De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen

Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, diverse parallel mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization revealed that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.

Cycle Threshold Values from Severe Acute Respiratory Syndrome Coronavirus-2 Reverse Transcription-Polymerase Chain Reaction Assays: Interpretation and Potential Use Cases

Reverse transcription-polymerase chain reaction (RT-PCR) tests for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), are approved for qualitative use. The cycle threshold (Ct) value reflects the concentration of viral RNA in the sample, with lower Ct values indicating higher levels of RNA. Caregivers may wish to use the Ct value to determine the progression of infection, how severe the infection will be, and whether the patient can transmit the virus. Variability of Ct values and the data supporting these uses should be considered when deciding whether and how to use Ct values in clinical care.

Predictive Value of Direct Disk Diffusion Testing from Positive Blood Cultures in a Children's Hospital and Its Utility in Antimicrobial Stewardship

Accurate and early susceptibility results could reduce overuse of broad-spectrum antibiotics for empirical treatment of bacteremia. Direct disk diffusion testing (dDD) using nonstandardized inocula directly from blood cultures could facilitate earlier narrowing of antibiotics. To determine the predictive value of dDD compared with standardized antimicrobial susceptibility testing (AST), we performed a retrospective cohort study of 582 blood cultures from 495 pediatric patients with bacteremia. Positive and negative predictive value (PPV: number of isolates susceptible by both dDD and AST divided by the total number of isolates susceptible by dDD; NPV: number of isolates not susceptible [either intermediate or resistant] by both dDD and AST divided by the total number of isolates not susceptible by dDD), sensitivity, specificity, and 95% confidence interval were calculated for each bacterium-antibiotic combination. We evaluated the Antibiotic Spectrum Index of prescribed antibiotics to assess change in antibiotic prescribing after availability of Gram stain, dDD, and AST results. dDD results were available a median of 21 h before AST results. dDD had PPVs of ≥96% for most organism-antibiotic pairs, including 100% (CI 96 to 100%) for Staphylococcus aureus with oxacillin and 99% (CI 93 to 100%) for Enterobacterales with ceftriaxone. NPVs of dDD were variable and frequently lower than the PPV. Very major errors and major errors occurred in 31/5,454 (0.6%) and 231/5,454 (4.2%) organism-antibiotic combinations, respectively. Antibiotics were narrowed in 30% of cases after a dDD result and a further 25% of cases after AST result. dDD is highly predictive of susceptibility for many common organism-antibiotic combinations and provides actionable information one day earlier than standard susceptibility approaches. dDD has the potential to facilitate earlier deescalation to narrow-spectrum antibiotic treatment.

Can We Test Our Way Out of the COVID-19 Pandemic?

Frequent, low-cost, universal testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with quarantine of those with a positive result has been suggested as a strategy to address the coronavirus disease 2019 (COVID-19) pandemic in the United States. Specifically, home or community use of tests that use paper strip detection devices, which may have reduced sensitivity for SARS-CoV-2, has been advocated. There are several potential challenges or problems with this strategy, including the limited availability of such tests, consequences of incorrect test results, difficulties with adherence to testing, and the questionable accuracy of such tests for detection of infectious people. Because of these, we think it is premature to strongly advocate for such a testing strategy, as the adverse consequences may outweigh any benefits. High-quality outcome data demonstrating the efficacy of this testing strategy are needed before widespread implementation.

Practical guide for pediatric pulmonologists on imaging management of pediatric patients with COVID-19

Understanding of coronavirus disease 2019 is rapidly evolving with new articles on the subject daily. This flood of articles can be overwhelming for busy practicing clinicians looking for key pieces of information that can be applied in daily practice. This review article synthesizes the reported imaging findings in pediatric Coronavirus disease 2019 (COVID-19) across the literature, offers imaging differential diagnostic considerations and useful radiographic features to help differentiate these entities from COVID-19, and provides recommendations for requesting imaging studies to evaluate suspected cases of pediatric COVID-19.

Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients

Probiotics are routinely administered to hospitalized patients for many potential indications1 but have been associated with adverse effects that may outweigh their potential benefits2-7. It is particularly alarming that probiotic strains can cause bacteremia8,9, yet direct evidence for an ancestral link between blood isolates and administered probiotics is lacking. Here we report a markedly higher risk of Lactobacillus bacteremia for intensive care unit (ICU) patients treated with probiotics compared to those not treated, and provide genomics data that support the idea of direct clonal transmission of probiotics to the bloodstream. Whole-genome-based phylogeny showed that Lactobacilli isolated from treated patients' blood were phylogenetically inseparable from Lactobacilli isolated from the associated probiotic product. Indeed, the minute genetic diversity among the blood isolates mostly mirrored pre-existing genetic heterogeneity found in the probiotic product. Some blood isolates also contained de novo mutations, including a non-synonymous SNP conferring antibiotic resistance in one patient. Our findings support that probiotic strains can directly cause bacteremia and adaptively evolve within ICU patients.

What Is the Future of Clinical Microbiology?

Clinical microbiology has advanced tremendously in the past 10 years. In this comic, the role of technology, the need for skilled microbiologists, and the meaning of progress in clinical microbiology are considered.

Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections

Staphylococcus aureus is an early colonizer in the lungs of individuals with cystic fibrosis (CF), but surprisingly, only a limited number of genomes from CF-associated S. aureus isolates have been sequenced. Here, we present the whole-genome sequences of 65 S. aureus isolates obtained from 50 individuals with CF.

Ceftaroline pharmacokinetics and pharmacodynamics in patients with cystic fibrosis

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is a prevalent pathogen in patients with cystic fibrosis (CF) associated with increased morbidity. Ceftaroline fosamil is an intravenous (IV) cephalosporin with activity against MRSA. There are minimal data regarding dosing in the CF population. The objective of this study was to determine the pharmacokinetic and pharmacodynamic profile of IV ceftaroline in patients with CF.

METHODS

We conducted a single-center prospective study of children and young adults with CF receiving ceftaroline (15mg/kg IV up to 600mg every 8h) as part of treatment for a CF pulmonary exacerbation between June 2016 and April 2017. Seven patients were enrolled for a total of 10 treatment courses. For each treatment course, up to 8 plasma samples were assayed for ceftaroline using ultra-high performance liquid chromatography with mass spectrometry. Maximum plasma concentration, systemic clearance, and elimination half-life were calculated. The area under the curve (AUC) above the minimum inhibitory concentration (MIC) and the percent time above the MIC (%fT>MIC) were determined for each subject using MICs of 0.5, 1, and 2μg/mL and the measured MIC if available.

RESULTS

The mean (SD) age for the 7 patients was 20.3 (8.0) years. Mean (SD) maximum plasma concentration of ceftaroline was 22.7 (9.6) μg/mL, systemic clearance 7.9 (3.3) L/h, and half-life 1.1 (0.4) hours. Using a MIC of 1 μg/mL, accepted as the MIC 90 of MRSA isolates, AUC above MIC mean (SD) was 53.6 (19.5) μg·h/mL, mean (SD) %fT>MIC was 75.7 (10.4), and all subjects had >60%fT>MIC.

CONCLUSIONS

In this cohort of CF patients, mean ceftaroline half-life was 1.1h, which is notably lower than the general population. The dosing regimen studied, which exceeds the recommended dosing in the non-CF population, was adequate to achieve >60% time above the MIC in all patients.

Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung

Bacterial populations diversify during infection into distinct subpopulations that coexist within the human body. Yet, it is unknown to what extent subpopulations adapt to location-specific selective pressures as they migrate and evolve across space. Here we identify bacterial genes under local and global selection by testing for spatial co-occurrence of adaptive mutations. We sequence 552 genomes of the pathogen Stenotrophomonas maltophilia across 23 sites of the lungs from a patient with cystic fibrosis. We show that although genetically close isolates colocalize in space, distant lineages with distinct phenotypes separated by adaptive mutations spread throughout the lung, suggesting global selective pressures. Yet, for one gene (a distant homologue of the merC gene implicated in metal resistance), mutations arising independently in two lineages colocalize in space, providing evidence for location-specific selection. Our work presents a general framework for understanding how selection acts upon a pathogen that colonizes and evolves across the complex environment of the human body.

The authors sequence the genomes of 552 bacterial isolates sampled across 23 sites of the lungs of a patient with cystic fibrosis, and identify bacterial genes under global and location-specific adaptation.

The aetiology of diarrhoea, pneumonia and respiratory colonization of HIV-exposed infants randomized to breast- or formula-feeding

BACKGROUND

Diarrhoea and pneumonia are common causes of childhood death in sub-Saharan Africa but there are few studies describing specific pathogens.

OBJECTIVES

The study aimed to describe the pathogens associated with diarrhoea, pneumonia and oropharyngeal colonization in children born to HIV-infected women (HIV-exposed infants).

METHODS

The Mashi Study randomized 1200 HIV-infected women and their infants to breastfeed for 6 months with ZDV prophylaxis or formula-feed with 4 weeks of ZDV. Children were tested for HIV by PCR at 1, 4, 7, 9 and 12 months and by ELISA at 18 months. Pre-defined subsets of children were sampled during episodes of diarrhoea (n = 300) and pneumonia (n = 85). Stool was tested for bacterial pathogens, rotavirus and parasites. Children with pneumonia underwent bacterial blood culture, and testing of nasopharyngeal aspirates for viral pathogens by PCR. Oropharyngeal swabs were collected from a consecutive subset of 561 infants at the routine 3-month visit for bacterial culture.

RESULTS

The median age (range) at sampling was 181 days for diarrhoea (0-730) and 140 days for pneumonia (2-551). Pathogens were identified in 55 (18%) children with diarrhoea and 32 (38%) with pneumonia. No differences in pathogens by child HIV status (HIV-infected vs HIV-uninfected) or feeding strategy were identified. Campylobacter was the most common diarrhoeal pathogen (7%). Adenovirus (22%) and other viruses (19%) were the primary pathogens isolated during pneumonias. More formula-fed infants had oropharyngeal colonization by pathogenic Gram-negative bacteria (16.8% vs 6.2%, P = 0.003), which was associated with a non-significant increased risk of pneumonia (OR 2.2, 95% CI 0.8-5.7).

CONCLUSION

A trend toward oropharyngeal bacterial colonization was observed in formula-fed infants. Although viruses were most commonly detected during pneumonia, respiratory colonization by Gram-negative bacteria may have contributed to pneumonia in formula-fed infants.

