Tracheal Aspirates Research Articles

COVID-19-associated pulmonary aspergillosis (CAPA): identification of Aspergillus species and determination of antifungal susceptibility profiles.

Among the co-infectious agents in COVID-19 patients, Aspergillus species cause invasive pulmonary aspergillosis (IPA). IPA is difficult to diagnose and is associated with high morbidity and mortality. This study is aimed at identifying Aspergillus spp. from sputum and tracheal aspirate (TA) samples of COVID-19 patients and at determining their antifungal susceptibility profiles. A total of 50 patients with COVID-19 hospitalized in their intensive care units (ICU) were included in the study. Identification of Aspergillus isolates was performed by phenotypic and molecular methods. ECMM/ISHAM consensus criteria were used for IPA case definitions. The antifungal susceptibility profiles of isolates were determined by the microdilution method. Aspergillus spp. was detected in 35 (70%) of the clinical samples. Among the Aspergillus spp., 20 (57.1%) A. fumigatus, six (17.1%) A. flavus, four (11.4%) A. niger, three (8.6%) A. terreus, and two (5.7%) A. welwitschiae were identified. In general, Aspergillus isolates were susceptible to the tested antifungal agents. In the study, nine patients were diagnosed with possible IPA, 11 patients were diagnosed with probable IPA, and 15 patients were diagnosed with Aspergillus colonization according to the used algorithms. Serum galactomannan antigen positivity was found in 11 of the patients diagnosed with IPA. Our results provide data on the incidence of IPA, identification of Aspergillus spp., and its susceptibility profiles in critically ill COVID-19 patients. Prospective studies are needed for a faster diagnosis or antifungal prophylaxis to manage the poor prognosis of IPA and reduce the risk of mortality.

Evaluation of presence of clone ST131 and biofilm formation in ESBL producing and non-producing Escherichia coli strains.

Escherichia coli ST131 is a pandemic clone associated with multidrug resistance, starting with beta-lactamase production and fluoroquinolone resistance in the first place, leading to significant systemic infections. Clones that develop due to the frequency of antimicrobial resistance and the rate of spread in our country are important issues that need to be investigated. This study aims to investigate the incidence of ST131which is a "high-risk pandemic clone E. coli" in ESBL-producing and non-ESBL-producing strains, as well as their biofilm-forming abilities and antibiotic resistance rates. A total of 86 E. coli isolates were used in the study. Bacterial identifications were performed by conventional and automated methods. The double disc synergy method was used to demonstrate the presence of ESBL. Molecular studies in all E. coli strains were performed by real-time PCR method. 86 strains were studied, of which 83.72% were urine, 6.98% were wound, 4.65% were blood, and 2.33% were tracheal aspirate and sputum. 79.07% of these strains were ESBL-positive. 58.1% of the strains were female, whereas 41.9% were male patients, and the average age was 46.2. Out of 86 strains, 38.72% were ST131 positive, the H30 subclone was detected in 27.27% of them, and the H30-Rx subclone was detected in all of the H30 subclone positive strains. The presence of the ESBL resistance gene was detected at the rate of TEM 41.86%, SHV 37.21%, CTX-M 36.04%, and OXA 4.65%. Most commonly SHV gene (54.54%) was seen in ST131 clone-positive samples. Finally, while it was found that 48.83% of the strains formed biofilm by any method, biofilm formation was detected in 69.7% of the samples that were positive for the ST131 clone. Our study can reveal the dramatic prevalence of the ESBL-producing E. coli strains along with the high-risk ST131 clone, the dominance of the H30Rx subclone of this risky clone, as well as the importance of the influence of resistance mechanisms along with resistance and biofilm.

A case-control study of atypical guttural pouch empyema in Arabian foals.

