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Background: The Centers for Disease Control and Prevention’s Emerging Infections Program conducts active laboratory- and population-based surveillance for carbapenem-resistant Enterobacterales (CRE) and extended spectrum beta-lactamase-producing Enterobacterales (ESBL-E). To better understand the U.S. epidemiology of these organisms among children, we determined the incidence of pediatric CRE and ESBL-E cases and described their clinical characteristics. Methods: Surveillance was conducted among children <18 years of age for CRE from 2016–2020 in 10 sites, and for ESBL-E from 2019–2020 in 6 sites. Among catchment-area residents, an incident CRE case was defined as the first isolation of Escherichia coli, Enterobacter cloacae complex, Klebsiella aerogenes, K. oxytoca, or K. pneumoniae in a 30-day period resistant to ≥1 carbapenem from a normally sterile site or urine. An incident ESBL-E case was defined as the first isolation of E. coli, K. pneumoniae, or K. oxytoca in a 30-day period resistant to any third-generation cephalosporin and non-resistant to all carbapenems from a normally sterile site or urine. Case records were reviewed. Results: Among 159 CRE cases, 131 (82.9%) were isolated from urine and 19 (12.0%) from blood; median age was 5 years (IQR 1–10) and 94 (59.1%) were female. Combined CRE incidence rate per 100,000 population by year ranged from 0.47 to 0.87. Among 207 ESBL-E cases, 160 (94.7%) were isolated from urine and 6 (3.6%) from blood; median age was 6 years (IQR 2–15) and 165 (79.7%) were female. Annual ESBL incidence rate per 100,000 population was 26.5 in 2019 and 19.63 in 2020. Incidence rates of CRE and ESBL-E were >2-fold higher in infants (children <1 year) than other age groups. Among those with data available, CRE cases were more likely than ESBL-E cases to have underlying conditions (99/158 [62.7%] versus 59/169 [34.9%], P<0.0001), prior healthcare exposures (74/158 [46.8%] versus 38/169 [22.5%], P<0.0001), and be hospitalized for any reason around time of their culture collection (75/158 [47.5%] versus 38/169 [22.5%], P<0.0001); median duration of admission was 18 days [IQR 3–103] for CRE versus 10 days [IQR 4–43] for ESBL-E. Urinary tract infection was the most frequent infection for CRE (89/158 [56.3%]) and ESBL-E (125/169 [74.0%]) cases. Conclusion: CRE infections occurred less frequently than ESBL-infections in U.S. children but were more often associated with healthcare risk factors and hospitalization. Infants had highest incidence of CRE and ESBL-E. Continued surveillance, infection prevention and control efforts, and antibiotic stewardship outside and within pediatric care are needed
The incidence of infections from extended-spectrum β-lactamase (ESBL)–producing Enterobacterales (ESBL-E) is increasing in the United States. We describe the epidemiology of ESBL-E at 5 Emerging Infections Program (EIP) sites.
During October–December 2017, we piloted active laboratory- and population-based (New York, New Mexico, Tennessee) or sentinel (Colorado, Georgia) ESBL-E surveillance. An incident case was the first isolation from normally sterile body sites or urine of Escherichia coli or Klebsiella pneumoniae/oxytoca resistant to ≥1 extended-spectrum cephalosporin and nonresistant to all carbapenems tested at a clinical laboratory from a surveillance area resident in a 30-day period. Demographic and clinical data were obtained from medical records. The Centers for Disease Control and Prevention (CDC) performed reference antimicrobial susceptibility testing and whole-genome sequencing on a convenience sample of case isolates.
We identified 884 incident cases. The estimated annual incidence in sites conducting population-based surveillance was 199.7 per 100,000 population. Overall, 800 isolates (96%) were from urine, and 790 (89%) were E. coli. Also, 393 cases (47%) were community-associated. Among 136 isolates (15%) tested at the CDC, 122 (90%) met the surveillance definition phenotype; 114 (93%) of 122 were shown to be ESBL producers by clavulanate testing. In total, 111 (97%) of confirmed ESBL producers harbored a blaCTX-M gene. Among ESBL-producing E. coli isolates, 52 (54%) were ST131; 44% of these cases were community associated.