Evaluation of the C6 Lyme Enzyme Immunoassay for the Diagnosis of Lyme Disease in Children and Adolescents

BACKGROUND

The commercially-available C6 Lyme enzyme immunoassay (EIA) has been approved to replace the standard whole-cell sonicate EIA as a first-tier test for the diagnosis of Lyme disease and has been suggested as a stand-alone diagnostic. However, the C6 EIA has not been extensively studied in pediatric patients undergoing evaluation for Lyme disease.

METHODS

We collected discarded serum samples from children and adolescents (aged ≤21 years) undergoing conventional 2-tiered testing for Lyme disease at a single hospital-based clinical laboratory located in an area endemic for Lyme disease. We performed a C6 EIA on all collected specimens, followed by a supplemental immunoblot if the C6 EIA result was positive but the whole-cell sonicate EIA result was negative. We defined a case of Lyme disease as either a clinician-diagnosed erythema migrans lesion or a positive standard 2-tiered serologic result in a patient with symptoms compatible with Lyme disease. We then compared the performance of the C6 EIA alone and as a first-tier test followed by immunoblot, with that of standard 2-tiered serology for the diagnosis of Lyme disease.

RESULTS

Of the 944 specimens collected, 114 (12%) were from patients with Lyme disease. The C6 EIA alone had sensitivity similar to that of standard 2-tiered testing (79.8% vs 81.6% for standard 2-tiered testing; P = .71) with slightly lower specificity (94.2% vs 98.8% 2; P < .002). Addition of a supplemental immunoblot improved the specificity of the C6 EIA to 98.6%.

CONCLUSIONS

For children and adolescents undergoing evaluation for Lyme disease, the C6 EIA could guide initial clinical decision making, although a supplemental immunoblot should still be performed.

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

Advances in sequencing have enabled the identification of mutations acquired by bacterial pathogens during infection^1-10. However, it remains unclear whether adaptive mutations fix in the population or lead to pathogen diversification within the patient^11,12. Here, we study the genotypic diversity of Burkholderia dolosa within people with cystic fibrosis by re-sequencing individual colonies and whole populations from single sputum samples. Extensive intra-sample diversity reveals that mutations rarely fix within a patient's pathogen population—instead, diversifying lineages coexist for many years. When strong selection is acting on a gene, multiple adaptive mutations arise but neither sweeps to fixation, generating lasting allele diversity that provides a recorded signature of past selection. Genes involved in outer-membrane components, iron scavenging and antibiotic resistance all showed this signature of within-patient selection. These results offer a general and rapid approach for identifying selective pressures acting on a pathogen in individual patients based on single clinical samples.

Yield of fungal surveillance cultures in pediatric hematopoietic stem cell transplant patients: a retrospective analysis and survey of current practice

BACKGROUND

Fungal surveillance cultures (FSCs) have been proposed as predictors for development of invasive fungal disease (IFD) and identifiers of the causative organism, although data supporting these are limited and predate universal initiation of antifungal prophylaxis. We aimed to define the epidemiology of fungal colonization and investigate the utility of FSCs for predicting IFD in recipients of pediatric hematopoietic stem cell transplantation (HSCT).

METHODS

FSCs performed from 2007 to 2011 on HSCT patients and laboratory and clinical data were reviewed, and incidence of IFD was determined. Descriptive analyses of culture results were performed to determine the yield of FSCs and their utility. A Web-based survey of national pediatric HSCT providers was undertaken to evaluate current practice and the relevance of our results.

RESULTS

Five thousand six hundred eighteen FSCs from nares, throat, and stool from 360 patients were processed. Of these, 14.8% were positive: 30.3% from stool, 13.2% from throat, and 0.9% from nares; 64.4% of patients had >1 positive FSCs. Thirty (8.3%) patients had IFD. IFD occurred in 7.9% and 10.1% of patients with positive and negative FSCs, respectively (P = .25). Antifungal coverage was changed in 69 patients (29.9%) after positive FSC; 8.6% developed IFD (n = 2 of 6 pathogen concordance with FSC) compared with 6.7% (P = .59) who had no treatment change (n = 3 of 11 concordance). The response rate to the survey was 70.8%; 40% of institutions reported performing routine FSC. Twenty-five percent of providers would not change management based on FSC results; overall rating of usefulness of FSCs was low.

CONCLUSIONS

Although FSCs are commonly performed for pediatric HSCT patients, they have limited utility for predicting IFD.

Polymerase chain reaction test for Clostridium difficile toxin B gene reveals similar prevalence rates in children with and without inflammatory bowel disease

OBJECTIVE

Clinicians often evaluate for Clostridium difficile infection (CDI) in patients with inflammatory bowel disease (IBD) presenting with exacerbations. A highly sensitive polymerase chain reaction (PCR) test for the toxin B gene of C difficile is increasingly used to diagnose CDI. The aim of this study was to determine the prevalence of positive C difficile PCR results in children and young adults with and without active IBD compared with patients with non-IBD gastrointestinal disease.

METHODS

Fecal samples were obtained from patients with ulcerative colitis (UC, n = 76) or Crohn disease (CD, n = 69) and 51 controls followed in our gastroenterology program. Samples were analyzed for C difficile using a PCR test for the C difficile toxin B gene (BD GeneOhm Cdiff assay). Proportions of positive tests in each group were compared using the Pearson χ2 test.

