David Haslam

A sustained quality improvement program reduces nephrotoxic medication-associated acute kidney injury

Exposure to nephrotoxic medication is among the most common causes of acute kidney injury (AKI) in hospitalized patients. Here we conducted a prospective quality improvement project implementing a systematic Electronic Health Record screening and decision support process (trigger) in our quaternary pediatric inpatient hospital. Eligible patients were noncritically ill hospitalized children receiving an intravenous aminoglycoside for more than 3 days or more than 3 nephrotoxins simultaneously (exposure) from September 2011 through March 2015. Pharmacists recommended daily serum creatinine monitoring in exposed patients after appearance on the trigger report and AKI was defined by the Kidney Disease Improving Global Outcomes AKI criteria. A total of 1749 patients accounted for 2358 separate hospital admissions during which a total of 3243 episodes of nephrotoxin exposure were identified with 170 patients (9.7%) experiencing 2 or more exposures. A total of 575 individual AKI episodes occurred over the 43-month study period. Overall, the exposure rate decreased by 38% (11.63-7.24 exposures/1000 patient days), and the AKI rate decreased by 64% (2.96-1.06 episodes/1000 patient days). Assuming initial baseline exposure rates would have persisted without our project implementation, we estimate 633 exposures and 398 AKI episodes were avoided. Thus, systematic surveillance for nephrotoxic medication exposure and near real-time AKI risk can lead to sustained reductions in avoidable harm. These interventions and outcomes are translatable to other pediatric and nonpediatric hospitalized settings.

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

ABSTRACT The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing (r 2 = −0.60) and MSS (r 2 = −0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge.

Use of Shotgun Metagenome Sequencing To Detect Fecal Colonization with Multidrug-Resistant Bacteria in Children

ABSTRACT Prevention of multidrug-resistant (MDR) bacterial infections relies on accurate detection of these organisms. We investigated shotgun metagenome sequencing for the detection of methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), and MDR Enterobacteriaceae. Fecal metagenomes were analyzed from high-risk inpatients and compared to those of low-risk outpatients and controls with minimal risk for a MDR bacterial infection. Principal-component analysis clustered patient samples into distinct cohorts, confirming that the microbiome composition was significantly different between cohorts (P = 0.006). Microbial diversity and relative anaerobe abundance were preserved in outpatients compared to those in controls. Relative anaerobe abundance was significantly reduced in inpatients compared to that in outpatients (P = 0.006). Although the potential for MDR bacteria was increased in inpatients and outpatients compared to that in controls (P < 0.001), there was no difference between inpatients and outpatients. However, 9 (53%) inpatients had colonization with a MDR bacterium that was not identified by culture. Unlike culture, shotgun sequencing quantitatively characterizes the burdens of multiple MDR bacteria relative to all of the microbiota within the intestinal community. We propose consideration of key microbiome features, such as diversity and relative anaerobe abundance, in addition to the detection of MDR bacteria by shotgun metagenome sequencing as a novel method that might better identify patients who are at increased risk of a MDR infection.

Healthcare Burden, Risk Factors, and Outcomes of Mucosal Barrier Injury Laboratory-Confirmed Bloodstream Infections after Stem Cell Transplantation

