Bacterial Lower Respiratory Tract Infections Research Articles

Disposable Peptidoglycan-Specific Biosensor for Noninvasive Real-Time Detection of Broad-Spectrum Gram-Positive Bacteria in Exhaled Breath Condensates.

Rapidly identifying and quantifying Gram-positive bacteria are crucial to diagnosing and treating bacterial lower respiratory tract infections (LRTIs). This work presents a field-deployable biosensor for detecting Gram-positive bacteria from exhaled breath condensates (EBCs) based on peptidoglycan recognition using an aptamer. Dielectrophoretic force is employed to enrich the bacteria in 10 s without additional equipment or steps. Concurrently, the measurement of the sensor's interfacial capacitance is coupled to quantify the bacteria during the enrichment process. By incorporation of a semiconductor condenser, the whole detection process, including EBC collection, takes about 3 min. This biosensor has a detection limit of 10 CFU/mL, a linear range of up to 105 CFU/mL and a selectivity of 1479:1. It is cost-effective and disposable due to its low cost. The sensor provides a nonstaining, culture-free and PCR-independent solution for noninvasive and real-time diagnosis of Gram-positive bacterial LRTIs.

Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis.

In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.

1269. Prospective Evaluation of a Machine Learning Model that Guides Indication for Antibiotics in Lower Respiratory Tract Infections

Abstract Background Over-prescribing of antibiotics for suspected acute bacterial lower respiratory tract infections (abLRTI) is prevalent. A classification model that can identify instances when antibiotics should be initiated or withheld was previously developed with promising results (80% accuracy). This, however, was based on a retrospective dataset. We conducted a prospective evaluation of this model in the hospital antimicrobial stewardship unit (ASU) to validate its performance and compare its effectiveness against current ASU strategies. Methods Inpatients audited by the hospital ASU between 10 January and 23 March 2023 (twice weekly) were enrolled into this study. Relevant patient information (e.g., clinical notes, radiology reports, vital signs) was extracted from our hospital’s electronic data repository for model inference. The presence of abLRTI as determined by the model, the patient’s primary care team and ASU review were compared. Cases that saw differing opinions between any of the three operators were subsequently reviewed by an independent Infectious Diseases physician, who provided the ground truth for that case. Results A total of 851 cases were included, of which 235 (27.6%) had true abLRTI. The model was most accurate in determining the presence versus absence of abLRTI (734/851, 86.3%), while ASU review and primary care team were correct in only 698 (82.0%) and 677 (79.6%) cases respectively. Primary care team demonstrated greatest sensitivity in the suspicion for abLRTI (91.9%); unfortunately, it also over-diagnosed abLRTI in 155 (42%) patients. Among these false-positive cases, the model rightly rejected presence of abLRTI in 126 (81.3%) patients whereas only 66 (64.1%) of them were identified by ASU. ASU outperformed the model in having a lower false-negative rate when abLRTI is suspected (17.3% vs. 22.0%). Conclusion The model displayed consistent performance in a prospective cohort. Findings support its value in guiding decisions on antibiotic initiation for suspected abLRTI. Deploying this model to augment current ASU capabilities should be strongly considered. Disclosures All Authors: No reported disclosures

2588. Burden of Mortality and Antimicrobial Resistance of Bacterial Pathogens Associated with Lower Respiratory Tract and Other Thorax Infection in United States in 2019: A Systematic Analysis