RESULTS

The prevalence of positive PCR results was 11.6% in patients with CD, 18.4% in patients with UC, and 11.8% in controls (P = 0.25). There were no significant differences in the prevalence of positive C difficile results among patients with IBD with and without active disease or among patients with and without diarrhea.

CONCLUSIONS

Positive C difficile PCR results occur with similar frequency in patients with IBD with and without active disease and in patients with other gastrointestinal diseases. A positive result in a highly sensitive PCR assay that detects low copy numbers of a toxin gene in C difficile may reflect colonization in a subset of patients with IBD, confounding clinical decision making in managing disease exacerbations.

Impact of in-hospital enteroviral polymerase chain reaction testing on the clinical management of children with meningitis

BACKGROUND

Enteroviral meningitis is a common cause of meningitis in children which requires only supportive care.

OBJECTIVE

To evaluate the impact of implementing an in-hospital enteroviral polymerase chain reaction (EVPCR) testing protocol on the clinical management of children with meningitis.

DESIGN

Retrospective cohort study.

POPULATION

Children <19 years old with meningitis.

INTERVENTION

EVPCR testing differed by time period: send-out testing protocol from July 1, 2006-June 23, 2008 (pre-period) versus in-house testing protocol from June 24, 2008-June 30, 2010 (post-period).

MEASUREMENTS

Test turnaround time, test utilization, length of stay, and duration of parenteral antibiotics.

RESULTS

Of the 441 study patients, 216 (49%) presented during the post-period. Median age was 2.9 months (interquartile range, 1.5-96 months). Test turnaround time decreased with the in-house test (53 hours pre vs 13 hours post, P < 0.001), and test utilization increased (28% pre vs 62% post, P < 0.001). Among children with a positive EVPCR test, both length of stay (44 hours pre vs 28 hours post, P = 0.005) and duration of parenteral antibiotics (48 hours pre vs 36 hours post, P = 0.04) decreased in the post-period. No change in either of these outcomes was observed in children with meningitis and a negative EVPCR test.

CONCLUSION

In-house EVPCR testing reduced test turnaround time, increased test utilization, and reduced both length of stay and duration of parenteral antibiotics for children with a positive result. Clinicians caring for children with meningitis should have access to in-hospital EVPCR testing.

Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection

BACKGROUND

New therapeutic targets for antibiotic-resistant bacterial pathogens are desperately needed. The bacterial surface polysaccharide poly-β-(1-6)-N-acetyl-glucosamine (PNAG) mediates biofilm formation by some bacterial species, and antibodies to PNAG can confer protective immunity. By analyzing sequenced genomes, we found that potentially multidrug-resistant bacterial species such as Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomonas maltophilia, and the Burkholderia cepacia complex (BCC) may be able to produce PNAG. Among patients with cystic fibrosis patients, highly antibiotic-resistant bacteria in the BCC have emerged as problematic pathogens, providing an impetus to study the potential of PNAG to be targeted for immunotherapy against pan-resistant bacterial pathogens.

METHODS

The presence of PNAG on BCC was assessed using a combination of bacterial genetics, microscopy, and immunochemical approaches. Antibodies to PNAG were tested using opsonophagocytic assays and for protective efficacy against lethal peritonitis in mice.

RESULTS

PNAG is expressed in vitro and in vivo by the BCC, and cystic fibrosis patients infected by the BCC species B. dolosa mounted a PNAG-specific opsonophagocytic antibody response. Antisera to PNAG mediated opsonophagocytic killing of BCC and were protective against lethal BCC peritonitis even during coinfection with methicillin-resistant Staphylococcus aureus.

CONCLUSIONS

Our findings raise potential new therapeutic options against PNAG-producing bacteria, including even pan-resistant pathogens.

A high-throughput screen identifies a new natural product with broad-spectrum antibacterial activity

Due to the inexorable invasion of our hospitals and communities by drug-resistant bacteria, there is a pressing need for novel antibacterial agents. Here we report the development of a sensitive and robust but low-tech and inexpensive high-throughput metabolic screen for novel antibiotics. This screen is based on a colorimetric assay of pH that identifies inhibitors of bacterial sugar fermentation. After validation of the method, we screened over 39,000 crude extracts derived from organisms that grow in the diverse ecosystems of Costa Rica and identified 49 with reproducible antibacterial effects. An extract from an endophytic fungus was further characterized, and this led to the discovery of three novel natural products. One of these, which we named mirandamycin, has broad-spectrum antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae, methicillin-resistant Staphylococcus aureus, and Mycobacterium tuberculosis. This demonstrates the power of simple high throughput screens for rapid identification of new antibacterial agents from environmental samples.

Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA

Pneumococcal type 1 pilus proteins have been proposed as potential vaccine candidates. Following conjugate pneumococcal vaccination, the prevalence of the pneumococcal type 1 pilus declined dramatically, a decline associated with the elimination of vaccine-type (VT) strains. Here we show that between 2004 and 2007, there has been a significant increase in pilus prevalence, now exceeding rates from the pre-conjugate vaccine era. This increase is primarily due to non-VT strains. These emerging piliated non-VT strains are mostly novel clones, with some exceptions. The rise in pilus type 1 frequency across multiple distinct genetic backgrounds suggests that the pilus may confer an intrinsic advantage.