Upper respiratory disease was reported over many seasons in Arabian foals on a single stud farm in the Middle East. Affected foals were noted to have mucopurulent nasal discharge, cough, fever and tachypnea. All affected foals had been empirically treated with a macrolide and rifampicin, by the referring veterinarian without improvement. On endoscopic examination, all affected foals had significant guttural pouch empyema (GPE). (1) To document a previously unreported presentation of guttural pouch empyema (GPE) in a family of juvenile Arabian foals; (2) To document the cytological and microbial composition of the empyema; (3) To identify clinical signs significantly correlated with the presence of GPE, as predictors for the need for guttural pouch (GP) endoscopy; (4) To demonstrate successful resolution of the identified syndrome with mechanical GP lavage and evidence based antimicrobial use, improving antibiotic stewardship and the one-health approach to respiratory disease in this demographic of foals. Evaluation and scoring of clinical signs, upper airway endoscopy and thoracic ultrasound were performed in 14 affected foals and 10 age-matched controls, followed by comparative tracheal and guttural pouch sputum culture and cytological evaluation. Therapeutic GP lavage was performed and response to therapy monitored. GPE, cranioventrally distributed ultrasonographic lesions and opportunistic pathogen infection suggested a primary lesion of GPE with aspiration of GP discharge into the lungs. GP lavage resolved the empyema and associated clinical signs in all cases. Cytological examination of tracheal and guttural pouch aspirates revealed a neutrophilic exudate with lipid-laden phagocytes, suggestive of engulfed milk. Bacteriology revealed a high prevalence of Streptococcus equi ssp. zooepidemicus admixed with other opportunistic pathogens. Streptococcus equi ssp. equi was not isolated in any case.

Mechanical hyperinflation maneuver and intracranial compliance of critical neurological patients: protocol for a randomized controlled equivalence trial

BackgroundMechanical hyperinflation maneuver (MHM) is a technique known for optimizing bronchial hygiene and respiratory mechanics; however, its effects on intracranial compliance are not known.MethodsSixty patients aged ≥ 18 years, with clinical diagnosis of acute stroke, confirmed by neuroimaging examination, with onset of symptoms within 72 h, under mechanical ventilation through tracheal tube, will participate in this study. Participants will be randomly allocated into 2 groups: experimental group (n = 30)—MHM plus tracheal aspiration—and control group (n = 30)—tracheal aspiration only. Intracranial compliance will be measured by a non-invasive technique using Brain4care BcMM-R-2000 sensor. This will be the primary outcome. Results will be recorded at 5 times: T0 (start of monitoring), T1 (moment before MHM), T2 (moment after the MHM and before tracheal aspiration), T3 (moment after tracheal aspiration), T4, and T5 (monitoring 10 and 20 min after T3). Secondary outcomes are respiratory mechanics and hemodynamic parameters.DiscussionThis study will be the first clinical trial to examine the effects and safety of MHM on intracranial compliance measured by non-invasive monitoring. Limitation includes the impossibility of blinding the physical therapist who will supervise the interventions. It is expected with this study to demonstrate that MHM can improve respiratory mechanics and hemodynamic parameters and provide a safe intervention with no changes in intracranial compliance in stroke patients.

EVALUATION OF TRACHEAL ASPIRATE CULTURES IN PATIENTS FOLLOWED WITH HOME MECHANICAL VENTILATORS

Introduction: In recent years, there has been an increase in the use of mechanical ventilators at home. In this study, we aimed to investigate the underlying diseases, admission complaints, microorganisms that isolated in samples taken from tracheal aspirate (TA) cultures and their resistance to antibiotics in patients followed up with mechanical ventilators at home.
 Methods: Between January 1, 2020 and January 1, 2021, TA cultures, identification of bacteria and their antibiotic susceptibilities were evaluated by VITEK 2 (bioMeriux, France) automated identification system. The patients' age, gender, underlying diseases, duration of home ventilator use, complaints, and laboratory data were reviewed retrospectively from the patient files.
 Results: Of the 91 prediagnosed ventilator-associated pneumonia (VAP) patients examined in the study, 72 (79%) were male and 19 (21%) were female. The ages of the patients ranged from 5 to 212 month, with a mean age of 91,64 ± 64,07 month. The most common reason for referral was fever and dyspnea and 43.76% of the patients were diagnosed with cerebral palsy/epilepsy and 10.4% with syndromes.
 Of the samples; 12 (13.3%) were defined as Gram-positive and 79 (86.7%) as Gram-negative. Pseudomonas aeruginosa was detected in 44 (48.4%) samples, S. marcescens in 9 (9.9%) and Klebsiella in 8 (8.8%) samples. Staph aureus was detected in 12 (13.3%) samples. Carbapenem resistance was 18.75% for P. auriginosa, 16% for Klebsiella, 12.5 for E.coli and 12% for Acinetobacter baumani.
 Conclusion: TA culture should be taken from patients with home mechanic ventilator (HMV) who admitted with signs of infection such as fever and respiratory distress and treatment should be arranged according to the result. It was observed that the TA culture antibiotic resistance rates of the patients followed up with HMV at home was lower than the TA cultures sent from the patients hospitalized in the intensive care unit.