Abstract Background Detailed information about the impact of bacterial antimicrobial resistance (AMR) on Lower Respiratory Tract and other thorax Infections (LRTIs) is currently unavailable. It is important to have precise data on bacterial AMR to develop effective programs and policies for controlling AMR and to use antibiotics prudently for optimal treatment of LRTI patients. The primary objective of this research is to present extensive estimates of the mortality due to "bacterial pathogens" and its "AMR" of LRTIs in the United States in 2019. Methods Mortality data associated with bacterial antimicrobial resistance and lower respiratory tract infection (LRTI) pathogens were acquired from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) in 2019. Results In United States, there were 88089 deaths (95% uncertainty interval [UI]: 66909-117145) due to bacterial pathogens in LRIT in 2019. Highest number of deaths observed due to Staphylococcus aureus (34.04%), followed by Streptococcus pneumoniae (18.30%), Pseudomonas aeruginosa (12.48%) in LRTI in 2019. There were 10984 deaths attributed to and 46482 deaths associated with bacterial AMR in LRTI in 2019. Conclusion Bacterial pathogens causing LRTIs are a significant cause of mortality in the United States. Moreover, antimicrobial resistance (AMR) among these pathogens has become a growing concern, exacerbating the burden of LRTI-related deaths. The implementation of such measures, along with the promotion of antimicrobial stewardship, can help to mitigate the impact of LRTI-associated deaths and preserve the effectiveness of available antimicrobial agents for the future. Disclosures All Authors: No reported disclosures

Are there differences in the relationship between respiratory rate and oxygen saturation between patients with COVID-19 and those without COVID-19? Insights from a cohort-based correlational study

BackgroundPhysicians have observed patients with COVID-19 without respiratory distress despite marked hypoxaemia and extensive radiographic abnormalities, a controversial phenomenon called ‘silent hypoxaemia’. We aimed to compare the relationship between RR...

A qualitative investigation of paediatric intensive care staff attitudes towards the diagnosis of lower respiratory tract infection in the molecular diagnostics era

BackgroundIn the past decade, molecular diagnostic syndromic arrays incorporating a range of bacterial and viral pathogens have been described. It is unclear how paediatric intensive care unit (PICU) staff diagnose lower respiratory tract infection (LRTI) and integrate diagnostic array results into antimicrobial decision-making.MethodsAn online survey with eleven questions was distributed throughout paediatric intensive care societies in the UK, continental Europe and Australasia with a total of 755 members. Participants were asked to rate the clinical factors and investigations they used when prescribing for LRTI. Semi-structured interviews were undertaken with staff who participated in a single-centre observational study of a 52-pathogen diagnostic array.ResultsSeventy-two survey responses were received; most responses were from senior doctors. Whilst diagnostic arrays were used less frequently than routine investigations (i.e. microbiological culture), they were of comparable perceived utility when making antimicrobial decisions. Prescribers reported that for arrays to be clinically impactful, they would need to deliver results within 6 h for stable patients and within 1 h for unstable patients to inform their immediate decision to prescribe antimicrobials. From 16 staff interviews, we identified that arrays were helpful for the diagnosis and screening of bacterial LRTI. Staff reported it could be challenging to interpret results in some cases due to the high sensitivity of the test. Therefore, results were considered within the context of the patient and discussed within the multidisciplinary team.ConclusionsDiagnostic arrays were considered of comparable value to microbiological investigations by PICU prescribers. Our findings support the need for further clinical and economic evaluation of diagnostic arrays in a randomised control trial.Trial registrationClinicaltrials.gov, NCT04233268. Registered on 18 January 2020.

Host test based on tumor necrosis factor-related apoptosis-inducing ligand, interferon gamma-induced protein-10 and C-reactive protein for differentiating bacterial and viral respiratory tract infections in adults: diagnostic accuracy study