Swine-origin influenza a (H1N1) viral infection in children: initial chest radiographic findings

PURPOSE

To evaluate initial chest radiographic findings of swine-origin influenza A (S-OIV) (also known as H1N1) viral infection in children.

MATERIALS AND METHODS

This was an institutional review board-approved, HIPAA-compliant retrospective study of 108 patients who had microbiologically confirmed S-OIV infection and available initial chest radiographs obtained between April 2009 and October 2009. The final study group was divided on the basis of clinical course (group 1, outpatients without hospitalization [n = 72]; group 2, inpatients with brief hospitalization [n = 22]; group 3, inpatients with intensive care unit admission [n = 14]). Two pediatric radiologists blinded to patient group and lung parenchymal, airway, pleural, hilar, and mediastinal abnormalities systematically reviewed initial chest radiographs. Lung parenchyma and airways were evaluated for pattern (peribronchial markings, consolidation, and ground-glass, nodular, and reticular opacity), distribution, and extent of abnormalities. Radiographs were assessed for presence of pleural effusions or lymphadenopathy. Medical records were reviewed for underlying medical conditions and patient outcomes. Association between frequency of underlying medical conditions and clinical course of S-OIV infection among study groups was evaluated with the Pearson chi(2) test.

RESULTS

The frequency of normal chest radiographs was significantly higher in group 1 (n = 48) than in groups 2 (n = 1) and 3 (n = 0) (P < .001, Pearson chi(2) test). Among patients with abnormal radiographs, the most common finding in group 1 was prominent peribronchial markings with hyperinflation (n = 17), whereas the most common findings in groups 2 (n = 12) and 3 (n = 12) were bilateral, symmetric, and multifocal areas of consolidation, often associated with ground-glass opacities. Nodular opacities, reticular opacities, pleural effusion, or lymphadenopathy were not observed in any patient. An increased frequency of underlying medical conditions was observed in patients with greater severity of illness due to S-OIV infection (group 3, 71%; group 2, 59%; group 1, 31%) (P = .003, Pearson chi(2) test). All 84 patients with available follow-up information have fully recuperated from S-OIV infection.

CONCLUSION

Initial chest radiographs in children with a mild and self-limited clinical course of S-OIV infection are often normal, but they may demonstrate prominent peribronchial markings with hyperinflation. Bilateral, symmetric, and multifocal areas of consolidation, often associated with ground-glass opacities, are the predominant radiographic findings in pediatric patients with a more severe clinical course of S-OIV infection. (c) RSNA, 2009.

Relative impact of influenza and respiratory syncytial virus in young children

OBJECTIVE

We measured the relative impact of influenza and respiratory syncytial virus (RSV) infections in young children in terms of emergency department (ED) visits, clinical care requirements, and overall resource use.

METHODS

Patients who were aged <or=7 years and treated in the ED of a tertiary care pediatric hospital for an acute respiratory infection were enrolled during 2 winter seasons between 2003 and 2005. We quantified health care resource use for children with influenza or RSV infections, and extrapolated results to estimate the national resource use associated with influenza and RSV infections.

RESULTS

Nationally, an estimated 10.2 ED visits per 1000 children were attributable to influenza and 21.5 visits per 1000 to RSV. Children who were aged 0 to 23 months and infected with RSV had the highest rate of ED visits with 64.4 visits per 1000 children. Significantly more children required hospitalization as a result of an RSV infection compared with influenza, with national hospitalization rates of 8.5 and 1.4 per 1000 children, respectively. The total number of workdays missed yearly by caregivers of children who required ED care was 246965 days for influenza infections and 716404 days for RSV infections.

CONCLUSION

For young children, RSV is associated with higher rates of ED visits, hospitalization, and caregiver resource use than is influenza. Our results provide data on the large number of children who receive outpatient care for influenza and RSV illnesses and serve to inform analyses of prevention programs and treatments for both influenza and RSV disease.

Epidemiology and risk factors for Staphylococcus aureus colonization in children in the post-PCV7 era

BACKGROUND

The incidence of community-associated methicillin-resistant Staphylococcus aureus (MRSA) has risen dramatically in the U.S., particularly among children. Although Streptococcus pneumoniae colonization has been inversely associated with S. aureus colonization in unvaccinated children, this and other risk factors for S. aureus carriage have not been assessed following widespread use of the heptavalent pneumococcal conjugate vaccine (PCV7). Our objectives were to (1) determine the prevalence of S. aureus and MRSA colonization in young children in the context of widespread use of PCV7; and (2) examine risk factors for S. aureus colonization in the post-PCV7 era, including the absence of vaccine-type S. pneumoniae colonization.

METHODS

Swabs of the anterior nares (S. aureus) were obtained from children enrolled in an ongoing study of nasopharyngeal pneumococcal colonization of healthy children in 8 Massachusetts communities. Children 3 months to <7 years of age seen for well child or sick visits in primary care offices from 11/03-4/04 and 10/06-4/07 were enrolled. S. aureus was identified and antibiotic susceptibility testing was performed. Epidemiologic risk factors for S. aureus colonization were collected from parent surveys and chart reviews, along with data on pneumococcal colonization. Multivariate mixed model analyses were performed to identify factors associated with S. aureus colonization.

