Whole Genome Sequencing Detects Minimal Clustering Among Escherichia coli Sequence Type 131-H30 Isolates Collected From United States Children's Hospitals.
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ABSTRACT:
SUBMITTER: Miles-Jay A
PROVIDER: S-EPMC7996643 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
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Whole Genome Sequencing Detects Minimal Clustering Among Escherichia coli Sequence Type 131-H30 Isolates Collected From United States Children's Hospitals.
Miles-Jay Arianna A Weissman Scott J SJ Adler Amanda L AL Baseman Janet G JG Zerr Danielle M DM
Journal of the Pediatric Infectious Diseases Society 20210301 2
We applied whole genome sequencing to identify putative transmission clusters among clinical multidrug-resistant Escherichia coli sequence type 131-H30 isolates from 4 United States children's hospitals. Of 126 isolates, 17 were involved in 8 putative transmission clusters; 4 clusters showed evidence of healthcare-associated epidemiologic linkages. Geographic clustering analyses showed weak geographic clustering. ...[more]
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Project description:BackgroundEmerging antimicrobial-resistant Escherichia coli represent mainly the nested (fluoroquinolone-resistant [FQR]) H30R and H30Rx subclones within sequence type 131 (ST131). Intestinal colonization and within-household transmission may underlie H30R's emergence.MethodsWe screened fecal samples from 741 volunteers (383 veterans, 358 household members, including pets) for ST131 and FQR E. coli (FQREC) and used molecular profiling to resolve unique strains. Selected strains underwent PCR-based detection of phylogroups, sequence types (STs), H30, H30Rx, and 53 virulence genes (VGs). Within-household strain sharing was compared with household, host, and bacterial characteristics. Fecal isolates were compared with clinical isolates.ResultsColonization prevalence was 5.1% for H30R, 8% for ST131 (67% FQREC), and 10% for FQREC (52% ST131). ST131 isolates exhibited more VGs than non-ST131 isolates. Strain sharing (27% of multisubject households, 18% of corresponding subjects) was associated with the elderly, FQREC, H30R, H30Rx, ST73, and specific VGs. Fecal ST131 and FQREC isolates resembled contemporaneous and historical clinical isolates according to all studied traits.ConclusionsVeterans and their human household members commonly carry and extensively share FQREC, predominantly H30R, thereby likely facilitating the ST131 pandemic. Strain sharing corresponds with multiple bacterial characteristics, including FQ resistance and specific VGs, which may promote intestinal colonization and/or host-to-host transmission.
| S-EPMC7184911 | biostudies-literature
Project description:Background:Escherichia coli sequence type (ST) 131-H30 is a globally important pathogen implicated in rising rates of multidrug resistance among E. coli causing extraintestinal infections. Previous studies have focused on adults, leaving the epidemiology of H30 among children undefined. Methods:We used clinical data and isolates from a case-control study of extended-spectrum cephalosporin-resistant E. coli conducted at 4 US children's hospitals to estimate the burden and identify host correlates of infection with H30. H30 isolates were identified using 2-locus genotyping; host correlates were examined using log-binomial regression models stratified by extended-spectrum cephalosporin resistance status. Results:A total of 339 extended-spectrum cephalosporin-resistant and 1008 extended-spectrum cephalosporin-susceptible E. coli isolates were available for analyses. The estimated period prevalence of H30 was 5.3% among all extraintestinal E. coli isolates (95% confidence interval [CI], 4.6%-7.1%); H30 made up 43.3% (81/187) of extended-spectrum β-lactamase (ESBL)-producing isolates in this study. Host correlates of infection with H30 differed by extended-spectrum cephalosporin resistance status: Among resistant isolates, age ≤5 years was positively associated with H30 infection (relative risk [RR], 1.83 [95% CI, 1.19-2.83]); among susceptible isolates, age ≤5 years was negatively associated with H30 (RR, 0.48 [95% CI, .27-.87]), while presence of an underlying medical condition was positively associated (RR, 4.49 [95% CI, 2.43-8.31]). Conclusions:ST131-H30 is less common among extraintestinal E. coli collected from children compared to reported estimates among adults, possibly reflecting infrequent fluoroquinolone use in pediatrics; however, it is similarly dominant among ESBL-producing isolates. The H30 subclone appears to disproportionately affect young children relative to other extended-spectrum cephalosporin-resistant E. coli.