ObjectivesTo assess the performance of a test (called BV), integrating the blood levels of three immune proteins into a score, to differentiate bacterial from viral infection among adults with suspected lower respiratory tract infection (LRTI). MethodsProspective diagnostic accuracy study, enrolling febrile adults >18 years with LRTI signs or symptoms for less than 7 days presenting to several hospitals' emergency departments in Israel. The main exclusion criterion was immunodeficiency. Reference standard diagnosis (bacterial/viral/indeterminate) was based on three experts independently reviewing comprehensive patient data including follow-up data. BV generated three results: viral infection or other nonbacterial condition (0 ≤ score < 35), equivocal (35 ≤ score ≤ 65) and bacterial infection including co-infection (65 < score ≤ 100). BV performance was assessed against the reference standard with indeterminate reference standard and equivocal BV cases removed. ResultsOf 490 enrolled patients, 415 met eligibility criteria (median age 56 years, interquartile range 35). The reference standard classified 104 patients as bacterial, 210 as viral and 101 as indeterminate. BV was equivocal in 9.6% (30/314). Excluding indeterminate reference standard diagnoses and equivocal BV results, BV's sensitivity for bacterial infection was 98.1% (101/103; 95% confidence interval 95.4–100), specificity 88.4% (160/181; 83.7–93.1) and negative predictive value 98.8% (160/162; 97.1–100). DiscussionBV exhibited high diagnostic performance for febrile adults with suspected LRTI among patients with reference standard diagnoses of bacterial or viral LRTI.

Quantitative Value of Bacteria Associated with Leukocytes in Differential Diagnosis of Lower Respiratory Tract Infection in Children, in Comparison to Sputum Culture and Procalcitonin.

The mortality and morbidity rates in children with lower respiratory tract infection (LRTI) remain high. To describe the number of bacteria that is associated with leukocytes in differential diagnosis of bacterial, mycoplasma, and viral LRTI in children. Sputum smears were Gram stained for counting single-morphology bacteria associated with leukocytes. The differential diagnostic values of bacterial number were assessed in children with LRTI. The area under the receiver operating characteristic (ROC) curve was 0.95 for bacterial number in the differential diagnosis of bacterial infection from mycoplasma and viral infections. The area under the ROC curve was 0.62 for procalcitonin and 0.94 for bacterial number in the differential diagnosis of bacterial infection from mycoplasma infection. The number of bacteria associated with leukocytes in sputum was valuable and rapid in differential diagnosis of bacterial infection in children with suspected bacterial, mycoplasma, and viral LRTI.

Evaluation of Pathogens and Antibiotic Resistance Profiles Isolated from Lower Respiratory Tract Samples

Objective: In this study, we aimed to guide clinicians in planning empirical treatment and contribute to regional data by presenting bacterial lower respiratory tract infection agents and antibiotic resistance profiles. Methods: All lower respiratory tract samples from patients admitted to our laboratory between January 01 and December 31, 2021 were evaluated retrospectively. Bacterial identification and susceptibility tests were performed using the VITEK 2 automated system and evaluated in accordance with the recommendations of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Results: Significant growth was detected in 461 of 923 lower respiratory tract samples. Antibiotic susceptibility test results of 340 samples were evaluated after excluding the repeated samples of same patient. Gram negative bacteria was isolated in 309 (90.9%), Staphylococcus aureus in 17 (5%) and Candida albicans in 14 (4.1%) of 340 samples. The most frequently isolated Gram-negative bacteria were Pseudomonas aeruginosa (121, 39.2%), Acinetobacter baumannii (88, 28.5%), Klebsiella pneumoniae (64, 20.7%) and Escherichia coli (36, 11.6%), respectively. Resistance rates of A. baumannii isolates to carbapenems, piperacillin/tazobactam, ceftazidime and fluoroquinolones were found to be over 90%, and higher resistance was observed in intensive care units (ICU) than in wards. Conclusion: The increased antibiotic resistance observed in lower respiratory tract infections from hospitalized patients in ICUs, is remarkable. As a result, knowing the causative agents and current resistance profiles is important, especially for hospitalized patients in ICUs, in order to initiate appropriate empirical treatment and to ensure treatment success. The data obtained from our study will guide clinicians in planning empirical treatment.