Cytomegalovirus reactivation with high viral load in a patient of coronavirus disease 2019 acute respiratory distress syndrome: a case report

IntroductionCytomegalovirus establishes life-long latency after primary infection in childhood. Cytomegalovirus reactivation has been well reported in immune-compromised patients; however, in the last few years it has been observed that cytomegalovirus reactivation also occurs in critically ill patients without exogenous immunosuppression, which increases length of intensive care unit stay and mortality rate.Case reportA 63-year-old Indian male, without any known comorbidity, developed severe coronavirus disease 2019 and was admitted to the intensive care unit. He received remdesivir, tocilizumab, steroids, anticoagulants, and empiric antibiotics over the next 3 weeks. However, his clinical condition did not improve much, and during the 9th week of illness his condition started deteriorating and routine bacterial cultures, fungal cultures, and cytomegalovirus real-time polymerase chain reaction on blood were negative. His clinical condition worsened rapidly, which led to the need for invasive mechanical ventilation. Tracheal aspirate bacterial and fungal culture showed no growth, but cytomegalovirus real-time polymerase chain reaction showed 21,86,000 copies/mL in tracheal aspirates. After 4 weeks of ganciclovir treatment, the patient improved clinically and was discharged. Currently he is doing well and able to do his routine activity without the need of oxygen.ConclusionTimely management with ganciclovir is associated with favorable outcome in cytomegalovirus infection. Thus, it can be suggested that treatment should be initiated with ganciclovir if a patient with coronavirus disease 2019 has high cytomegalovirus load in tracheal aspirates, along with unexplained and prolonged clinical and/or radiological features.

Epidemiology and Multidrug Resistance of Pseudomonas aeruginosa and Acinetobacter baumanni Isolated from Clinical Samples in Ethiopia.

A. baumannii and P. aeruginosa are important nosocomial pathogens in health-care settings. Both are intrinsically resistant to many drugs and are able to become resistant to the virtually most antimicrobial agents. An increasing prevalence of infections caused by multidrug-resistant isolates has been reported in many countries. An institutional-based cross-sectional five-year retrospective study was conducted to assess the antimicrobial resistance trend of P. aeruginosa and A. baumani. 893 A. baumani and 729 P. aeruginosa isolates were included in the study. Conventional method was used for identification and antimicrobial susceptibility was determined by Kirby-Bauer disc-diffusion method. The isolates were from suspected bloodstream infections, wound infections, urinary tract, or surgical site nosocomial infections. Socio-demographic and other variables of interest were collected using a structured check list from a patient record data. Data were analyzed using SPSS version 26 software. P value <0.05 was considered statistically significant. A total of 1622 A. baumanii and P. aeruginosa were isolated from various clinical specimens recorded from the year 2017-2021. Out of which A. baumanni was 893 (60.6%) and P. aeruginosa was 729 (39.4%). Blood was the major source of the isolates (18.3%), followed by urine (16%), and tracheal aspirate (10.6%). Antimicrobial resistance among A. baumanni over the five years were; ampicillin (86% to 92%), ceftriaxone (66.7% to 82.2%), and ciprofloxacin (58.5% to 66.7%). In P. aeruginosa a significant increase in resistance was seen from 2017 to 2021 to Amoxicillin-clavulanate (74.1% to 84.2%), chloramphenicol (62% to 81.9%), and gentamicin (40% to 44.8%). A five-year antimicrobial resistance trend analysis of A. baumanni and P. aeruginosa showed increasing multi drug resistance and resistance to highly potent antimicrobial agents in Ethiopia. It should be addressed with infection control measures, surveillance, and alternative new therapeutic strategies to circumvent the spread of multi-drug resistance.

Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae among clinical isolates in Turaif general hospital, northern borders- Saudi Arabia.