| S-EPMC5848265 | biostudies-literature
Project description:BackgroundThe prevalence of tranexamic acid (TXA) use for trauma and other conditions in children is unknown.ObjectivesThe objective of this study was to describe the use of TXA in United States (US) children's hospitals for children in general, and specifically for trauma.MethodsWe conducted a secondary analysis of a large, administrative database of 36 US children's hospitals. We included children <18 years of age who received TXA (based on pharmacy charge codes) between 2009 and 2013. Patients were grouped into the following diagnostic categories: trauma, congenital heart surgery, scoliosis surgery, craniosynostosis/craniofacial surgery, and other, based on the International Classification of Diseases, Ninth Revision principal procedure and diagnostic codes. TXA administration and dosage, in-hospital clinical variables, and diagnostic and procedure codes were documented.ResultsA total of 35,478 pediatric encounters with a TXA charge were included in the study cohort. The proportions of children who received TXA were similar across the years 2009 to 2013. Only 110 encounters (0.31%) were for traumatic conditions. Congenital heart surgery accounted for more than one-half of the encounters (22,863; 64%). Overall, the median estimated weight-based dose of TXA was 22.4 mg/kg (interquartile range, 7.3-84.9 mg/kg).ConclusionsWe identified a wide frequency of use and range of doses of TXA for several diagnostic conditions in children. The use of TXA among injured children, however, appears to be rare despite its common use and efficacy among injured adults. Additional work is needed to identify appropriate indications for TXA and provide dosage guidelines among children with a variety of conditions, including trauma.
| S-EPMC4912435 | biostudies-literature
Project description:ObjectiveTo identify demographic, clinical, and hospital factors associated with mortality on readmission within 180 days following an inpatient hospitalization.Study designWe conducted a retrospective cohort study including 33 US children's hospitals in the Pediatric Health Information System from January 2010 to June 2020. Our primary outcome was death during readmission within 180 days of an index hospitalization among children aged 0-18 years. Illness severity during the index hospitalization was defined according to the All Patient-Refined Diagnosis-Related Group-categorized illness severity (ie, minor, moderate, or major/extreme). We performed multivariable logistic regression analysis to identify factors during the index hospitalization associated with mortality during readmission.ResultsAmong 2 677 111 children discharged, 337 385 (12.6%) were readmitted within 180 days of the index hospitalization and 2913 (0.8%) died during readmission. More than one-quarter (26.2%) of deaths among children who were readmitted and died occurred within 10 days after discharge from the index hospitalization. Factors independently associated with mortality during readmission included multiple complex chronic conditions, index admissions lasting >7 days, moderate or severe/extreme illness during the index hospitalization, and public insurance. Children whose race was reported as Black had greater odds of mortality during readmission compared with children of other races.ConclusionsAmong hospitalized children, several demographic and clinical factors present during index hospitalizations were associated with mortality during readmission. Greater odds of mortality during readmission among children whose race was reported as Black likely reflects disparities in social determinants of health and clinical care. Interventions to reduce mortality during readmission may target high-risk populations in the period immediately following discharge.
| S-EPMC9233053 | biostudies-literature
Project description:Objective:To investigate the molecular characteristics of carbapenem-resistant Enterobacteriaceae (CRE) from county hospitals in China. Materials and Methods:Forty-three sequential non-duplicate CRE strains (including 33 Klebsiella pneumoniae isolates, 4 Enterobacter cloacae isolates, 3 Escherichia coli isolates, 1 Serratia marcescens, 1 Morganella morganii and 1 Citrobacter freundii) were collected from 4 county hospitals and 2 municipal hospitals. Antimicrobial susceptibility testing was conducted by broth microdilution method, using 3-aminophenylboronic acid and EDTA and the modified carbapenem inactivation method (mCIM) to screen phenotype of carbapenemase. ?-Lactamases were characterized by polymerase chain reaction (PCR) and DNA sequencing. The transferability of bla NDM-5 was investigated by transformation experiment. Clonal relatedness was evaluated by pulsed-field gel electrophoresis and multilocus sequence typing . Results:The results of antimicrobial susceptibility testing indicated that 43 CRE strains were resistant to most of the antimicrobial agents, except tigecycline and colistin. Overall, 93%, 93%, and 97.7% of these strains were resistant to imipenem, meropenem, and ertapenem, respectively. PCR and DNA sequencing indicated that 67.4% (29/43) were bla KPC-2 positive isolates, in which 3.4% (1/29) was coproduced with bla NDM-1. In addition, 7.0% (3/43), 4.7% (2/43), 4.7% (2/43), 2.3% (1/43), 2.3% (1/43) were bla NDM-1, bla NDM-16, bla NDM-4, bla NDM-5, bla IMP-4 positive isolates, respectively. The 29 bla KPC-2-positive isolates belonged to 12 different PFGE type and designated as ST11 (n=20) and ST15, ST39, ST116, ST667, ST2245, ST2338. The plasmid bearing bla NDM-5 could be transferred into recipient E. coli J53 through transformation. Conclusion:Our study indicated the dissemination of CRE between the tertiary hospitals and secondary hospitals.
