Nasopharyngeal Codetection of Haemophilus influenzae and Streptococcus pneumoniae Shapes Respiratory Syncytial Virus Disease Outcomes in Children.

BACKGROUND: The role of nasopharyngeal bacteria in respiratory syncytial virus (RSV) disease has been underestimated. We measured the frequency and burden of respiratory bacteria in the upper respiratory tract of infants with RSV infection over 7 respiratory seasons, and their impact on clinical outcomes. METHODS: Children <2 years old with mild (outpatients, n=115) or severe (inpatients, n=566) RSV infection, and matched healthy controls (n=161) were enrolled. Nasopharyngeal samples were obtained for RSV, Streptococcus pneumoniae, Staphylococcus aureus, Moraxella catarrhalis, and Haemophilus influenzae detection and quantitation by PCR. Multivariable models were constructed to identify variables predictive of severe disease. RESULTS: S. pneumoniae, H. influenzae, and M. catarrhalis, but not S. aureus, were detected more frequently in RSV-infected children (84%) than healthy controls (46%; P<.001). Detection of S. pneumoniae and/or H. influenzae was associated with fever, more frequent antibiotic treatment, worse radiologic findings, and higher neutrophil counts (P<.01). In adjusted analyses, S. pneumoniae/H. influenzae codetection was independentlyassociated with greater odds of hospitalization, higher disease severity scores, need for supplemental oxygen, and longer hospitalization. CONCLUSIONS: Nasopharyngeal codetection of S. pneumoniae and H. influenzae in infants with RSV infection is associated with increased disease severity.

Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection.

RATIONALE: Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and hospitalizations in infants worldwide. Known risk factors, however, incompletely explain the variability of RSV disease severity, especially among healthy children. We postulate that the severity of RSV infection is influenced by modulation of the host immune response by the local bacterial ecosystem. OBJECTIVES: To assess whether specific nasopharyngeal microbiota (clusters) are associated with distinct host transcriptome profiles and disease severity in children less than 2 years of age with RSV infection. METHODS: We characterized the nasopharyngeal microbiota profiles of young children with mild and severe RSV disease and healthy children by 16S-rRNA sequencing. In parallel, using multivariable models, we analyzed whole-blood transcriptome profiles to study the relationship between microbial community composition, the RSV-induced host transcriptional response, and clinical disease severity. MEASUREMENTS AND MAIN RESULTS: We identified five nasopharyngeal microbiota clusters characterized by enrichment of either Haemophilus influenzae, Streptococcus, Corynebacterium, Moraxella, or Staphylococcus aureus. RSV infection and RSV hospitalization were positively associated with H. influenzae and Streptococcus and negatively associated with S. aureus abundance, independent of age. Children with RSV showed overexpression of IFN-related genes, independent of the microbiota cluster. In addition, transcriptome profiles of children with RSV infection and H. influenzae- and Streptococcus-dominated microbiota were characterized by greater overexpression of genes linked to Toll-like receptor and by neutrophil and macrophage activation and signaling. CONCLUSIONS: Our data suggest that interactions between RSV and nasopharyngeal microbiota might modulate the host immune response, potentially affecting clinical disease severity.

Superiority of transcriptional profiling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults.

BACKGROUND: Distinguishing between bacterial and viral lower respiratory tract infection (LRTI) remains challenging. Transcriptional profiling is a promising tool for improving diagnosis in LRTI. METHODS: We performed whole blood transcriptional analysis in 118 patients (median age [interquartile range], 61 [50-76] years) hospitalized with LRTI and 40 age-matched healthy controls (median age, 60 [46-70] years). We applied class comparisons, modular analysis, and class prediction algorithms to identify and validate diagnostic biosignatures for bacterial and viral LRTI. RESULTS: Patients were classified as having bacterial (n = 22), viral (n = 71), or bacterial-viral LRTI (n = 25) based on comprehensive microbiologic testing. Compared with healthy controls, statistical group comparisons (P < .01; multiple-test corrections) identified 3376 differentially expressed genes in patients with bacterial LRTI, 2391 in viral LRTI, and 2628 in bacterial-viral LRTI. Patients with bacterial LRTI showed significant overexpression of inflammation and neutrophil genes (bacterial > bacterial-viral > viral), and those with viral LRTI displayed significantly greater overexpression of interferon genes (viral > bacterial-viral > bacterial). The K-nearest neighbors algorithm identified 10 classifier genes that discriminated between bacterial and viral LRTI with a 95% sensitivity (95% confidence interval, 77%-100%) and 92% specificity (77%-98%), compared with a sensitivity of 38% (18%-62%) and a specificity of 91% (76%-98%) for procalcitonin. CONCLUSIONS: Transcriptional profiling is a helpful tool for diagnosis of LRTI.