Mucosal barrier injury laboratory-confirmed bloodstream infections (MBI-LCBIs) lead to significant morbidity, mortality, and healthcare resource utilization in hematopoietic stem cell transplant (HSCT) patients. Determination of the healthcare burden of MBI-LCBIs and identification of patients at risk of MBI-LCBIs will allow researchers to identify strategies to reduce MBI-LCBI rates. The objective of our study was to describe the incidence, risk factors, timing, and outcomes of MBI-LCBIs in hematopoietic stem cell transplant patients. We performed a retrospective analysis of 374 patients who underwent HSCT at a large free-standing academic childrens hospital to determine the incidence, risk factors, and outcomes of patients that developed a bloodstream infection (BSI) including MBI-LCBI, central line-associated BSI (CLABSI), or secondary BSI in the first year after HSCT. Outcome measures included nonrelapse mortality (NRM), central venous catheter removal within 7 days of positive culture, shock, admission to the pediatric intensive care unit (PICU) within 48 hours of positive culture, and death within 10 days of positive culture. One hundred seventy BSIs were diagnosed in 100 patients (27%): 80 (47%) MBI-LCBIs, 68 (40%) CLABSIs, and 22 (13%) secondary infections. MBI-LCBIs were diagnosed at a significantly higher rate in allogeneic HSCT patients (18% versus 7%, Pu2009=u2009.007). Reduced-intensity conditioning (OR, 1.96; Pu2009=u2009.015) and transplant-associated thrombotic microangiopathy (OR, 2.94; Pu2009=u2009.0004) were associated with MBI-LCBI. Nearly 50% of all patients with a BSI developed septic shock, 10% died within 10 days of positive culture, and nearly 25% were transferred to the PICU. One-year NRM was significantly increased in patients with 1 (34%) and more than 1 (56%) BSIs in the first year post-HSCT compared with those who did not develop BSIs (14%) (Pu2009≤ .0001). There was increased 1-year NRM in patients with at least 1 MBI-LCBI (OR, 1.94; Pu2009=u2009.018) and at least 1 secondary BSI (OR, 2.87; Pu2009=u2009.0023) but not CLABSIs (OR, 1.17; Pu2009=u2009.68). Our data demonstrate that MBI-LCBIs lead to substantial use of healthcare resources and are associated with significant morbidity and mortality. Reduction in frequency of MBI-LCBI should be a major public health and scientific priority.

A fast and robust protocol for metataxonomic analysis using RNAseq data

BackgroundMetagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, primarily from 16S rRNA gene sequencing and DNAseq, to identify microorganisms and viruses within a complex mixture. With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make metatranscriptomic data sufficient for metataxonomics, new analytical workflows are needed to deal with sparse and taxonomically less informative sequencing data.ResultsWe present a new protocol, IMSA+A, for accurate taxonomy classification based on metatranscriptome data of any read length that can efficiently and robustly identify bacteria, fungi, and viruses in the same sample. The new protocol improves accuracy by using a conservative reference database, employing a new counting scheme, and by assembling shotgun reads. Assembly also reduces analysis runtime. Simulated data were utilized to evaluate the protocol by permuting common experimental variables. When applied to the real metatranscriptome data for mouse intestines colonized by ASF, the protocol showed superior performance in detection of the microorganisms compared to the existing metataxonomics tools. IMSA+A is available at https://github.com/JeremyCoxBMI/IMSA-A.ConclusionsThe developed protocol addresses the need for taxonomy classification from RNAseq data. Previously not utilized, i.e., unmapped to a reference genome, RNAseq reads can now be used to gather taxonomic information about the microbiota present in a biological sample without conducting additional sequencing. Any metatranscriptome pipeline that includes assembly of reads can add this analysis with minimal additional cost of compute time. The new protocol also creates an opportunity to revisit old metatranscriptome data, where taxonomic content may be important but was not analyzed.

Utility of a routine urinalysis in children who require clean intermittent catheterization