Enterobacteriaceae that produce extended-spectrum beta-lactamase (ESBL) are quickly spreading, posing a threat to world healthcare. 138 gram-negative bacteria were collected from different samples (stool, urine, wound, blood, tracheal aspirate, catheter tip, vaginal swab, sputum, and tracheal aspirate) from hospitalized patients. Samples were subcultured and identified in accordance with their biochemical reactions and culture characteristics. Against all the isolated Enterobacteriaceae, an antimicrobial susceptibility test was performed. VITEK®2 system, phenotypic confirmation, and Double-Disk Synergy Test (DDST) had been utilized to identify the ESBLs. Of the 138 samples studied, the prevalence of ESBL-producing infections among the clinical samples of the present study was 26.8 % (n = 37). E. coli was the commonest ESΒL producer at 51.4% (n = 19) followed by K. pneumoniae at 27% (n = 10). The potential risk factors for the ESBL development that produces bacteria were as follows, patients with the presence of indwelling devices, previous history of hospital admission, and usage of antibiotics. ESBL is statistically (p ≤ 0.05) higher among the patients with indwelling devices, ICU admission, who had a previous hospital admission in the last 6 months as well as who was given antibiotics (quinolones and/or cephalosporins) in the last 6 months. One hundred thirty-two (95.7%) of ESBL isolates were resistant to amoxicillin, while the lowest resistance was for fosfomycin (15.2%). ESBL-producing Enterobacteriaceae are highly prevalent in Turaif General Hospital setting with some potential risk factors. A strict policy to be made available on the usage of antimicrobials in hospitals and clinics should be established.

Pseudomonas aeruginosa in tracheal aspirate: Colonization, infection, and recurrence.

Pseudomonas aeruginosa respiratory infections are challenging, and the risk of recurrence is a frequent problem. The aim of this study was to investigate the risk factors associated with the presence of P.aeruginosa, and the risk factors related to the recurrence and death of lower airway infections in inpatients in a Brazilian hospital. Retrospective cohort with inpatients that had a sample of airways culture (tracheal aspirate or bronchoalveolar lavage) with the detection of P.aeruginosa. The patients with clinical criteria of infection were classified as ventilator-associated, hospital-acquired, or community-acquired pneumonia. P.aeruginosa in respiratory samples without symptoms was considered colonization. The antimicrobial treatment adequacy and the clinical data were evaluated. Outcome variables included mortality and recurrence. One hundred and fifty-four patients were included in the study, most of them were men, and the majority (102) were considered infected. The average length of stay was superior to 30 days. Previous pulmonary disease was associated with the occurrence of colonization. Aminoglycosides were the most active drug according to susceptibility tests and were successfully used as monotherapy. Septic shock was a risk factor for death in the infected patients. The use of adequate antimicrobial therapy was associated with major survival, independent of the infection classification. It is possible to evaluate clinical data associated with recurrence and mortality in patients with different lung infections by P.aeruginosa. Aminoglycoside monotherapy is safe and effective in P.aeruginosa respiratory infections.

Neutrophil extracellular traps promote bronchopulmonary dysplasia-like injury in neonatal mice via the WNT/β-catenin pathway.

Bronchopulmonary dysplasia (BPD) is one of the most common and severe chronic diseases in preterm infants. Premature infants are susceptible to BPD due to immature lungs and adverse perinatal episodes of infection, hyperoxia, and mechanical ventilation. Neutrophils are the first line of host defence, and the release of neutrophil extracellular traps (NETs) is an important strategy to immobilize and kill invading microorganisms. This study examined whether NETs were associated with BPD in preterm infants and contributed to hyperoxia-induced lung injury in neonatal mice via the WNT/β-catenin pathway. In this study, we found that preterm infants with BPD had higher levels of NETs in their tracheal aspirates than those without BPD. Neonatal mice treated with NETs after birth exhibited BPD-like changes in their lungs. Furthermore, the levels of Aquaporin 5 (AQP5) and surfactant-associated protein C (SPC), which represent alveolar differentiation and development, were significantly lower than those in the controls. The WNT/β-catenin pathway is one of the most well-known signalling pathways involved in lung growth. We found that the expression of the target genes c-MYC, cyclin D, and vascular endothelial growth factor (VEGF) and the important proteins WNT3a and β-catenin significantly decreased. Moreover, heparin, which is a NET inhibitor, attenuated changes in gene and protein expression, thereby attenuating BPD-like changes. This finding indicates that NETs are associated with BPD and can induce BPD-like changes in neonatal mice via the WNT/β-catenin pathway.