In vitro activity of cefpodoxime against Russian clinical isolates of Haemophilus influenzae, Streptococcus pneumoniae and Streptococcus pyogenes

Objective. To determine in vitro activity of oral III generation cephalosporin cefpodoxime against clinical isolates of Haemophilus influenzae, Streptococcus pneumoniae and Streptococcus pyogenes isolated from patients with community-acquired respiratory tract infections in different regions of the Russian Federation. Materials and Methods. The study included isolates of bacterial pathogens of community-acquired respiratory tract infections isolated from outpatients and hospitalized patients in different regions of the Russian Federation. A total of 558 isolates were included in the study, including 184 isolates of H. influenzae, 186 isolates of S. pneumoniae and 188 isolates of S. pyogenes. Species identification was performed using the MALDI-TOF mass spectrometry (Bruker Daltonics, Germany), for S. pneumoniae identification was also performed taking into account the morphology of colonies on blood agar, the presence of α-hemolysis, negative catalase reaction, sensitivity to optochin and positive results of latex-agglutination using DrySpot kit (OXOID, UK). Antimicrobial susceptibility to cefpodoxime and comparative antimicrobials was determined using broth microdilution method; interpretation of susceptibility testing results was performed in accordance with the recommendations of EUCAST, v.13.0. Data analysis and visualization were performed using the online platform AMRcloud. Results. Despite the generally low incidence of antibiotic resistance in the tested H. influenzae isolates, cefpodoxime, to which all tested isolates were susceptible, was superior to all other oral antibiotics in terms of in vitro activity: aminophenocillins (R – 8.7%), amoxicillin/clavulanate (R – 1.1%), co-trimoxazole (R – 31.5%), levofloxacin (R – 3.8%), moxifloxacin (R – 3.8%), tetracycline (R – 11%), cefixime (R – 2.2%), ceftibuten (R – 3.3%). Among the studied S. pneumoniae isolates, 81.7% were susceptible to cefpodoxime. All isolates resistant to penicillin, amoxicillin and ceftriaxone were also resistant to cefpodoxime. Cefpodoxime was inferior to levofloxacin (R – 0%), moxifloxacin (R – 0%), linezolid (R – 0%), vancomycin (R – 0%), ertapenem (R – 8.6%), ceftaroline (R – 2.3%), and chloramphenicol (R – 3.2%) in terms of in vitro activity against S. pneumoniae. However, all these drugs are either not available in oral form or have a less favorable safety profile compared to cefpodoxime. When compared with other III generation oral cephalosporins cefixime and ceftibuten, the activity of cefpodoxime against S. pneumoniae was significantly higher based on MIC50/90 values (cefixime – 0.125⁄8 mg/l, ceftibuten – 2/≥ 128 mg/l, cefpodoxime – 0.06/4 mg/l) and MICs range (cefixime – 0.06/≥ 128 mg/l, ceftibuten – 0.06/≥ 128 mg/l, cefpodoxime – 0.03/32 mg/l). No strains resistant to β-lactam antibiotics were detected among the tested S. pyogenes isolates. Based on the MIC50/90 values and the range of MIC values, the in vitro activity of cefpodoxime was higher than that of ceftibuten and comparable to that of cefixime. Conclusions. According to the results of our study, as well as in view of its pharmacokinetic profile, high safety and compliance, cefpodoxime can be considered as one of the options for oral therapy of community-acquired bacterial upper and lower respiratory tract infections.

330. BioFire ® FilmArray® Pneumonia Panel (PN) Results Compared to Standard Microbiologic Testing and Clinical Adjudication in Adults Hospitalized with Respiratory Illness.