BACKGROUNDnChildren who require clean intermittent catheterization (CIC) frequently have positive urine cultures. However, diagnosing a urinary tract infection (UTI) can be difficult, as there are no standardized criteria. Routine urinalysis (UA) has good predictive accuracy for UTI in the general pediatric population, but data are limited on the utility of routine UA in the population of children who require CIC.nnnOBJECTIVEnTo determine the utility of UA parameters (e.g. leukocyte esterase, nitrites, and pyuria) to predict UTI in children who require CIC, and identify a composite UA that has maximal predictive accuracy for UTI.nnnMETHODSnA cross-sectional study of 133 children who required CIC, and had a UA and urine culture sent as part of standard of care. Patients in the no-UTI group all had UA and urine cultures sent as part of routine urodynamics, and were asymptomatic. Patients included in the UTI group had growth of ≥50,000xa0colony-forming units/ml of a known uropathogen on urine culture, in addition to two or more of the following symptoms: fever, abdominal pain, back pain, foul-smelling urine, new or worse incontinence, and pain with catheterization. Categorical data were compared using Chi-squared test, and continuous data were compared with Students t-test. Sensitivity, specificity, and positive and negative predictive values were calculated for individual UA parameters, as well as the composite UA. Logistic regression was performed on potential composite UA models to identify the model that best fit the data.nnnRESULTSnThere was a higher proportion of patients in the no-UTI group with negative leukocyte esterase compared with the UTI group. There was a higher proportion of patients with UTI who had large leukocyte esterase and positive nitrites compared with the no-UTI group (Summary Figure). There was no between-group difference in urinary white blood cells. Positive nitrites were the most specific (84.4%) for UTI. None of the parameters had a high positive predictive value, while all had high negative predictive values. The composite model with the best Akaike information criterion was >10 urinary white blood cells and either moderate or large leukocyte esterase, which had a positive predictive value of 33.3 and a negative predictive value of 90.4.nnnCONCLUSIONnRoutine UA had limited sensitivity, but moderate specificity, in predicting UTI in children who required CIC. The composite UA and moderate or large leukocyte esterase both had good negative predictive values for the outcome of UTI.

Risk Factors for Staphylococcus aureus Acquisition in the Neonatal Intensive Care Unit: A Matched Case-Case-Control Study

OBJECTIVE To determine risk factors independent of length of stay (LOS) for Staphylococcus aureus acquisition in infants admitted to the neonatal intensive care unit (NICU). DESIGN Retrospective matched case-case-control study. SETTING Quaternary-care referral NICU at a large academic childrens hospital. METHODS Infants admitted between January 2014 and March 2016 at a level IV NICU who acquired methicillin resistant (MRSA) or susceptible (MSSA) S. aureus were matched with controls by duration of exposure to determine risk factors for acquisition. A secondary post hoc analysis was performed on the entire cohort of at-risk infants for risk factors identified in the primary analysis to further quantify risk. RESULTS In total, 1,751 infants were admitted during the study period with 199 infants identified as having S. aureus prevalent on admission. There were 246 incident S. aureus acquisitions in the remaining at-risk infant cohort. On matched analysis, infants housed in a single-bed unit were associated with a significantly decreased risk of both MRSA (P=.03) and MSSA (P=.01) acquisition compared with infants housed in multibed pods. Across the entire cohort, pooled S. aureus acquisition was significantly lower in infants housed in single-bed units (hazard ratio,=0.46; confidence interval, 0.34-0.62). CONCLUSIONS NICU bed design is significantly associated with S. aureus acquisition in hospitalized infants independent of LOS. Infect Control Hosp Epidemiol 2018;39:46-52.

