Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections.

Acute bacterial infections are often treated empirically, with the choice of antibiotic therapy updated during treatment. The effects of such rapid antibiotic switching on the evolution of antibiotic resistance in individual patients are poorly understood. Here we find that low-frequency antibiotic resistance mutations emerge, contract, and even go to extinction within days of changes in therapy. We analyzed Pseudomonas aeruginosa populations in sputum samples collected serially from 7 mechanically ventilated patients at the onset of respiratory infection. Combining short- and long-read sequencing and resistance phenotyping of 420 isolates revealed that while new infections are near-clonal, reflecting a recent colonization bottleneck, resistance mutations could emerge at low frequencies within days of therapy. We then measured the in vivo frequencies of select resistance mutations in intact sputum samples with resistance-targeted deep amplicon sequencing (RETRA-Seq), which revealed that rare resistance mutations not detected by clinically used culture-based methods can increase by nearly 40-fold over 5-12 days in response to antibiotic changes. Conversely, mutations conferring resistance to antibiotics not administered diminish and even go to extinction. Our results underscore how therapy choice shapes the dynamics of low-frequency resistance mutations at short time scales, and the findings provide a possibility for driving resistance mutations to extinction during early stages of infection by designing patient-specific antibiotic cycling strategies informed by deep genomic surveillance.

Trends in Pediatric Candidemia: Epidemiology, Anti-Fungal Susceptibility, and Patient Characteristics in a Children's Hospital.

Candida bloodstream infections (CBSIs) have decreased among pediatric populations in the United States, but remain an important cause of morbidity and mortality. Species distributions and susceptibility patterns of CBSI isolates diverge widely between children and adults. The awareness of these patterns can inform clinical decision-making for empiric or pre-emptive therapy of children at risk for candidemia. CBSIs occurring from 2006-2016 among patients in a large children's hospital were analyzed for age specific trends in incidence rate, risk factors for breakthrough-CBSI, and death, as well as underlying conditions. Candida species distributions and susceptibility patterns were evaluated in addition to the anti-fungal agent use. The overall incidence rate of CBSI among this complex patient population was 1.97/1000 patient-days. About half of CBSI episodes occurred in immunocompetent children and 14% in neonatal intensive care unit (NICU) patients. Anti-fungal resistance was minimal: 96.7% of isolates were fluconazole, 99% were micafungin, and all were amphotericin susceptible. Liposomal amphotericin was the most commonly prescribed anti-fungal agent included for NICU patients. Overall, CBSI-associated mortality was 13.7%; there were no deaths associated with CBSI among NICU patients after 2011. Pediatric CBSI characteristics differ substantially from those in adults. The improved management of underlying diseases and antimicrobial stewardship may further decrease morbidity and mortality from CBSI, while continuing to maintain low resistance rates among Candida isolates.

Improving antibiotic prescribing for pediatric acute respiratory tract infections: A cluster randomized trial to evaluate individual versus clinic feedback.

Objective: To assess the effect of individual compared to clinic-level feedback on guideline-concordant care for 3 acute respiratory tract infections (ARTIs) among family medicine clinicians caring for pediatric patients. Design: Cluster randomized controlled trial with a 22-month baseline, 26-month intervention period, and 12-month postintervention period. Setting and participants: In total, 26 family medicine practices (39 clinics) caring for pediatric patients in Virginia, North Carolina, and South Carolina were selected based upon performance on guideline-concordance for 3 ARTIs, stratified by practice size. These were randomly allocated to a control group (17 clinics in 13 practices) or to an intervention group (22 clinics in 13 practices). Interventions: All clinicians received an education session and baseline then monthly clinic-level rates for guideline-concordant antibiotic prescribing for ARTIs: upper respiratory tract infection (URI), acute bacterial sinusitis (ABS), and acute otitis media (AOM). For the intervention group only, individual clinician performance was provided. Results: Both intervention and control groups demonstrated improvement from baseline, but the intervention group had significantly greater improvement compared with the control group: URI (odds ratio [OR], 1.62; 95% confidence interval [CI], 1.37-1.92; P < 0.01); ABS (OR, 1.45; 95% CI, 1.11-1.88; P < 0.01); and AOM (OR, 1.59; 95% CI, 1.24-2.03; P < 0.01). The intervention group also showed significantly greater reduction in broad-spectrum antibiotic prescribing percentage (BSAP%): odds ratio 0.80, 95% CI 0.74-0.87, P < 0.01. During the postintervention year, gains were maintained in the intervention group for each ARTI and for URI and AOM in the control group. Conclusions: Monthly individual peer feedback is superior to clinic-level only feedback in family medicine clinics for 3 pediatric ARTIs and for BSAP% reduction. Trial registration: ClinicalTrials.gov identifier: NCT04588376, Improving Antibiotic Prescribing for Pediatric Respiratory Infection by Family Physicians with Peer Comparison.

