBAPENEM RESISTANT NONFERMENTING GRAM NEGATIVE BACILLI FROM PATIENTS WITH RESPIRATORY INFECTIONS IN THE INTENSIVE CARE UNITS

Resistance to carbapenems is commonly seen in nonfermenting gram negative bacilli (NFGNB). We document herein the prevalence of carbapenem resistance in NFGNB isolated from patients with respiratory tract infections in the intensive care units (ICUs). A total of 460 NFGNB were isolated from 606 endotracheal aspirate specimens during January through December 2003, of which 56 (12.2%) were found to be resistant to imipenem and meropenem. Of these, 24 (42.8%) were Pseudomonas aeruginosa, 8 (14.2%) were Acinetobacter spp. and 24 (42.8%) were other NFGNB. Stringent protocols such as antibiotic policies and resistance surveillance programs are mandatory to curb these bacteria in ICU settings.

Incidence of carbapenem resistant nonfermenting gram negative bacilli from patients with respiratory infections in the intensive care units

Resistance to carbapenems is commonly seen in nonfermenting gram negative bacilli (NFGNB). We document herein the prevalence of carbapenem resistance in NFGNB isolated from patients with respiratory tract infections in the intensive care units (ICUs). A total of 460 NFGNB were isolated from 606 endotracheal aspirate specimens during January through December 2003, of which 56 (12.2%) were found to be resistant to imipenem and meropenem. Of these, 24 (42.8%) were Pseudomonas aeruginosa , 8 (14.2%) were Acinetobacter spp. and 24 (42.8%) were other NFGNB. Stringent protocols such as antibiotic policies and resistance surveillance programs are mandatory to curb these bacteria in ICU settings