Low Diagnostic Utility of Frequent Serial Tracheal Aspirate Cultures in the PICU*

To determine the diagnostic outcomes of serial tracheal aspirate cultures (TACs) in the PICU. A retrospective chart review of TAC utilization was performed. Items recorded for each TAC included the time and date of culture acquisition, result, changes in microbial resistance patterns, antimicrobial therapy, and patient clinical course. A single urban tertiary care children's hospital in the United States. Patients admitted to the PICU from January 1, to October 31, 2021, for whom a TAC was performed. None. One hundred fifty unique subjects had 582 TACs performed during the study period, of which 145 (24.9%) were serially repeated within 72 hours. Of these serial TACs, 82 (56.6%) had no growth, 41 (28.3%) grew the same organism as the prior culture, with most (36/41) displaying no major change in antimicrobial susceptibilities, 11 (7.6%) grew a new organism previously grown during the admission, and 11 (7.6%) grew a new organism not previously grown during the admission. Overall, only 26 of these serial TACs (17.9%) provided new diagnostic information, whereas only five (3.4%) led to a change in management. Frequent serial TAC sampling in the PICU is common and infrequently yields new data that impact clinical decision-making. Considering worsening antimicrobial resistance and the role of diagnostic stewardship in mitigating it, these findings further support a 72-hour reassessment period before performing a repeat TAC in critically ill children.

Viewing both sides of the coin for infectious disease diagnosis.

Optimal management of lower respiratory tract infection relies on distinguishing infectious from noninfectious etiologies and identifying the microbiologic cause if applicable. This process is complicated by overlapping clinical symptoms and the colonizing lung microbiota. In a recent issue of the JCI, Mick, Tsitsiklis, and colleagues apply RNA-Seq to tracheal aspirates from critically ill children and demonstrate how integration of the host response with microbial identification results in a harmonious and accurate diagnostic classifier. Though promising, there are numerous barriers to realizing a combined host and pathogen diagnostic.

Bacterial co-infection in Covid-19 patients visiting a tertiary care hospital in Maharashtra

Background and objectives: Several patients with SARS-CoV-2 infection presents with bacterial co-infection. The aim of the present study was to determine the bacteria responsible for co-infection in Covid-19 infected patients visiting a tertiary care hospital of Maharashtra, India. Material and methods: A cross sectional study was conducted for 3 months at tertiary care center. Covid-19 patients attending the hospital were included in the study. All the specimens were collected either at the time of admission at outdoor or within 24-48 hours of admission. All the specimens were processed for culture and antibiotic susceptibility testing as per institutional policy and standard methods. Results: Total 200 samples were collected out of which 98 (49%) patients were diagnosed with bacterial co-infection. Majority of cases with bacterial co-infection were above 21 years of age. Culture was positive in 80%, 66.7%, 49.2% and 38.8% of tracheal aspirate, pus, blood and urine samples respectively. Out of 98 cases of bacterial co-infection, 62.2% and 37.8% had infection with Gram negative and positive bacteria respectively. Most common organism isolated was Klebsiella pneumoniae (20.4%) followed by Enterococcus species (14.3%). Over 70% of Klebsiella pneumoniae isolates were resistant to aminoglycosides, cephalosporins, fluroquinolones and carbapenems while 100% Acinetobacter was resistant to all antimicrobials tested. Among 57 Of the Gram negative isolates, 5 and 24 isolates were positive for ESBL carbapenemase respectively. Conclusion: The study revealed that bacterial co-infection was present in considerable proportion of Covid-19 patients and the organisms responsible were resistant to several antimicrobial agents. IMC J Med Sci. 2023; 17(2):006. DOI: https://doi.org/10.55010/imcjms.17.016 *Correspondence: Sahjid Mukhida, Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, India-411018. E-mail: drssmukhida@rediffmail.com

Distribution and antifungal resistance rate of yeast isolated from various samples