RESULTS

Among 1,968 children, the mean age (SD) was 2.7 (1.8) years, 32% received an antibiotic in the past 2 months, 2% were colonized with PCV7 strains and 24% were colonized with non-PCV7 strains. The prevalence of S. aureus colonization remained stable between 2003-04 and 2006-07 (14.6% vs. 14.1%), while MRSA colonization remained low (0.2% vs. 0.9%, p = 0.09). Although absence of pneumococcal colonization was not significantly associated with S. aureus colonization, age (6-11 mo vs. > or =5 yrs, OR 0.39 [95% CI 0.24-0.64]; 1-1.99 yrs vs. > or =5 yrs, OR 0.35 [0.23-0.54]; 2-2.99 yrs vs. > or =5 yrs, OR 0.45 [0.28-0.73]; 3-3.99 yrs vs. > or =5 yrs, OR 0.53 [0.33-0.86]) and recent antibiotic use were significant predictors in multivariate models.

CONCLUSION

In Massachusetts, S. aureus and MRSA colonization remained stable from 2003-04 to 2006-07 among children <7 years despite widespread use of pneumococcal conjugate vaccine. S. aureus nasal colonization varies by age and is inversely correlated with recent antibiotic use.

Prospective multicenter study of the viral etiology of bronchiolitis in the emergency department

Objectives:  To determine the viral etiology of bronchiolitis and clinical characteristics of children age < 2 years presenting to the emergency department (ED) with bronchiolitis.

Methods:  The authors conducted a 14‐center prospective cohort study during 2005–2006 of ED patients age < 2 years with bronchiolitis. The study was conducted in 10 states as part of the Emergency Medicine Network. Researchers collected nasopharyngeal aspirates and conducted structured interviews, medical record reviews, and 2‐week follow‐up telephone calls. Samples were tested using reverse transcription polymerase chain reaction for respiratory syncytial virus (RSV), rhinovirus (RV), human metapneumovirus (hMPV), and influenza viruses (Flu).

Results:  Testing of 277 samples revealed 176 (64%) positive for RSV, 44 (16%) for RV, 26 (9%) for hMPV, 17 (6%) for Flu A, and none for Flu B. When children were categorized as RSV only, RV only, RV and RSV, and all others (hMPV, Flu, no identified virus), children with RV only were more likely to be African American (19, 62, 14, and 40%, respectively; p < 0.001) and have a history of wheezing (23, 52, 21, and 15%, respectively; p = 0.01). In multivariate models, children with RV were more likely to receive corticosteroids (odds ratio [OR] 3.5; 95% confidence interval [CI] = 1.5 to 8.15). The duration of illness may be shorter for children with RV (Days 8, 3, 6, and 8; p = 0.07).

Conclusions:  In this multicenter study, RSV was the most frequent cause of bronchiolitis (64%). RV was present in 16%, and these children have a distinct profile in terms of demographics, medical history, and ED treatment.

Association of the pneumococcal pilus with certain capsular serotypes but not with increased virulence

The recent discovery of a mobile genetic element encoding a pilus-like structure in Streptococcus pneumoniae and the demonstration of a role for the pilus in virulence in mice have led to the proposal of the use of the pilus as a candidate pneumococcal vaccine. We examined the frequency of occurrence of the pneumococcal pilus, as determined by the presence of the rrgC gene, and analyzed its association with virulence, capsular serotypes, and multilocus sequence types in the American Indian pneumococcal collection and isolates of S. pneumoniae from blood cultures collected at Children's Hospital Boston. Overall, 21.4% of strains in the American Indian collection had the rrgC gene, but there was no difference between isolates obtained from the nasopharynx and those obtained from sterile sites (blood or cerebrospinal fluid). Vaccine-type strains were significantly more likely than non-vaccine-type strains to have this pilus gene (P < 0.001). Among isolates with identical multilocus sequence types, there was a high concordance (95%) between the multilocus sequence type and the presence or the absence of rrgC. Finally, in the era of the pneumococcal conjugate vaccine, the frequency of rrgC in isolates from Children's Hospital Boston has decreased significantly (42.8% before 2000 versus 21.3% after 2000; P = 0.019). Therefore, our data show that the pilus is present in a minority of strains and is associated with certain serotypes and that its frequency has been reduced by the conjugate pneumococcal vaccine.

Influenza and other respiratory virus-related emergency department visits among young children

BACKGROUND

Influenza and other winter respiratory viruses cause substantial morbidity among children. Previous estimates of the burden of illness of these viruses have neglected to include the emergency department, where a large number of patients seek acute care for respiratory illnesses. This study provides city- and statewide population estimates of the burden of illness attributable to respiratory viruses for children receiving emergency department-based care for respiratory infections during the winter months.

METHODS

The number of patients < or = 7 years of age presenting to the emergency department of an urban tertiary care pediatric hospital with acute respiratory infections was estimated by using a classifier based on presenting complaints. The rates of specific viral infections in this population were estimated by using the rates of positivity for respiratory syncytial virus, influenza virus, parainfluenza virus, adenovirus, and enterovirus. Local emergency department market share and US Census data enabled determination of the rates of emergency department visits in the Boston, Massachusetts, area and in Massachusetts.