Occult bloodstream infections in adults: a "benign" entity.

BACKGROUND: Patients with septic episodes whose blood cultures turn positive after being sent home from emergency departments (EDs) are recognized as having occult bloodstream infections (BSI). The incidence, etiology, clinical circumstances, and outcome of occult BSI in children are well known, but, to our knowledge, data in adult patients are scarce. We analyzed the episodes of occult BSI in adult patients at our institution. METHODS: This is a retrospective cohort study (September 2010 to September 2012), in adult patients discharged from the ED in whom blood cultures turned positive. Patients were evaluated according to a preestablished protocol. RESULTS: We recorded 4025 cases of significant BSI in the ED and 113 patients with adult occult BSI. In other words, the incidence of occult BSI in the ED was 2.8 per 100 episodes. The predominant microorganisms were gram-negative bacteria (57%); Escherichia coli was the most common (41%), followed by gram-positive bacteria (29%), anaerobes (6.9%), polymicrobial (6.1%), and yeasts (0.8%). The most frequent suspected origin was urinary tract infection (53%), and most infections were community acquired (63.7%). Of the 105 patients that we were able to trace, 54 (42.5%) were asymptomatic and were receiving adequate antibiotic treatment at the time of the call, and 65 (51.2%) had persistent fever or were not receiving adequate antibiotic treatment. CONCLUSIONS: Occult BSI is relatively common in patients in the adult ED. Despite the need for readmission of a fairly high proportion of patients, occult BSI behaves as a relatively benign entity.

Young infants display heterogeneous serological responses and extensive but reversible transcriptional changes following initial immunizations.

Infants necessitate vaccinations to prevent life-threatening infections. Our understanding of the infant immune responses to routine vaccines remains limited. We analyzed two cohorts of 2-month-old infants before vaccination, one week, and one-month post-vaccination. We report remarkable heterogeneity but limited antibody responses to the different antigens. Whole-blood transcriptome analysis in an initial cohort showed marked overexpression of interferon-stimulated genes (ISGs) and to a lesser extent of inflammation-genes at day 7, which normalized one month post-vaccination. Single-cell RNA sequencing in peripheral blood mononuclear cells from a second cohort identified at baseline a predominantly naive immune landscape including ISGhi cells. On day 7, increased expression of interferon-, inflammation-, and cytotoxicity-related genes were observed in most immune cells, that reverted one month post-vaccination, when a CD8+ ISGhi and cytotoxic cluster and B cells expanded. Antibody responses were associated with baseline frequencies of plasma cells, B-cells, and monocytes, and induction of ISGs at day 7.

Resistance to voriconazole due to a G448S substitution in Aspergillus fumigatus in a patient with cerebral aspergillosis.

A voriconazole-resistant isolate of Aspergillus fumigatus was recovered from an immunocompetent patient receiving long-term antifungal therapy for cerebral aspergillosis. A G448S amino acid substitution in the azole target (Cyp51A) was identified as the cause of the resistance phenotype. This article describes the first isolation of a voriconazole-resistant A. fumigatus isolate from an immunocompetent patient in Spain.

Vancomycin MICs do not predict the outcome of methicillin-resistant Staphylococcus aureus bloodstream infections in correctly treated patients.

BACKGROUND: Recent studies have reported a greater probability of vancomycin treatment failure in methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections caused by strains with a vancomycin MIC ≥ 1.5 mg/L. However, previous reports included patients treated without adjustments based on vancomycin serum levels and with different methods to evaluate MICs, which may render different results. METHODS: Over a 5 year period (2005-09), vancomycin MICs were determined for 361 MRSA isolates recovered from 309 patients with bloodstream infection using microdilution and the Etest simultaneously. The relationship between the vancomycin MICs determined by each method was assessed. To assess the outcome of patients treated with vancomycin, 104 patients for whom serum vancomycin levels had been determined were selected. RESULTS: The percentage of MRSA strains with MIC values ≥ 1.5 mg/L according to the Etest was 66.5% compared with only 3.6% according to microdilution. No correlation between mortality and any MIC value obtained with either method was observed, independently of the vancomycin serum levels measured. CONCLUSIONS: There is a poor correlation between vancomycin MIC values obtained by microdilution and by Etest. No association between mortality rate and any MIC value was observed, not even in patients with suboptimal vancomycin trough serum levels. These data do not support replacing or complementing the standard microdilution test with the Etest for determination of MICs of vancomycin in microbiology laboratories.