Objective: Yeast causes hospital-acquired infections at increasing rates, which can cause serious mortality, especially in patients with a suppressed immune system. This study aimed to determine the species distribution and antifungal resistance rates of yeast isolated in a hospital. Material and Methods: Isolated yeasts from clinical specimens of patients who received inpatient treatment in different clinics in our hospital between 1 December 2019 and 30 September 2020 were examined. In all of these isolates, species identification was made with an automated system in addition to classical methods. Additionally, the antifungal susceptibility of yeast against amphotericin B, flucytosine, Fluconazole, micafungin, caspofungin, and Voriconazole was investigated using an automated system. Results: In the study, yeasts isolated from 183 clinical samples, including 64 vagen, 62 blood, 28 urine, 12 wounds, eight tracheal aspirates, five peritoneal fluids, three catheters and one cerebrospinal fluid (CSF) samples were included. Of these isolates, 93 were Candida albicans (50,82%), 40 were Candida parapsilosis (21,86%), 17 were Candida tropicalis (9,29%), eight were Candida glabrata (4,37%), eight were Stephanoascus ciferrii (4,37%), five were Candida lusitaniae (2,19%), four were Candida famata (2,19%), four were Cryptococcus laurentii (2,19%) and four were Candida krusei ( 2,19%). Antifungal susceptibility testing was performed in 103 of the isolates. The highest resistance was found against Fluconazole, with 16.8%, and the lowest resistance was against flucytosine, with 2.2%. Antifungal resistance rates of Fluconazole, Voriconazole, amphotericin B, flucytosine, caspofungin and micafungin were found as 16.8%, 8.2%, 6.1%, 2.2%, 2.9% and 6.8% respectively. Conclusion: Due to the increasing frequency of fungal infections due to long-term hospitalization, it has been concluded that identifying the causative species and reporting the antifungal susceptibility status is important in monitoring the change in resistance rates and guiding the treatment.

Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.

BACKGROUNDLower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging because noninfectious respiratory illnesses appear clinically similar and because existing microbiologic tests are often falsely negative or detect incidentally carried microbes, resulting in antimicrobial overuse and adverse outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and treatment remains unclear.METHODSWe used tracheal aspirate RNA-Seq to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n = 117) or of noninfectious respiratory failure (n = 50). We then developed a classifier that integrates the host LRTI probability, abundance of respiratory viruses, and dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.RESULTSThe host classifier achieved a median AUC of 0.967 by cross-validation, driven by activation markers of T cells, alveolar macrophages, and the interferon response. The integrated classifier achieved a median AUC of 0.986 and increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n = 94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those.CONCLUSIONLower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.FUNDINGSupport for this study was provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Heart, Lung, and Blood Institute (UG1HD083171, 1R01HL124103, UG1HD049983, UG01HD049934, UG1HD083170, UG1HD050096, UG1HD63108, UG1HD083116, UG1HD083166, UG1HD049981, K23HL138461, and 5R01HL155418) as well as by the Chan Zuckerberg Biohub.

Multiomics endotyping of preterm infants with bronchopulmonary dysplasia and pulmonary hypertension-A pilot study.

Pulmonary hypertension associated with bronchopulmonary dysplasia is a severe complication of preterm birth resulting in high mortality of up to 50% within the first 2 years of life. There is a direct relationship between bronchopulmonary dysplasia severity and incidence of associated pulmonary hypertension. However, it is challenging to clinically characterize severe bronchopulmonary dysplasia with and without pulmonary hypertension and there is need for better understanding of the two entities. Our main objective is to identify markers to help understand biological processes and characterize infants with pulmonary hypertension associated with bronchopulmonary dysplasia using tracheal aspirates. We conducted an unbiased multiomic analysis of tracheal aspirates via microRNA(miRNA) polymerase chain reaction arrays, RNA sequencing, and mass spectrometry proteomics in preterm infants with severe bronchopulmonary dysplasia with and without pulmonary hypertension (n = 46). Our pilot study analysis revealed 12 miRNAs (hsa-miR-29a, has-miR-542-3p, has-miR-624, has-miR-183, hsa-miR-501-3p, hsa-miR-101, hsa-miR-3131, hsa-miR-3683, hsa-miR-3193, hsa-miR-3672, hsa-miR-3128, and hsa-miR-1287), 6 transcripts (IL6, RPL35P5, HSD3B7, RNA5SP215, OR2A1-AS1, and RNVU1-19), and 5 proteins (CAPS, AAT, KRT5, SFTPB, and LGALS3BP) with significant differential expression in preterm infants with severe lung disease with pulmonary hypertension when compared with infants with severe lung disease but no pulmonary hypertension. Pathway analysis of the integrated multiomic expression signatures revealed NFkB, VEGF, SERPINA1, IL6, and ERK1/2 as target molecules and cellular development, cellular growth and proliferation, and cellular movement as key affected molecular functions. Our multiomic analysis of tracheal aspirates revealed a comprehensive thumbprint of miRNAs, mRNAs, and proteins that could help endotype infants with severe lung disease and pulmonary hypertension.