RESULTS

During the 11-year study period, the mean yearly number of patients < or = 7 years of age presenting to the study emergency department during the winter season was 17397. On the basis of the respiratory classifier, the mean number of patients with an acute respiratory infection was 6923, or 398 per 1000 emergency department visits. In the city population, the mean number of emergency department visits for acute respiratory infections was 17906, which is equivalent to 113.9 per 1000 children residing in the city, and in the state population the mean number was 61529, or 94.5 per 1000 children residing in the state. At the state level, 23114 of the visits were for respiratory syncytial virus, 5650 for influenza, 1751 for parainfluenza virus, 2848 for adenovirus, and 798 for enterovirus. For patients 6 to 23 months of age in the state population, there were 19860 emergency department visits for acute respiratory infections, or 168 per 1000 children in this age group, with 6235 visits resulting from respiratory syncytial virus and 2112 resulting from influenza.

CONCLUSION

There is a high incidence of emergency department visits for infectious respiratory illnesses among children. This important component of health care use should be included in estimates of the burden of illness attributable to influenza and other winter respiratory viruses.

Impact ofBurkholderia dolosaon Lung Function and Survival in Cystic Fibrosis

RATIONALE

Chronic infection with Burkholderia cepacia complex bacteria in cystic fibrosis is associated with accelerated decline in pulmonary function and increased mortality. Clinical implications of the recently characterized genomovar VI, B. dolosa, are unknown.

OBJECTIVES

Characterization of impact of B. dolosa on pulmonary function and mortality in cystic fibrosis.

METHODS

We compared patients chronically infected with B. dolosa (n = 31) with unmatched patients with B. multivorans (n = 24) and with age- and sex-matched control subjects without Burkholderia species (n = 58). We analyzed rates of pulmonary function decline (% predicted FEV(1)) using a random effects model assuming segmented linear trends. All available FEV(1) measurements from 5 yr (median, 4.8) before until 2.5 yr (median, 1.5) after the first positive culture for Burkholderia (reference date) were analyzed. Survival was compared using the Kaplan-Meier method and proportional hazards model.

MEASUREMENTS AND MAIN RESULTS

Baseline FEV(1) and rate of decline were similar in the cohorts. Decline in FEV(1) after the reference date accelerated in patients with B. dolosa (-2.3 percentage points/yr pre vs. -7.1 post, p = 0.002), but was unchanged in the B. multivorans and control patients (-2.3 vs. -0.8 post, p = 0.38, and -2.1 pre vs. -0.5 post, p = 0.20, respectively). The probability of dying within 18 mo of the reference date was 13, 7, and 3% for B. dolosa, B. multivorans, and control patients, respectively (B. dolosa vs. control hazard ratio, 10.8; 95% confidence interval, 1.3-92.8; p = 0.03).

CONCLUSIONS

B. dolosa chronic infection in cystic fibrosis is associated with accelerated loss of lung function and decreased survival.

Validation of syndromic surveillance for respiratory infections

Study objective

A key public health question is whether syndromic surveillance data provide early warning of infectious outbreaks. One cause for skepticism is that biological correlates of the administrative and clinical data used in these systems have not been rigorously assessed. This study measures the value of respiratory data currently used in syndromic surveillance systems to detect respiratory infections by comparing it against criterion standard viral testing within a pediatric population.

Methods

We conducted a longitudinal study with prospective validation in the emergency department (ED) of a tertiary care children’s hospital. Children aged 7 years or younger who presented with a respiratory syndrome or who were tested for respiratory syncytial virus (RSV), influenza virus, parainfluenza virus, adenovirus, or enterovirus between January 1993 and June 2004 were included. We assessed the predictive ability of the viral tests by fitting generalized linear models to respiratory syndrome counts.

Results

Of 582,635 patient visits, 89,432 (15.4%) were for respiratory syndromes, and of these, 7,206 (8.1%) patients were tested for the viruses of interest. RSV was significantly related to respiratory syndrome counts (adjusted rate ratio [RR] 1.33; 95% confidence interval [CI] 1.04 to 1.71). In multivariate models including all viruses tested, influenza virus was also a significant predictor of respiratory syndrome counts (RR 1.47; 95% CI 1.03 to 2.10). This model accounted for 81.6% of the observed variability in respiratory syndrome counts.

Conclusion

Respiratory syndromic surveillance data strongly correlate with virologic test results in a pediatric population, providing evidence of the biologic validity of such surveillance systems. Real-time outbreak detection systems relying on syndromic data may be an important adjunct to the current set of public health systems for the detection and surveillance of respiratory infections.