Abstract Background Inability to define microbial etiology of lower respiratory tract infection (LRTI) leads to unnecessary antibiotic use. Though multiplex PCR improves viral detection, bacterial LRTI diagnosis remains problematic. We evaluated the clinical utility of BioFire ® FilmArray ® Pneumonia (PN) Panel which detects 8 viruses, 3 atypical and 15 pathogenic bacteria by semi-quantitative PCR to inform bacterial diagnosis. Methods As part of a study to distinguish bacterial from non-bacterial LRTI in hospitalized adults, clinical, laboratory, and X-ray data were collected. Adequate sputa (&amp;lt; 10 Epithelial &amp; &amp;gt;25 PMNs) processed by Gram stain and culture were tested with FilmArray® PN. Microbial LRTI etiology (viral alone, bacterial with or without concomitant viruses, or indeterminate) was adjudicated by a four physician panel using all clinical data except bacterial PCR results. Bacterial PCR was compared to Gram stain and culture and clinical adjudication. Results From 737 illnesses evaluated, 423 sputa were collected and 201 deemed adequate and were tested with FilmArray® PN. Most common discharge diagnoses were pneumonia (24%), AECOPD (21%), viral illness (13%) and asthma exacerbations (9%). FilmArray® PN detected 155 typical bacteria, 9 atypical and 101 viruses. Most bacterial detections were monomicrobial (58%) often with concomitant viruses (43%). Compared to Gram stain and culture, FilmArray® PN detected more bacterial pathogens and was less affected by antibiotics. (Figure) Cases were adjudicated as viral Alone (37), bacterial (93) and indeterminate (71). Bacteria were detected by PCR in 41% of viral and 96% of bacterial cases, p=0.0001 and 76% of indeterminate cases. In cases with no bacteria detected by PCR, only 4 (9%) were adjudicated as bacterial; all deemed caused by anaerobic bacteria which are not included in the PCR panel. Comparing bacterial vs. non-bacterial (Viral + Indeterminate), FilmArray® PN bacterial PCR had 96% sensitivity, 36% specificity, 56% positive predictive value and 91% negative predictive value. Finally, sputum PCR detected 4 mycoplasma and 56 viral infections missed by standard of care testing. FigureRelationship of Gram Stain and Time on Antibiotics to Bacterial Culture and Bacterial PCR Results Conclusion Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria. Disclosures Ann R. Falsey, MD, BioFire Diagnostics: Grant/Research Support|Janssen: Grant/Research Support|Merck, Sharp and Dohme: Grant/Research Support|Novavax: Advisor/Consultant|Pfizer: Grant/Research Support Angela R. Branche, MD, Cyanvac: Grant/Research Support|GSK: Advisor/Consultant|Janssen: Advisor/Consultant|Merck: Expert Testimony|Pfizer: Grant/Research Support Edward E. Walsh, MD, Janssen: Advisor/Consultant|Janssen: Grant/Research Support|Janssen: Honoraria|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support.

Antimicrobial prescribing for children in China: data from point prevalence surveys in 18 tertiary centres in China in 2016–2017

ObjectivesThe reports on evaluating the classification of antibiotic agents prescribed for Chinese children by combining WHO’s and China’s administrative categories were rare. This study aimed to investigate the pattern of...

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

BackgroundAntimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing.MethodsWe studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients).ResultsCompared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47–87%) and specificity of 95% (CI 85–99%). For gram-negative bacteria, sensitivity was 100% (CI 87–100%) and specificity 64% (CI 48–78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform.ConclusionsmNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens.

Lower Respiratory Tract Infections in Pediatric Patients with Severe Neurological Impairments: Clinical Observations and Perspectives in a Palliative Care Unit.

Pediatric palliative care (PPC) patients with a severe neurologic impairment (SNI) suffer considerable morbidity and increased mortality from lower respiratory tract infections (LRTIs). The indication and choice of antibiotic therapy for bacterial LRTIs are often challenging given the lack of evidence-based treatment recommendations for this vulnerable patient population. We conducted an observational study before the SARS-CoV-2 pandemic in an eight-bed pediatric palliative care inpatient unit. During two years of surveillance, we diagnosed and treated 33 cases of a bacterial LRTI in patients with an SNI; 5 patients were hospitalized with an LRTI more than once. Two patients died from complications due to LRTIs during hospitalization. Three patients (15%) were colonized with multidrug-resistant organisms. An initial antibiotic treatment failed in one-third of the cases; a successful therapy of the LRTI was achieved with broad-spectrum and extended-spectrum penicillins (n = 13; in combination with β-lactamase inhibitors for n = 5 cases), cephalosporins (n = 13: n = 4 second-generation and n = 9 third-generation cephalosporins; in combination with other substances for n = 5 cases), ciprofloxacin (n = 3), and meropenem plus vancomycin (n = 2) or meropenem (n = 1). A respiratory specimen was obtained in 66.7% of cases with P. aeruginosa, E. coli, and K. pneumoniae accounting for the majority of the detected species. In most cases, there was no definite confirmation that the LRTI was caused by the species detected. The diagnostics and treatment of bacterial LRTIs in PPC patients with an SNI are challenging. The lack of controlled studies and the heterogeneity of this population often necessitate an individual approach. This lack of controlled studies may partly be compensated by a set of diagnostic and antibiotic stewardship criteria.