Nonalcoholic steatohepatitis and the intestinal microbiota

Nonalcoholic steatohepatitis (NASH), characterized by fatty infiltration of the liver, hepatocellular injury, and hepatic inflammation, is a major cause of liver failure. The pathogenesis of NASH is incompletely understood, but generally occurs in individuals with preexisting nonalcoholic fatty liver disease (NAFLD) or uncomplicated steatosis. Whereas most individuals with NAFLD will not develop liver disease, at least 10% progress to NASH and a large portion of these individuals develop cirrhosis and, ultimately, liver failure. Understanding which factors drive progression from simple steatosis to NASH is profoundly important. In this regard, the intestinal microbial community has become a major focus of investigation for its potential role in inciting liver inflammation and injury. In humans, the intestine plays hosts to a dense microbial community (the microbiota) comprised of thousands of species. The gut microbiota are collectively an intense biochemical reactor, generating byproducts that can cross the intestinal mucosa to the portal circulation and directly to the liver. Whereas some microbial metabolites are undoubtedly beneficial, others are suspected to stimulate inflammation or cause hepatocellular injury. Most notable in this regard is lipopolysaccharide (LPS), a component of the cell wall of Gram-negative bacteria and an exceptionally potent stimulus for inflammatory cytokines. LPS can be detected in plasma of obese patients where it has been correlated with the degree of liver injury, suggesting a link between microbiota-derived LPS and progression to NASH. Several animal models of NASH support the contribution of LPS to liver inflammation. Other metabolite levels are affected by microbiota biochemical activities and some of these and are felt to contribute to NASH, such as short-chain fatty acids, ethanol, and bile acids. Consistent with a role for the gut microbiota in liver disease, animal models reveal that antibiotic treatment, probiotics, and prebiotics can delay disease progression. Treatment of patients with the antibiotic, rifaximin, decreased markers of hepatic injury in patients with NASH. Despite these intriguing findings, the precise contribution of intestinal microbes to progression from NAFLD to NASH remains unclear. Studies examining microbial species in the human microbiota have been inconsistent, in some cases reporting completely opposite associations between NASH and specific intestinal microbes. Previous studies have found that Bacteroides and Proteobacteria, which includes Escherichia coli and other Enterobacteraciae, are most commonly different between patients with NASH compared to those without, but the direction of the associations has not been consistent. For example, abundance of Bacteroides was either significantly increased, significantly decreased, or not significantly different between patients with NASH compared to healthy controls or those with NAFLD. The study by Del Chierico et al., in the current issue of HEPATOLOGY, provides a rich new data set, which, from associations between intestinal microbes, fecal metabolites, and liver disease, are explored anew. The investigators studied both the gut microbiota and the metabolite composition of feces from patients with obesity (n 5 8), NAFLD (n 5 27), or NASH (n 5 26) and compared these to healthy age-matched controls (n 5 54). As has been observed by other Abbreviations: LPS, lipopolysaccharide; NAFLD, nonalcoholic fatty liver disease; NASH, nonalcoholic steatohepatitis; PLS-DA, partial least squares discriminant analysis.

Performance of the check-points check-MDR CT103XL assay utilizing the CDC/FDA antimicrobial resistance isolate bank

The Check-MDR CT103XL beta-lactamase assay was validated for use in the clinical microbiology laboratory using two CDC-FDA Antimicrobial Resistant Isolate Bank panels (133 gram-negative bacilli known beta-lactamase genes). The CT103XL detected most reported resistance genes (123 of 136 genes) and additionally identified several resistance genes not reported by the CDC. Discrepant results were confirmed via whole genome sequencing.

Frequency of Multidrug-Resistant Organisms Cultured From Urine of Children Undergoing Clean Intermittent Catheterization

BackgroundnChildren undergoing CIC frequently have positive urine culture results and receive many antimicrobial agents. Subsequently, this population is at high risk for infections caused by antimicrobial-resistant bacteria. Resistant pathogens, such as vancomycin-resistant Enterococcus (VRE), carbapenem-resistant Enterobacteriaceae (CRE), and organisms that produce extended-spectrum β-lactamases (ESBLs), which are third-generation cephalosporin resistant (3GCR), are of particular concern.nnnMethodsnIn this retrospective study, all urine culture results and antimicrobial-susceptibility testing results were obtained between January 2008 and December 2014 from the electronic health record of children ≤18 years of age who were undergoing CIC (n = 14 832). Isolates were identified as VRE, CRE, or 3GCR. Organisms of the same type that were obtained in the same year and with identical antibiotic susceptibilities from the same patient were excluded. Simple linear regression was used to determine the association between year and rates of resistance.nnnResultsnA total of 3997 positive culture results were included in this analysis. Of all Enterococcus isolates for which susceptibility results were available, 4.6% were VRE, 11.1% of all isolates that belonged to the Enterobacteriaceae family were 3GCR, and 0.4% of eligible isolates were CRE. There were significantly higher rates of resistance to third-generation cephalosporins and CRE in 2014 than in 2008 (P < .01). Simple linear regression revealed a significant association between year and rate for resistance to third-generation cephalosporins but not for CRE or VRE. The rate of increase in resistance to third-generation cephalosporins in patients who required CIC was higher than that in patients who did not need CIC.nnnConclusionsnThe rate of resistance to third-generation cephalosporins has increased significantly in the past 7 years in children undergoing CIC, which indicates that careful monitoring is warranted for continued increases in antimicrobial-resistant organisms in this unique patient population.