Bacteriological Profile and Antibiogram of Respiratory Tract Infections in a Tertiary Care Hospital, Bangladesh

Background: Respiratory tract infections (RTIs) are significant health concern for mortality and morbidity in many developing countries. Proper identification of causative pathogens and their antibiotic susceptibility testing is needed to select appropriate antibiotic therapy for management of the patient suffering from RTI. The study was aimed to determine the spectrum of bacterial pathogen causing respiratory tract infections with their antibiogram in Dhaka Medical College hospital (DMCH), Dhaka, Bangladesh. Methods: This observational study was conducted from October 2018 to March 2019 in DMCH. Respiratory tract specimens (sputum, tracheal aspirate and throat swab) sent to the Microbiology laboratory for culture and sensitivity test were included in this study. Data regarding information of the patients, isolated organisms and sensitivity reports were collected from the records of the Microbiology laboratory. Results: Out of 580 processed specimens, 64.66% yielded significant growth of organisms of which 88.80% were gram negative and 11.20% were gram positive bacteria. Pseudomonas spp was the most commonly (31.47%) isolated organism followed by Klebsiella spp (23.47%), Escherichia coli (15.20%) and Staphylococcus aureus (8.53%). Gram negative bacteria were mostly resistant to amoxicillin followed by fluoroquinolones, cotrimoxazole, cephalosporins whereas colistin, carbapenems and piperacillin/tazobactum were the most sensitive antibiotics against them. Among gram negative bacteria, 31.23% were extended spectrum beta lactamase (ESBL) producing organisms and Klebsiella spp were the most commonly isolated ESBL producers. Majority of gram positive bacteria were resistant to fluoroquinolones and co-trimoxazole but all Staphylococcus aureus were susceptible to vancomycin and linezolid followed by teicoplanin (84%) and 37.5% of them were Methicillin resistant (MRSA). Conclusion: Gram negative bacteria were predominant where Pseudomonas spp and Klebsiella spp were most commonly isolated organisms. Most of the bacteria showed high resistance to commonly used antibiotics and this antimicrobial resistance is a matter of concern for the treatment of respiratory tract infections. Bangladesh Medical Res Counc Bull 2023; 49(1): 15-21

Clinicomicrobiological Profile of Infections by Achromobacter: An Emerging Nosocomial Pathogen in Indian Hospitals.

Achromobacter causes opportunistic nosocomial infections in immunocompromised patients with high mortality. It is underreported as it is often misidentified by conventional microbiological methods. The aim of the study is to access the clinicomicrobiological profile and antibiogram of Achromobacter spp. from clinical isolates. It is an observational study done from July 2020 to December 2021 in our hospital. All nonduplicate isolates of Achromobacter from blood and respiratory samples were initially identified with VITEK-2 GN card system and further confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antibiogram and treatment outcomes were also studied. Achromobacter spp. was isolated from 14 patients. Blood samples yielded most isolates (71.4%; n = 10) followed by tracheal aspirate and bronchoalveolar lavage fluid. Bacteremia followed by pneumonia was the most common clinical manifestation of Achromobacter infection. All the isolates were identified as A. xylosoxidans denitrificans and showed 100% susceptibility to minocycline and piperacillin-tazobactam. Diabetes mellitus and malignancy were the most common underlying condition in these patients. A favorable outcome was seen in 78.6% of the individuals with timely institution of antibiotics and proper diagnosis. Infections due to Achromobacter are on the rise in developing countries like India. Resistance to many classes of antimicrobials makes its treatment more challenging therefore it should always be guided by antibiograms. The present study highlights the significance of this rare bacterium in patients with malignancies in India and advocates greater vigilance toward appropriate identification of this organism.