Multidrug-resistant bacteria with ESBL genes: a growing threat among people living with HIV/AIDS in Nepal

BackgroundBacterial opportunistic infections are common in people living with HIV/AIDS (PLHA). Besides HIV-TB co-infection, lower respiratory tract infections (LRTIs) due to multidrug-resistant (MDR) bacteria cause significant morbidity and mortality among PLHA. This study identified bacterial co-infection of the lower respiratory tract and detected plasmid-mediated blaTEM and blaCTX-M genes among Extended-Spectrum β-Lactamase (ESBL) producing isolates from sputum samples in PLHA.MethodsA total of 263 PLHA with LRTIs were enrolled in this study, out of which, 50 were smokers, 70 had previous pulmonary tuberculosis, and 21 had CD4 count < 200 cells/µl. Sputum samples collected from PLHA were processed with standard microbiological methods to identify the possible bacterial pathogens. The identified bacterial isolates were assessed for antibiotic susceptibility pattern using modified Kirby Bauer disk diffusion method following Clinical Laboratory Standard Institute (CLSI) guidelines. In addition, plasmid DNA was extracted from MDR and ESBL producers for screening of ESBL genes; blaCTX-M and blaTEM by conventional PCR method using specific primers.ResultsOf 263 sputum samples, 67 (25.48%) showed bacterial growth. Among different bacterial pathogens, Klebsiella pneumoniae, (17; 25.37%) was the most predominant, followed by Haemophillus influenzae, (14; 20.90%) and Escherichia coli, (12; 17.91%). A higher infection rate (4/8; 50%) was observed among people aged 61–70 years, whereas no infection was observed below 20 years. About 30.0% (15/50) of smokers, 32.86% (23/70) cases with previous pulmonary tuberculosis, and 52.38% (11/21) with CD4 count < 200 cells/µl had bacterial LRTIs. Among 53 bacterial isolates excluding H. influenzae, 28 isolates were MDR and 23 were ESBL producers. All ESBL producers were sensitive to colistin and polymyxin B. Among ESBL producers, 47.83% (11/23) possessed blaCTX-M, 8.6% (2/23) were positive for blaTEM gene, and 43.48% (10/23) possessed both ESBL genes.ConclusionThe increasing rate of MDR bacterial infections, mainly ESBL producers of LRTIs causes difficulty in disease management, leading to high morbidity and mortality of PLHA. Hence, it is crucial to know the antibiogram pattern of the isolates to recommend effective antimicrobial therapy to treat LRTIs in PLHA.

Long-term outcome and predictors of long-term outcome in patients with lupus nephritis managed at a tertiary hospital in Mumbai.