Appropriateness of Antibiotic Prescribing in United States Children's Hospitals: A National Point Prevalence Survey.

BACKGROUND: Studies estimate that 30%-50% of antibiotics prescribed for hospitalized patients are inappropriate, but pediatric data are limited. Characterization of inappropriate prescribing practices for children is needed to guide pediatric antimicrobial stewardship. METHODS: Cross-sectional analysis of antibiotic prescribing at 32 children's hospitals in the United States. Subjects included hospitalized children with ≥ 1 antibiotic order at 8:00 am on 1 day per calendar quarter, over 6 quarters (quarter 3 2016-quarter 4 2017). Antimicrobial stewardship program (ASP) physicians and/or pharmacists used a standardized survey to collect data on antibiotic orders and evaluate appropriateness. The primary outcome was the percentage of antibiotics prescribed for infectious use that were classified as suboptimal, defined as inappropriate or needing modification. RESULTS: Of 34 927 children hospitalized on survey days, 12 213 (35.0%) had ≥ 1 active antibiotic order. Among 11 784 patients receiving antibiotics for infectious use, 25.9% were prescribed ≥ 1 suboptimal antibiotic. Of the 17 110 antibiotic orders prescribed for infectious use, 21.0% were considered suboptimal. Most common reasons for inappropriate use were bug-drug mismatch (27.7%), surgical prophylaxis > 24 hours (17.7%), overly broad empiric therapy (11.2%), and unnecessary treatment (11.0%). The majority of recommended modifications were to stop (44.7%) or narrow (19.7%) the drug. ASPs would not have routinely reviewed 46.1% of suboptimal orders. CONCLUSIONS: Across 32 children's hospitals, approximately 1 in 3 hospitalized children are receiving 1 or more antibiotics at any given time. One-quarter of these children are receiving suboptimal therapy, and nearly half of suboptimal use is not captured by current ASP practices.

Antibiotic Susceptibility and Therapy in Central Line Infections in Pediatric Home Parenteral Nutrition Patients.

BACKGROUND: Patients receiving home parenteral nutrition (HPN) are at high-risk for central line-associated bloodstream infections (CLABSI). There are no published management guidelines, however, for the antibiotic treatment of suspected CLABSI in this population. Historical microbiology data may help inform empiric antimicrobial regimens in this population. OBJECTIVE: The aim of the study was to describe antimicrobial resistance patterns and determine the most appropriate empiric antibiotic therapy in HPN-dependent children experiencing a community-acquired CLABSI. METHODS: Single-center retrospective cohort study evaluating potential coverage of empiric antibiotic regimens in children on HPN who developed a community-acquired CLABSI. RESULTS: From October 1, 2011 to September 30, 2017, there were 309 CLABSI episodes among 90 HPN-dependent children with median age 3.8 years old.Fifty-nine percent of patients carried the diagnosis of surgical short bowel syndrome. Organisms isolated during these infections included 60% Gram-positive bacteria, 34% Gram-negative bacteria, and 6% fungi. Among all staphylococcal isolates, 51% were methicillin sensitive. Among enteric Gram-negative organisms, sensitivities were piperacillin-tazobactam 71%, cefepime 97%, and meropenem 99%. Organisms were sensitive to current institutional standard therapy with vancomycin and piperacillin-tazobactam in 69% of cases compared with vancomycin and cefepime or vancomycin an meropenem in 85% and 96% of cases (both P < 0.01). CONCLUSIONS: Empiric antimicrobial therapy for suspected CLABSI in HPN-dependent children should include therapy for methicillin-resistant staphylococci as well as enteric Gram-negative organisms. Future studies are needed to evaluate clinical outcomes based upon evidence-based antimicrobial regimens.

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.

Increased 30-Day Mortality Associated With Carbapenem-Resistant Enterobacteriaceae in Children.

In this multicenter study, we identified an increased risk of 30-day mortality among hospitalized children with carbapenem-resistant Enterobacteriaceae (CRE) isolated from clinical cultures compared with those with carbapenem-susceptible Enterobacteriaceae. We additionally report significant variation in antibiotic treatment for children with CRE infections with infrequent use of combination therapy.

Reducing Redundant Anaerobic Therapy Through Spaced Education and Antimicrobial Stewardship Interventions.