Donor-derived bacterial infections in lung transplant recipients in the era of multidrug resistance.

OBJECTIVES: Our aim was to analyze the prevalence of multidrug-resistant bacterial infections in lung transplant donors and to evaluate its influence on donor-derived bacterial infections. METHODS: We conducted a retrospective study of adult patients who underwent lung transplantation (2013-2016) at our hospital. Donor-derived bacterial infection was defined as the isolation of the same bacteria with identical antibiotic susceptibility patterns in the recipient and the perioperative cultures from the donor during the first month posttransplantation. We utilized a preventive antibiotic strategy adapted to the bacteria identified in donor cultures using systemic and nebulized antibiotics. RESULTS: 252 lung transplant recipients and 243 donors were included. In 138/243 (56.8%) donors, one bacterial species was isolated from at least one sample; graft colonization (118/243; 48.6%), blood cultures (5/243; 2.1%) and the contamination of preservation fluids (56/243; 23%). Multidrug-resistant bacteria were isolated from 12/243 (4.9%) donors; four Enterobacterales, four Stenotrophomonas maltophilia, three Pseudomonas aeruginosa and one methicillin-resistant Staphylococcus aureus. There was no transmission of these multidrug-resistant bacteria. Donor-derived infections, primarily tracheobronchitis due to non-MDR bacteria, were diagnosed in 7/253 (2.9%) recipients, with good clinical outcomes. CONCLUSIONS: The lungs of donors colonized with multidrug-resistant bacteria may be safely used when recipients receive prompt tailored antibiotic treatment.

Immune profiles provide insights into respiratory syncytial virus disease severity in young children.

Respiratory syncytial virus (RSV) is associated with major morbidity in infants, although most cases result in mild disease. The pathogenesis of the disease is incompletely understood, especially the determining factors of disease severity. A better characterization of these factors may help with development of RSV vaccines and antivirals. Hence, identification of a "safe and protective" immunoprofile induced by natural RSV infection could be used as a as a surrogate of ideal vaccine-elicited responses in future clinical trials. In this study, we integrated blood transcriptional and cell immune profiling, RSV loads, and clinical data to identify factors associated with a mild disease phenotype in a cohort of 190 children <2 years of age. Children with mild disease (outpatients) showed higher RSV loads, greater induction of interferon (IFN) and plasma cell genes, and decreased expression of inflammation and neutrophil genes versus children with severe disease (inpatients). Additionally, only infants with severe disease had increased numbers of HLA-DRlow monocytes, not present in outpatients. Multivariable analyses confirmed that IFN overexpression was associated with decreased odds of hospitalization, whereas increased numbers of HLA-DRlow monocytes were associated with increased risk of hospitalization. These findings suggest that robust innate immune responses are associated with mild RSV infection in infants.

What if there were no new antibiotics? A look at alternatives.

INTRODUCTION: Bacterial resistance to antibiotics is increasing worldwide, due to the emergence of multidrug-resistant strains. With this panorama, there is a serious danger that we may be entering the 'post-antibiotic era'. Areas covered: We assess why so few new classes of antibiotics have been developed in the past years and discuss a variety of treatments that may be able to replace antimicrobials: monoclonal antibodies, bacteriophages, stem cells and anti-virulence agents such as liposomes. Expert commentary: There are a series of economic, scientific-research and regulatory reasons for the scarcity of new antimicrobials. New approaches are needed to combat infections. Innovative strategies like Eco-Evo drugs and innovative delivery methods such as aerosol or nanoparticle administration require a new management paradigm, in combination with rapid molecular diagnostic tests. Biopharma, clinical researchers, regulatory agencies, governments and investors must work together in the attempts to achieve effective treatment for infections caused by MDR organisms.

Improved Sepsis Alert With a Telephone Call From the Clinical Microbiology Laboratory: A Clinical Trial.

