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Background Children affected by infectious diseases may not always have a detectable infectious etiology. Diagnostic uncertainty can lead to prolonged hospitalizations, inappropriately broad or extended courses of antibiotics, invasive diagnostic procedures, and difficulty predicting the clinical course and outcome. Cell-free plasma next-generation sequencing (cfNGS) can identify viral, bacterial, and fungal infections by detecting pathogen DNA in peripheral blood. This testing modality offers the ability to test for many organisms at once in a shotgun metagenomic approach with a rapid turnaround time. We sought to compare the results of cfNGS to conventional diagnostic test results and describe the impact of cfNGS on clinical care in a diverse pediatric population at a large academic children’s hospital. Methods We performed a retrospective chart review of hospitalized subjects at a tertiary pediatric hospital to determine the diagnostic yield of cfNGS and its impact on clinical care. Results We describe the clinical application of results from 142 cfNGS tests in the management of 110 subjects over an 8-month study period. In comparison to conventional testing as a reference standard, cfNGS was found to have a positive percent agreement of 89.6% and negative percent agreement of 52.3%. Furthermore, 32.4% of cfNGS results were directly applied to make a clinical change in management. Conclusions We demonstrate the clinically utility of cfNGS in the management of acutely ill children. Future studies, both retrospective and prospective, are needed to clarify the optimal indications for testing.

Compassion in interactions between physicians and patients can have a therapeutic effect independent of the technical medical treatment provided. However, training physicians to effectively communicate compassion is challenging. This study explores how medical students experienced training focused on interacting with patients by examining students’ reports of particularly memorable lessons. Six focus groups were conducted with medical students (total n = 48) in their fourth year of training. We report on responses from students to the question, “What was the most memorable lesson you have learned about interacting with patients?” Students discussed lessons aimed at patient-centered physical navigation, interpersonal navigation, and perspective taking. Concerns were raised that navigation techniques felt inauthentic and that perspective taking was too time consuming to be sustainable in actual practice. While perspective-taking exercises should motivate medical students to treat every patient with dignity by demonstrating the complexity of others’ lives, if students assume that full understanding is a prerequisite to delivery of compassionate care, they may dismiss explicit techniques of patient-centered care as inauthentic and perceive compassion and efficiency as mutually exclusive.

Influenza A (H1N1) pdm09 became the predominant circulating strain in the United States during the 2013-2014 influenza season. Little is known about the epidemiology of severe influenza during this season. A retrospective cohort study of severely ill patients with influenza infection in intensive care units in 33 US hospitals from September 1, 2013, through April 1, 2014, was conducted to determine risk factors for mortality present on intensive care unit admission and to describe patient characteristics, spectrum of disease, management, and outcomes. A total of 444 adults and 63 children were admitted to an intensive care unit in a study hospital; 93 adults (20.9%) and 4 children (6.3%) died. By logistic regression analysis, the following factors were significantly associated with mortality among adult patients: older age (>65 years, odds ratio, 3.1 [95% CI, 1.4-6.9], P=.006 and 50-64 years, 2.5 [1.3-4.9], P=.007; reference age 18-49 years), male sex (1.9 [1.1-3.3], P=.031), history of malignant tumor with chemotherapy administered within the prior 6 months (12.1 [3.9-37.0], P<.001), and a higher Sequential Organ Failure Assessment score (for each increase by 1 in score, 1.3 [1.2-1.4], P<.001). Risk factors for death among US patients with severe influenza during the 2013-2014 season, when influenza A (H1N1) pdm09 was the predominant circulating strain type, shifted in the first postpandemic season in which it predominated toward those of a more typical epidemic influenza season.

Background Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease burden consists of skin and soft tissue infections (SSTI) not associated with significant morbidity; however, CA-MRSA also causes severe, invasive infections resulting in significant morbidity and mortality. The broad range of disease severity may be influenced by bacterial genetic variation. Results We sequenced the complete genomes of 36 CA-MRSA clinical isolates from the predominant North American community acquired clonal type USA300 (18 SSTI and 18 severe infection-associated isolates). While all 36 isolates shared remarkable genetic similarity, we found greater overall time-dependent sequence diversity among SSTI isolates. In addition, pathway analysis of non-synonymous variations revealed increased sequence diversity in the putative virulence genes of SSTI isolates. Conclusions Here we report the first whole genome survey of diverse clinical isolates of the USA300 lineage and describe the evolution of the pathogen over time within a defined geographic area. The results demonstrate the close relatedness of clinically independent CA-MRSA isolates, which carry implications for understanding CA-MRSA epidemiology and combating its spread.

Sepsis, resulting from a dysregulated host immune response to invading pathogens, is the leading cause of mortality in critically ill patients worldwide. Immunomodulatory treatment for sepsis is currently lacking. Children with short bowel syndrome (SBS) may present with less severe symptoms during gram-negative bacteremia. We, therefore, tested the hypothesis that plasma from children with SBS could confer protection against Escherichia coli sepsis. We showed that SBS plasma at 5% and 10% concentrations significantly (p < 0.05) inhibited the production of both TNF-α and IL-6 induced by either E. coli- or LPS-stimulated host cells when compared to plasma from healthy controls. Furthermore, mice treated intravenously with select plasma samples from SBS or healthy subjects had reduced proinflammatory cytokine levels in plasma and a significant survival advantage after E. coli infection. However, SBS plasma was not more protective than the plasma of healthy subjects, suggesting that children with SBS have other immunomodulatory mechanisms, in addition to neutralizing antibodies, to alleviate their symptoms during gram-negative sepsis.

Abstract Background Osteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children. Methods This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children’s hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon’s discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site. Results We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS. Conclusions In this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens. We evaluate the utility of next-generation sequencing in comparison to operative culture to detect a pathogen in acute pediatric osteomyelitis and septic arthritis.

The etiologic agents of community-acquired pneumonia (CAP) vary by age and presenting signs and symptoms. Viral pathogens are far more common than bacterial pathogens as agents of CAP in children, particularly in the preschool-aged population. However, given a clinical presentation of high fever, rales, and a focal infiltrate on chest radiograph, typical bacterial CAP pathogens are most likely. Although the advent of polysaccharide-protein conjugate vaccines has altered the epidemiology of bacterial CAP, Streptococcus pneumoniae remains the most common cause, with strains demonstrating far less penicillin resistance than those isolated prior to widespread use of the pneumococcal conjugate vaccine. Amoxicillin is the first-line agent for oral empiric therapy in the outpatient setting as it provides adequate coverage for most pneumococcal isolates. A familiarity with the common pathogens and treatment regimens of CAP is important given the prevalence of disease in children and the potential for significant morbidity and mortality.

Atypical pneumonia can occur at any age in the pediatric population and accounts for a significant percentage of community-acquired pneumonia (CAP). However, there are classic epidemiologic clues and presenting symptoms that help distinguish atypical pneumonias from other causes of CAP. In general, atypical pneumonia is more common in school-aged children and adolescents. Atypical pneumonias often have a subacute onset and an insidious course. They frequently begin with nonspecific extrapulmonary symptoms, progress to have predominantly lower respiratory tract symptoms, and end with protracted cough. The degree of illness during the lower respiratory tract phase is often less than one would expect given the findings on pulmonary examination. This clinical course characterizes the atypical pneumonias and has led to the colloquialism \"walking pneumonia.\" Atypical pneumonias are caused by a set of unique organisms and the typical age of infection, presenting symptoms, and disease course vary by pathogen.