| S-EPMC7183775 | biostudies-literature
Project description:BackgroundChildren may be hospitalized at general hospitals or freestanding children's hospitals. Knowledge about how inpatient care differs at these hospitals is important to inform national research and quality efforts.ObjectiveTo describe the volume and characteristics of pediatric hospitalizations at acute care general and freestanding children's hospitals in the United States.Design, patients, and settingCross-sectional study of hospitalizations in the United States among children <18 years, excluding in-hospital births, using the Healthcare Cost and Utilization Project's 2012 Kids' Inpatient Database.MeasurementWe examined differences between hospitalizations at general and freestanding children's hospitals, applying weights to generate national estimates. Reasons for hospitalization were categorized using a pediatric grouper, and differences in hospital volumes were assessed for common diagnoses.ResultsA total of 1,407,822 (standard deviation 50,456) hospitalizations occurred at general hospitals, representing 71.7% of pediatric hospitalizations. Hospitalizations at general hospitals accounted for 63.6% of hospital days and 50.0% of pediatric inpatient healthcare costs. Median volumes of pediatric hospitalizations, per hospital, were significantly lower at general hospitals than freestanding children's hospitals for common medical and surgical diagnoses. Although the most common reasons for hospitalization were similar, the most costly conditions differed.ConclusionsIn 2012, more than 70% of pediatric hospitalizations occurred at general hospitals in the United States. Differences in patterns of care at general hospitals and freestanding children's hospitals may inform clinical programs, research, and quality improvement efforts. Journal of Hospital Medicine 2016;11:743-749. © 2016 Society of Hospital Medicine.
| S-EPMC5467435 | biostudies-literature
Project description:BackgroundEscherichia coli sequence type 131 (ST131), with its multidrug-resistance-associated H30R1 and H30Rx clonal subsets, causes most antimicrobial-resistant E. coli infections in the U.S., especially among veterans. The activity of ceftolozane-tazobactam (C/T), a new beta-lactamase inhibitor agent, against ST131 strains, and E. coli isolates from veterans, is undefined.MethodsWe determined broth microdilution MICs for C/T and five comparators-piperacillin-tazobactam (TZP) levofloxacin (LVX), gentamicin (GEN), ceftazidime (CAZ), and meropenem (MEM)-for 595 clinical E. coli isolates, collected in 2011 from 24 Veterans Affairs Medical Centers across the U.S. Categorical resistance and MICs were compared statistically with resistance category (fluoroquinolone-susceptible, fluoroquinolone-resistant, and extended-spectrum beta-lactamase [ESBL]-producing) and with PCR-defined ST131, H30R1, and H30Rx status.ResultsResistance prevalence was ≤ 6% for C/T (6%) and MEM (0%), vs. from 8.0% (TZP) to 59% (LVX) for the other comparators. MICs generally increased by resistance category, from fluoroquinolone-susceptible through fluoroquinolone-resistant to ESBL, and by clonal subgroup, from non-ST131-H30 through H30R1 to H30Rx. For each comparator agent except MEM, although a significantly greater fraction of resistant than susceptible isolates were C/T-resistant, only a minority of comparator-resistant isolates were C/T-resistant (i.e., 9% if LEV-resistant, 12% if GEN-resistant, 21% if CAZ-resistant, 38% if TZP-resistant).ConclusionsC/T was broadly active against E. coli clinical isolates from veterans, notwithstanding significant variation by resistance category and ST131-H30R1/H30Rx status, outperforming all non-carbapenem comparators. C/T should prove useful as a carbapenem-sparing therapy for multidrug-resistant E. coli ST131 infections, including in veterans.