BACKGROUND: Decreasing the use of redundant anaerobic therapy is a key target for antimicrobial stewardship. Education techniques that optimize knowledge retention could be an important component of reducing these regimens. METHODS: We implemented a quality improvement project that incorporated spaced education to reduce the use of redundant anaerobic therapy. The initial interventions (November through December 2015) included education in a hospital-wide newsletter and review of redundant anaerobic regimens by the antimicrobial stewardship program. A spaced education module was then developed with the gastroenterology (GI) service, which had a relatively high rate of redundant anaerobic therapy use. Ten questions with teaching points were delivered to GI physicians at spaced intervals over 2 to 4 weeks (February through March 2016). Knowledge scores were compared at initial and final question presentation using generalized estimating equations. Interrupted time-series analysis was used to compare the rates of redundant-metronidazole-days per 1000 patient-days among patients in the patients admitted to the GI service and those in the non-GI group before and after the intervention. RESULTS: Of 66 GI physicians, 56 (85%) participated in the spaced education activity. After the intervention, their knowledge scores on all the questions improved, and their mean knowledge score increased from 57% to 86% (P < .001). Nearly all (91%) of the participants were very or generally satisfied with the activity. In the GI group, the rate of redundant-metronidazole-days decreased from 26.2 to 13.0 per 1000 patient-days (relative risk [RR], 0.45 [95% confidence interval (CI), 0.27-0.73]; P = .001). This rate in the non-GI group also decreased from 5.47 to 2.18 per 1000 patient-days (RR, 0.47 [95% CI, 0.36-0.60]; P < .001) after our interventions. CONCLUSIONS: Spaced education is an effective approach for teaching antimicrobial stewardship topics. Focused provider education was associated with a sustained reduction in the use of redundant anaerobic therapy.

Multicenter Study of the Risk Factors for Colonization or Infection with Carbapenem-Resistant Enterobacteriaceae in Children.

Carbapenem-resistant Enterobacteriaceae (CRE) are increasingly identified in children in the United States, but data on the epidemiology of CRE in this population are limited. The objectives of this study were to characterize the risk factors for colonization or infection with CRE and describe the microbiologic characteristics of pediatric CRE isolates. We performed a multicenter matched case-control study from January 2011 to October 2015 at three tertiary care pediatric centers. Case patients were hospitalized children with CRE isolated from clinical cultures and were matched in a 2:1 ratio to control patients with carbapenem-susceptible Enterobacteriaceae (CSE). Risk factors for colonization or infection with CRE were then evaluated using a multivariable conditional logistic regression. Additionally, we comprehensively reported the antimicrobial susceptibility pattern for CRE isolates. Sixty-three case patients were identified and matched to 126 control patients. On multivariable analysis, antipseudomonal antibiotic exposure within the previous 3 months (odds ratio [OR], 5.20; 95% confidence interval [CI], 1.71 to 15.9; P = 0.004), prior surgery (OR, 6.30; 95% CI, 1.83 to 21.6; P = 0.003), and mechanical ventilation (OR, 12.4; 95% CI, 1.26 to 122; P = 0.031) were identified as risk factors for colonization or infection with CRE. Pediatric CRE isolates demonstrated relatively low rates of resistance to amikacin (5%) and ciprofloxacin (25%). Our findings support an important role for antibiotic stewardship interventions limiting the unnecessary use of antipseudomonal antibiotics as a strategy to prevent widespread emergence of CRE in children. Future studies should further characterize molecular determinants of antibiotic resistance among pediatric CRE isolates.

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.

Long-Term Outcomes and Risk Factors Associated With Acute Encephalitis in Children.

BACKGROUND: Factors associated with poor outcomes of children with encephalitis are not well known. We sought to determine whether electroencephalography (EEG) findings, magnetic resonance imaging (MRI) abnormalities, or the presence of seizures at presentation were associated with poor outcomes. METHODS: A retrospective review of patients aged 0 to 21 years who met criteria for a diagnosis of encephalitis admitted between 2000 and 2010 was conducted. Parents of eligible children were contacted and completed 2 questionnaires that assessed current physical and emotional quality of life and neurological deficits at least 1 year after discharge. RESULTS: During the study period, we identified 142 patients with an International Classification of Diseases 9th Revision diagnosis of meningitis, meningoencephalitis, or encephalitis. Of these patients, 114 met criteria for a diagnosis of encephalitis, and 76 of these patients (representing 77 hospitalizations) had complete data available. Forty-nine (64%) patients were available for follow-up. Patients admitted to the intensive care unit were more likely to have abnormal EEG results (P = .001). The presence of seizures on admission was associated with ongoing seizure disorder at follow-up. One or more years after hospitalization, 78% of the patients had persistent symptoms, including 35% with seizures. Four (5%) of the patients died. Abnormal MRI findings and the number of abnormal findings on initial presentation were associated with lower quality-of-life scores. CONCLUSIONS: Encephalitis leads to significant morbidity and death, and incomplete recovery is achieved in the majority of hospitalized patients. Abnormal EEG results were found more frequently in critically ill children, patients with abnormal MRI results had lower quality-of-life scores on follow-up, and the presence of seizures on admission was associated with ongoing seizure disorder and lower physical quality-of-life scores.