BACTERIAL PROFILE AND ANTIBIOGRAM OF MICROORGANISMS ISOLATED FROM DIFFERENT BODY SITE INFECTIONS AMONG PATIENTS OF A PRIVATE HOSPITAL, KARACHI

Objective:It is crucial to keep an eye on current patterns of multi-drug resistance and extensively drug resistance at local level to facilitate physicians in making justified decision regarding empirical therapy during this era of rising superbugs. Material and Methods: This antibiogram was made up according to CLSI (Clinical Laboratory Standard Institute) M100 guidelines. Samples were received for a period of 2-years from June 2019-June 2021 at National Medical Center Karachi. These samples were urine, blood, pus, cerebrospinal fluid (CSF), central venous pressure (CVP) tip, sputum and tracheal aspirates. Results: Out of 10564 samples received, 4582 were positive for growth of microorganisms. Sample distribution patterns according to the frequency of positive growth of isolates were predominantly urine (58%) and blood (17%) followed by pus (8%) and pus swab (6%) 2% fluid and 2% tracheal secretions, and 7% others like tips growth. Blood cultures were mainly received from Intensive care unit (50%) followed by out-patients departments (34%). The pattern of resistance observed in Escherichia coli (E. coli) revealed ampicillin as the most resistant among all antibiotics (93%) followed by cefixime (77%). Most sensitive antibiotic was amikacin (99%). The Staphylococcus aureus isolates were highly susceptible to vancomycin and linezolid (100%) followed by gentamicin (89%) and chloramphenicol (85%). Vancomycin resistance was observed in Enterococcus faecium (8%). Conclusion: Antimicrobial resistance among gram negative and gram-positive bacteria is increasing. This has left us with fewer therapeutic options which in turn highlights the issue of antimicrobial resistance being a global health concern. This emphasizes the significance of surveillance of antimicrobial patterns, development of antibiograms and implementation of antibiotic stewardship programs by judicious use of antibiotics for prevention of further spread of antimicrobial resistance. Key Words: Antibiogram, Antimicrobial resistance, Multidrug resistance, Extensively drug resistance

Colonization and Antimicrobial resistance patterns of Potentially Pathogenic Micro-Organisms in tracheostomized patients

Introduction: Tracheostomy is one of the most common and ancient surgical procedure performed in the world but it is like a double-edged sword which not only facilitates respiration, but also impairs the natural resistant barrier, therebyaugmenting the colonization of other secondary pathogenic micro-organisms. Hence, it is important to know the patternof microbiological colonizers in tracheostomized patients, so that adequate empiric antimicrobial coverage can preventdevelopment of hospital acquired pneumonia. This study aims to identify various micro-organisms colonizing lower airway in tracheostomized patients.&#x0D; Materials and Methods: An observational cross-sectional study was conducted in a tertiary based teaching hospital in North Bengal, India during July 2021 to July 2022. A total of 56 patients were included in the study.&#x0D; Results: Positive Cultures on day 0 were found in 20.8% &amp; 65.6% of patients in wards and ICUs respectively. Out of the positive cultures isolated on day 0, Staphylococcus aureus was the most common organism (80%) obtained from ward patients whereas, Acinetobacter baumannii was most common organism (47.61%) in ICU admitted patients. On day 7, positive cultures were found in 66.6% &amp; 84.4% of admitted patients in wards and ICUs respectively. Staphylococcus aureus was again the most common organism obtained (56.25%) in wards whereas, Pseudomonas aeruginosa was the most common organism (44.44%) obtained in ICU admitted patients followed by Acinetobacter baumannii (33.33%).&#x0D; Conclusion: Culture positivity rates were higher in patients who were previously intubated in Intensive care unit, which establishes the fact that any procedure which warrants airway manipulations, increases the chance of hospital acquired infections. Antibiotic resistance is very common in ICU admitted patients and has a tendency to increase over time. Hence, upscaling of antibiotics is recommended only after proper sensitivity check of the tracheal aspirates.