Study the long-term outcome of the patients with LN and identify the baseline factors that can predict the long-term outcome of these patients. All biopsy-proven LN patients who attended our regular 'lupus nephritis' clinic from 2013 to 2021 were studied. Data of these patients were collected from the hospital patient records. Standard therapy was given as per the KDIGO guidelines, and the renal response was evaluated according to KDIGO outcome criteria. Cox' regression analysis was used to determine predictors of chronic kidney disease (persistent doubling of serum creatinine with creatinine ≥1.5mg%). Kaplan-Meier analysis was used for renal survival. Eighty patients with at least 1year of follow-up were included. Median age of onset was 24years (IQR18-35). Median follow up was 6.5years (IQR 3-10). World Health Organisation renal biopsy profile was Class I 1(1.2 %), Class II 6(7.5 %), Class III 9(11.2 %), Class IV 36(45 %), Class V 18(22.5 %) and Mixed Class IV + V 10 (12%). Complete remission was achieved in 63.75%, 70 % and 66.6% patients at 1, 2 and 5years, respectively. Survival with normal renal function was 88.5 %, 85.8% and 60 % at 5, 10 and 15years, respectively. Risk factors for poor outcome on univariate analysis were presence of Raynaud's phenomena-hazard ratio(HR) 7.78 (CI 1.944-31.207; p < .004), baseline hypertension-HR 5.356 (CI 1.479-19.403; p < .011), tubulointerstitial involvement-HR 1.076 (CI 1.032-1.222; p < .001), time to complete response-HR 1.036 (CI 1.036-1.067; p < .02 ), serum creatinine at 6months HR 10.51 (CI 2.19-50.39; p < .003), failure to achieve complete response at 2years HR 6.271 (CI 1.567-25.092; p < .009) and the number of nephritic flares HR 1.868(CI 1.103-3.164 ; p < .02). Renal relapses were quite common, with 1.8 flares per 10 patient-years of follow up. Infection was the most common cause of death, with bacterial lower respiratory infections and pulmonary tuberculosis being the most common. Apart from conventional risk factors, other predictive factors like the presence of Raynaud's phenomenon, tubulointerstitial fibrosis and tubular atrophy on kidney biopsy, and initial response to induction therapy by 6months have a significant impact on the long-term outcome in patients with LN.

Microbiologically confirmed infections and antibiotic-resistance in a national surveillance study of hospitalised patients who died with COVID-19, Italy 2020–2021

BackgroundPatients hospitalised for COVID-19 may present with or acquire bacterial or fungal infections that can affect the course of the disease. The aim of this study was to describe the microbiological characteristics of laboratory-confirmed infections in hospitalised patients with severe COVID-19.MethodsWe reviewed the hospital charts of a sample of patients deceased with COVID-19 from the Italian National COVID-19 Surveillance, who had laboratory-confirmed bacterial or fungal bloodstream infections (BSI) or lower respiratory tract infections (LRTI), evaluating the pathogens responsible for the infections and their antimicrobial susceptibility.ResultsAmong 157 patients with infections hospitalised from February 2020 to April 2021, 28 (17.8%) had co-infections (≤ 48 h from admission) and 138 (87.9%) had secondary infections (> 48 h). Most infections were bacterial; LRTI were more frequent than BSI. The most common co-infection was pneumococcal LRTI. In secondary infections, Enterococci were the most frequently recovered pathogens in BSI (21.7% of patients), followed by Enterobacterales, mainly K. pneumoniae, while LRTI were mostly associated with Gram-negative bacteria, firstly Enterobacterales (27.4% of patients, K. pneumoniae 15.3%), followed by A. baumannii (19.1%). Fungal infections, both BSI and LRTI, were mostly due to C. albicans. Antibiotic resistance rates were extremely high in Gram-negative bacteria, with almost all A. baumannii isolates resistant to carbapenems (95.5%), and K. pneumoniae and P. aeruginosa showing carbapenem resistance rates of 59.5% and 34.6%, respectively.ConclusionsIn hospitalised patients with severe COVID-19, secondary infections are considerably more common than co-infections, and are mostly due to Gram-negative bacterial pathogens showing a very high rate of antibiotic resistance.

Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis

BackgroundThe study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples.ResultsOur MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8–100%, respectively.ConclusionsOur MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections.