Impact of Mandatory Public Reporting of Central Line-Associated Bloodstream Infections on Blood Culture and Antibiotic Utilization in Pediatric and Neonatal Intensive Care Units.

BACKGROUND: As mandatory public reporting of healthcare-associated infections increases, there is concern that clinicians could attempt to decrease rates by avoiding the diagnosis of reportable infections. OBJECTIVE: To determine whether blood culture and antibiotic utilization changed after mandatory public reporting of central line-associated bloodstream infection (CLABSI). DESIGN: Interrupted time-series of blood culture and antibiotic rates before and after state-specific implementation of mandatory public reporting. We analyzed data from pediatric and neonatal intensive care units (ICUs) at 17 children's hospitals that contributed to the Pediatric Health Information System administrative database. We used multivariable regression with generalized linear mixed-effects models to determine adjusted rate ratios (ARRs) after implementation of mandatory public reporting. We conducted subgroup analysis on patients with central venous catheters. To assess temporal trends, we separately analyzed data from 4 pediatric hospitals in states without mandatory public reporting. RESULTS: There was no significant effect of mandatory public reporting on rates of blood culture (pediatric ICU ARR, 1.03 [95% CI, 0.82-1.28]; neonatal ICU ARR, 1.06 [0.85-1.33]) or antibiotic utilization (pediatric ICU ARR, 0.86 [0.72-1.04]; neonatal ICU ARR, 1.09 [0.87-1.35]). Results were similar in the subgroup of patients with central venous catheter codes. Hospitals with and without mandatory public reporting experienced small decreases in blood culture and antibiotic use across the study period. CONCLUSIONS: Mandatory public reporting of central line-associated bloodstream infection did not impact blood culture and antibiotic utilization, suggesting that clinicians have not shifted their practice in an attempt to detect fewer infections.

Outpatient course and complications associated with home oxygen therapy for mild bronchiolitis.

BACKGROUND: Home oxygen has been incorporated into the emergency department management of bronchiolitis in high-altitude settings. However, the outpatient course on oxygen therapy and factors associated with subsequent admission have not been fully defined. METHODS: We conducted a retrospective cohort study in consecutive patients discharged on home oxygen from the pediatric emergency department at Denver Health Medical Center from 2003 to 2009. The integration of inpatient and outpatient care at our study institution allowed comprehensive assessment of follow-up rates, outpatient visits, time on oxygen, and subsequent admission. Admitted and nonadmitted patients were compared by using a χ(2) test and multivariable logistic regression. RESULTS: We identified 234 unique visits with adequate follow-up for inclusion. The median age was 10 months (interquartile range [IQR]: 7-14 months). Eighty-three percent of patients were followed up within 24 hours and 94% within 48 hours. The median length of oxygen use was 6 days (IQR: 4-9 days), and the median number of associated encounters was 3 (range: 0-9; IQR: 2-3). Ninety-three percent of patients were on room air at 14 days. Twenty-two patients (9.4%) required subsequent admission. Fever at the initial visit (>38.0°C) was associated with admission (P < .02) but had a positive predictive value of 15.4%. Age, prematurity, respiratory rate, oxygen saturation, and history of previous bronchiolitis or wheeze were not associated with admission. CONCLUSIONS: There is a significant outpatient burden associated with home oxygen use. Although fever was associated with admission, we were unable to identify predictors that could modify current protocols.

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

Advances in sequencing technologies have enabled the identification of mutations acquired by bacterial pathogens during infection. However, it remains unclear whether adaptive mutations fix in the population or lead to pathogen diversification within the patient. Here we study the genotypic diversity of Burkholderia dolosa within individuals with cystic fibrosis by resequencing individual colonies and whole populations from single sputum samples. We find extensive intrasample diversity, suggesting that mutations rarely fix in a patient's pathogen population--instead, diversifying lineages coexist for many years. Under strong selection, multiple adaptive mutations arise, but none of these sweep 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 the selective pressures acting on a pathogen in individual patients based on single clinical samples.

Variability in the Diagnosis of Encephalitis by Pediatric Subspecialists: The Need For a Uniform Definition.

Research definitions of encephalitis vary widely. When surveyed on the criteria used in clinical diagnosis, 88 pediatric specialists demonstrated diverse responses, with pediatric neurologists and pediatric infectious disease specialists differing significantly in their consideration of cerebrospinal fluid pleocytosis and abnormal neuroimaging. Results emphasize the need for a uniform definition.