| S-EPMC6039045 | biostudies-literature
Project description:We analyzed 62 clinical isolates of streptogramin A-resistant (SGA(r)) Staphylococcus aureus collected between 1981 and 2001 in 14 hospitals located in seven French cities. These isolates, including five with decreased susceptibility to glycopeptides, were distributed into 45 antibiotypes and 38 SmaI genotypes. Each of these genotypes included between 1 and 11 isolates, the SmaI patterns of which differed by no more than three bands. Although numerous clones were identified, we observed the spread of monoclonal isolates either within the same hospital or within hospitals in distinct cities and at large time intervals. Hybridization with probes directed against 10 SGA(r) genes (vatA, vatB, vatC, vatD, vatE, vgaA, vgaB, vgaAv, vgbA, and vgbB) revealed six patterns: vgaAv (21 isolates), vatA-vgbA (24 isolates), vgaAv-vatB-vgaB (14 isolates), vgaAv-vatA-vgbA (1 isolate), vgaAv-vatA-vgbA-vatB-vgaB (1 isolate), and vgaA (1 isolate). We detected at least one SGA(r) determinant in all of the tested isolates. vgaAv, which is part of the recently characterized transposon Tn5406, was found in 59.7% of the tested isolates. Of the 16 streptogramin B-susceptible isolates, 14 carried vgaAv alone and were susceptible to the mixtures of streptogramins, whereas the 2 isolates carrying vgaAv-vatB-vgaB were resistant to these mixtures. vatA-vgbA was found on plasmids of the same apparent size in 26 (42%) of the tested clinical isolates from 18 unrelated SmaI genotypes. The possible dissemination of some of the multiple clones characterized in the present study with an expected increased selective pressure of streptogramins following the recent licensing of Synercid (quinupristin-dalfopristin) must be carefully monitored.
| S-EPMC149720 | biostudies-literature
Project description:Quantifying how close hospitals came to exhausting capacity during the outbreak of pandemic influenza A (H1N1) 2009 can help the health care system plan for more virulent pandemics. This ecologic analysis used emergency department (ED) and inpatient data from 34 US children's hospitals. For the 11-week pandemic (H1N1) 2009 period during fall 2009, inpatient occupancy reached 95%, which was lower than the 101% occupancy during the 2008-09 seasonal influenza period. Fewer than 1 additional admission per 10 inpatient beds would have caused hospitals to reach 100% occupancy. Using parameters based on historical precedent, we built 5 models projecting inpatient occupancy, varying the ED visit numbers and admission rate for influenza-related ED visits. The 5 scenarios projected median occupancy as high as 132% of capacity. The pandemic did not exhaust inpatient bed capacity, but a more virulent pandemic has the potential to push children's hospitals past their maximum inpatient capacity.
| S-EPMC3320222 | biostudies-literature
Project description:BackgroundEscherichia coli sequence type 131 (ST131), typically fluoroquinolone-resistant (FQ-R) and/or extended-spectrum ?-lactamase (ESBL)-producing, has emerged globally. We assessed its prevalence and characteristics among US veterans.MethodsIn 2011, 595 de-identified E. coli clinical isolates were collected systematically within 3 resistance groups (FQ-susceptible [FQ-S], FQ-R, and ESBL-producing) from 24 nationally distributed Veterans Affairs Medical Centers (VAMCs). ST131 and its H30 subclone were detected by polymerase chain reaction and compared with other E. coli for molecular traits, source, and resistance profiles.ResultsST131 accounted for 78% (184/236) of FQ-R and 64.2% (79/123) of ESBL-producing isolates, but only 7.2% (17/236) of FQ-S isolates (P < .001). The H30 subclone accounted for ?95% of FQ-R and ESBL-producing, but only 12.5% of FQ-S, ST131 isolates (P < .001). By back-calculation, 28% of VAMC E. coli isolates nationally represented ST131. Overall, ST131 varied minimally in prevalence by specimen type, inpatient/outpatient source, or locale; was the most prevalent ST, followed distantly by ST95 and ST12 (13% each); and accounted for ?40% (?-lactams), >50% (trimethoprim-sulfamethoxazole , multidrug), or >70% (ciprofloxacin, gentamicin) of total antimicrobial resistance. FQ-R and ESBL-producing ST131 isolates had higher virulence scores than corresponding non-ST131 isolates. ST131 pulsotypes overlapped extensively among VAMCs.ConclusionsAmong US veterans, ST131, primarily its H30 subclone, accounts for most antimicrobial-resistant E. coli and is the dominant E. coli strain overall. Possible contributors include multidrug resistance, extensive virulence gene content, and ongoing transmission. Focused attention to ST131, especially its H30 subclone, could reduce infection-related morbidity, mortality, and costs among veterans.
| S-EPMC3792724 | biostudies-literature