Early sepsis attention is a standard of care in many institutions and the role of different specialists is well recognized. However, the impact of a telephone call from a specialist in Clinical Microbiology upon blood cultures request has not been assessed to the best of our knowledge. We performed telephone calls followed by an interview with physicians and nurses in charge of adult patients (> 18 years old) whose blood cultures had just been received in the Microbiology Laboratory in a tertiary hospital. Patients were randomly classified in 2 different groups: group A (telephone call performed) and group B (no telephone call). At the end of the telephonic intervention, recommendations on the use of microbiology and biochemical tests as well as on the management and antibiotic therapy of sepsis were made if required. We included 300 patients. Of those fulfilling standard criteria of sepsis, 30.3% of the nurses and 50% of the physicians immediately recognized it. Advice to optimize the use of biochemical and microbiological tests was provided in 36% of the cases and to improve antimicrobial therapy in 57.6%. The median number of days of antibiotic use in groups A and B were, respectively, 6 days (IQR: 2-12) vs 9 days (IQR: 4-16) P = 0.008 and the median number of prescribed daily doses of antimicrobials (6 [IQR: 3-17] vs 10 [IQR: 5-22] P = 0.016) were lower in group A. We estimate a reduction, only in the use of antibiotic, of 1.8 million Euros per year. A telephone call with management advice, immediately after the arrival of blood cultures in the Microbiology Laboratory improves the recognition of sepsis and the use of diagnostic resources and reduces antimicrobial consumption and expenses.

Evaluation of GeneXpert MTB/RIF for the detection of Mycobacterium tuberculosis and resistance to rifampin in clinical specimens.

OBJECTIVES: GeneXpert (GX) is a novel real-time polymerase chain reaction assay for the simultaneous detection of Mycobacterium tuberculosis (MTB) and resistance to rifampin (RIF). We evaluated the performance of GX for direct detection of MTB in respiratory and non-respiratory specimens and assessed the ability of the assay to detect resistance to RIF in non-tuberculosis (TB) endemic country. METHODS: We analyzed 595 clinical samples in a 1550-bed tertiary hospital in Madrid, Spain. Specimens were processed using GX, auramine smear, conventional culture, and drug phenotypic susceptibility testing (DST) with MGIT SIRE (BD). RESULTS: Of the 595 clinical samples, 305 (51.3%) were non-respiratory and 290 (48.7%) were respiratory. In total, MTB was isolated in 81 specimens, 71 of which were positive with GX. The sensitivity, specificity, PPV, and NPV of the GX were: 97.1%, 98.6%, 95.7% and 99.1% for respiratory samples and 33.3%, 99.7%, 80.0% and 97.3% for non-respiratory. GX detected 8 RIF-resistant samples, but only 5 were confirmed by DST. CONCLUSIONS: GX is an accurate, easy-to-apply and rapid test to detect MTB, especially in smear-positive respiratory samples. Although is a useful tool for the rapid identification of RIF-resistant MTB strains, the rifampin resistant results should be confirmed by DST.

Listeriosis: An emerging public health problem especially among the elderly.

OBJECTIVES: To analyze the incidence trend of listeriosis, its present epidemiology and the potential benefit of aminoglycosides during the last two decades. METHODS: We reviewed all cases of invasive listeriosis detected during a 22-year period in a large tertiary hospital. Two equal periods of 11 years were compared. RESULTS: We detected 111 cases of listeriosis (32 during the first 11-year period and 79 during the second). Incidence of listeriosis increased significantly (from 4.66/10(6) inhabitants to 10.39/10(6) inhabitants; P = .001). In the second period, there were more patients >65 years (21.9%-45.6%; P = .02) and with no significant underlying diseases (0 vs. 16.5%; P = .02). Comparing clinical presentations between the two periods, primary bacteremia increased (40.6% vs. 55.7%), while central nervous system infections decreased (34.4% vs. 27.8%). Cotrimoxazole (SXT) use increased significantly in the second period (from 6.3% to 40.5%, P = .001) while the administration of aminoglycosides decreased (from 40.6% to 21.5%, P = .04). The use of combination therapy did not have any impact on mortality, however it did increase toxicity. CONCLUSIONS: Listeriosis should be considered an emerging health problem, especially among the elderly, including those with no underlying medical conditions. The use of aminoglycosides does not seem to be justified according to our data.