Myxovirus resistance protein A for discriminating between viral and bacterial lower respiratory tract infections in children – The TREND study

ObjectiveDiscriminating between viral and bacterial lower respiratory tract infection (LRTI) in children is challenging, leading to an excessive use of antibiotics. Myxovirus resistance protein A (MxA) is a promising biomarker for viral infections. The primary aim of the study was to assess differences in blood MxA levels between children with viral and bacterial LRTI. Secondary aims were to assess differences in blood MxA levels between children with viral LRTI and asymptomatic controls and to assess MxA levels in relation to different respiratory viruses. MethodsChildren with LRTI were enrolled as cases at Sachs' Children and Youth Hospital, Stockholm, Sweden. Nasopharyngeal aspirates and blood samples for analysis of viral PCR, MxA, and C-reactive protein were systematically collected from all study subjects in addition to standard laboratory/radiology assessment. Aetiology was defined according to an algorithm based on laboratory and radiological findings. Asymptomatic children with minor surgical disease were enrolled as controls. ResultsMxA levels were higher in children with viral LRTI (n = 242) as compared to both bacterial (n = 5) LRTI (p <0.01, area under the curve (AUC) 0.90, 95% CI: 0.81 to 0.99), and controls (AUC 0.92, 95% CI: 0.88 to 0.95). In the subgroup of children with pneumonia diagnosis, a cutoff of MxA 430 μg/l discriminated between viral (n = 29) and bacterial (n = 4) aetiology with 93% (95% CI: 78–99%) sensitivity and 100% (95% CI: 51–100%) specificity (AUC 0.98, 95% CI: 0.94 to 1.00). The highest MxA levels were seen in cases PCR positive for influenza (median MxA 1699 μg/l, interquartile range: 732 to 2996) and respiratory syncytial virus (median MxA 1115 μg/l, interquartile range: 679 to 2489). DiscussionMxA accurately discriminated between viral and bacterial aetiology in children with LRTI, particularly in the group of children with pneumonia diagnosis, but the number of children with bacterial LRTI was low.

Role of procalcitonin in diagnosis of community acquired pneumonia in Children

BackgroundThe role of serum Procalcitonin (PCT) in adults in diagnosis of Community acquired pneumonia (CAP) is well established, however, role in pediatric CAP remains controversial.ObjectivesThe objective of this study was to investigate the utility of serum procalcitonin in differentiating bacterial community-acquired lower respiratory tract infection from non-bacterial respiratory infection in children; radiologically confirmed pneumonia was used as the reference. In addition, we assessed the utility of adding the PCT assay to the clinical criteria for diagnosis of pneumonia.Study designSubanalysis of a larger prospective,multicentriccohort study.ParticipantsChildren, 2 months to 59 months of age, attending paediatric OPD of 5 urban tertiary care hospitals, suffering from acute respiratory infection (ARI).InterventionDetailed clinical history and examination findings of enrolled children were recorded on predesigned case record form. Samples for PCT were obtained at admission and were measured centrally at the end of the study except for one site using VIDAS® B.R.A.H.M.S PCT kit (Biomerieux SA, France).OutcomesSensitivity and specificity of procalcitonin for diagnosis of radiologically confirmed pneumonia.ResultsSerum Procalcitonin was measured in 370 patients; median (IQR) age of these children being 12 (7, 22) months, 235 (63.5%) were boys. The median (IQR) serum procalcitonin concentration was 0.1(0.05, 0.4) ng/mL.Sensitivity and specificity of raised PCT (> 0.5 ng/mL) for pneumonia as per any CXR abnormalities were 29.7% and87.5%,(P < 0.001) respectively. Raised PCT was also significantly associated with consolidation (34.5%,79.2%,P < 0.02)and pleural effusion(54.6%,79%,P < 001). Adding PCT to the existing clinical criteria of WHO did not improve the sensitivity for diagnosis of pneumonia. PCT was significantly higher in children with severe pneumonia.ConclusionPositive PCT (> 0.5 ng/mL) is significantly associated with radiographic pneumonia but not with pneumonia based on WHO criteria.However, it can act as a surrogate marker for severe pneumonia.