Pathology of human metapneumovirus infection: insights into the pathogenesis of a newly identified respiratory virus

Human metapneumovirus (hMPV) is a recently discovered human virus that causes significant respiratory infections. Pathologic features of hMPV infection have not been described. A total of 1257 pediatric respiratory samples submitted for routine clinical virologic testing were additionally tested for hMPV by reverse transcriptase polymerase chain reaction (PCR). Pathology specimens, available in 6 of 53 hMPV-positive patients, were examined by light and electron microscopy and included 6 bronchoalveolar lavage (BAL) and 3 lung biopsy specimens from 6 patients (3 girls and 3 boys) ranging in age from 1 to 16 years. BAL from three patients performed within 4 days of the positive hMPV assay showed epithelial degenerative changes and eosinophilic cytoplasmic inclusions within epithelial cells, multinucleate giant cells, and histiocytes. Inclusions were not seen in three patients with BAL performed = 1 month from the time of their positive assay. Lung biopsy, performed in three patients, all = 1 month from the time of their positive assay, showed chronic airway inflammation and intraalveolar foamy and hemosiderin-laden macrophages; all three patients had an underlying pulmonary/systemic disorder. Our findings delineate the clinicopathologic features in hMPV-infected patients undergoing anatomic sampling, which may provide diagnostic guidance to a practicing pathologist. Further, they contribute toward understanding the pathogenesis of hMPV infection.

Cerebrospinal latex agglutination fails to contribute to the microbiologic diagnosis of pretreated children with meningitis

We conducted a 10-year retrospective study of all children who had cerebrospinal fluid latex agglutination testing for bacterial antigens performed at 1 tertiary care urban children's hospital. Of the 176 patients with culture-negative meningitis who were pretreated with antibiotics before lumbar puncture, none had a positive latex agglutination study (0 of 176; 95% confidence interval, 0-2%). Latex agglutination studies identified no additional cases of bacterial meningitis beyond those identified by culture in pretreated patients. Clinical decision-making algorithms for the management of pretreated patients at risk for bacterial meningitis should not include latex agglutination testing.

Detection of multiple macrolide- and lincosamide-resistant strains of Streptococcus pyogenes from patients in the Boston area

Macrolide (including erythromycin and azithromycin) and lincosamide (including clindamycin) antibiotics are recommended for treatment of penicillin-allergic patients with Streptococcus pyogenes pharyngitis. Resistance to erythromycin in S. pyogenes can be as high as 48% in specific populations in the United States. Macrolide and lincosamide resistance in S. pyogenes is mediated by several different genes. Expression of the erm(A) or erm(B) genes causes resistance to erythromycin and inducible or constitutive resistance to clindamycin, respectively, whereas expression of the mef(A) gene leads to resistance to erythromycin but not clindamycin. We studied the resistance of S. pyogenes to erythromycin and clindamycin at an urban tertiary-care hospital. Of 196 sequential isolates from throat cultures, 15 (7.7%) were resistant to erythromycin. Three of these were also constitutively resistant to clindamycin and had the erm(B) gene. Five of the erythromycin-resistant isolates were resistant to clindamycin upon induction with erythromycin and had the erm(A) gene. The remaining seven erythromycin-resistant isolates were susceptible to clindamycin even upon induction with erythromycin and had the mef(A) gene. Pulsed-field gel electrophoresis analysis and emm typing demonstrated that the erythromycin-resistant S. pyogenes comprised multiple strains. These results demonstrate that multiple mechanisms of resistance to macrolide and lincosamide antibiotics are present in S. pyogenes strains in the United States.

Human metapneumovirus in children tested at a tertiary-care hospital

BACKGROUND

Respiratory infections are the leading cause of outpatient visits in the United States, but the etiology of many of these infections is unknown. Human metapneumovirus (hMPV) is a recently discovered virus that causes respiratory infections.

METHODS

Respiratory specimens obtained from patients <or=18 years old, between 1 October 2000 and 31 August 2002, were tested for hMPV. The results of testing for other viruses and epidemiological information were obtained from the hospital databases. A logistic regression model, including sex and age of the patient and year and season in which the specimen was obtained, was used to determine the factors associated with hMPV infection.

RESULTS

hMPV was detected in 6.2% of patients tested and was significantly more common among children 3-24 months old than in older or younger children. The seasonal occurrence of hMPV was similar to that of respiratory syncytial virus and influenza virus, with most cases occurring in the winter and spring. In this tertiary care-center population, patients with hMPV infection often had underlying chronic conditions.

CONCLUSIONS

hMPV is common among young children with apparent respiratory infections, suggesting that it is a significant cause of symptomatic respiratory infections.

Resistance of group B streptococcus to selected antibiotics, including erythromycin and clindamycin

Resistance of group B streptococcus (GBS) to antibiotics, particularly erythromycin and clindamycin, was studied. Erythromycin resistance was present in 22% of GBS isolates, and these isolates were constitutively resistant, inducibly resistant, or sensitive to clindamycin. Erythromycin and clindamycin MICs were related to the presence of ermA, ermB, or mefA genes.

Cutting edge: inducible costimulator protein regulates both Th1 and Th2 responses to cutaneous leishmaniasis

The CD28 family member inducible costimulator protein (ICOS) has an important role in T cell differentiation and Ig class switching. To investigate the role of ICOS in vivo, ICOS-/- mice were infected s.c. with Leishmania mexicana. While wild-type mice developed large, cutaneous lesions, the growth of lesions and tissue histopathology was significantly delayed in ICOS-/- mice. ICOS-/- mice exhibited marked decreases in both Th1 and Th2 cytokine production and profound defects in L. mexicana-specific Ig isotype class switching to IgG1 and IgG2a and reduced total IgE levels. Our findings indicate that ICOS is a key regulator of both Th1 and Th2 responses and has a role in controlling cutaneous L. mexicana infection.