The burden of ESBL-E was high across surveillance sites, with nearly half of cases acquired in the community. EIP has implemented ongoing ESBL-E surveillance to inform prevention efforts, particularly in the community and to watch for the emergence of new ESBL-E strains.
Using a machine-learning model, we examined drivers of antibiotic prescribing for antibiotic-inappropriate acute respiratory illnesses in a large US claims data set. Antibiotics were prescribed in 11% of the 42 million visits in our sample. The model identified outpatient setting type, patient age mix, and state as top drivers of prescribing.
Background: Automated testing instruments (ATIs) are commonly used by clinical microbiology laboratories to perform antimicrobial susceptibility testing (AST), whereas public health laboratories may use established reference methods such as broth microdilution (BMD). We investigated discrepancies in carbapenem minimum inhibitory concentrations (MICs) among Enterobacteriaceae tested by clinical laboratory ATIs and by reference BMD at the CDC. Methods: During 2016–2018, we conducted laboratory- and population-based surveillance for carbapenem-resistant Enterobacteriaceae (CRE) through the CDC Emerging Infections Program (EIP) sites (10 sites by 2018). We defined an incident case as the first isolation of Enterobacter spp (E. cloacae complex or E. aerogenes), Escherichia coli, Klebsiella pneumoniae, K. oxytoca, or K. variicola resistant to doripenem, ertapenem, imipenem, or meropenem from normally sterile sites or urine identified from a resident of the EIP catchment area in a 30-day period. Cases had isolates that were determined to be carbapenem-resistant by clinical laboratory ATI MICs (MicroScan, BD Phoenix, or VITEK 2) or by other methods, using current Clinical and Laboratory Standards Institute (CLSI) criteria. A convenience sample of these isolates was tested by reference BMD at the CDC according to CLSI guidelines. Results: Overall, 1,787 isolates from 112 clinical laboratories were tested by BMD at the CDC. Of these, clinical laboratory ATI MIC results were available for 1,638 (91.7%); 855 (52.2%) from 71 clinical laboratories did not confirm as CRE at the CDC. Nonconfirming isolates were tested on either a MicroScan (235 of 462; 50.9%), BD Phoenix (249 of 411; 60.6%), or VITEK 2 (371 of 765; 48.5%). Lack of confirmation was most common among E. coli (62.2% of E. coli isolates tested) and Enterobacter spp (61.4% of Enterobacter isolates tested) (Fig. 1A), and among isolates testing resistant to ertapenem by the clinical laboratory ATI (52.1%, Fig. 1B). Of the 1,388 isolates resistant to ertapenem in the clinical laboratory, 1,006 (72.5%) were resistant only to ertapenem. Of the 855 nonconfirming isolates, 638 (74.6%) were resistant only to ertapenem based on clinical laboratory ATI MICs. Conclusions: Nonconfirming isolates were widespread across laboratories and ATIs. Lack of confirmation was most common among E. coli and Enterobacter spp. Among nonconfirming isolates, most were resistant only to ertapenem. These findings may suggest that ATIs overcall resistance to ertapenem or that isolate transport and storage conditions affect ertapenem resistance. Further investigation into this lack of confirmation is needed, and CRE case identification in public health surveillance may need to account for this phenomenon.
Background: Certain nursing home (NH) resident care tasks have a higher risk for multidrug-resistant organisms (MDRO) transfer to healthcare personnel (HCP), which can result in transmission to residents if HCPs fail to perform recommended infection prevention practices. However, data on HCP-resident interactions are limited and do not account for intrafacility practice variation. Understanding differences in interactions, by HCP role and unit, is important for informing MDRO prevention strategies in NHs. Methods: In 2019, we conducted serial intercept interviews; each HCP was interviewed 6–7 times for the duration of a unit’s dayshift at 20 NHs in 7 states. The next day, staff on a second unit within the facility were interviewed during the dayshift. HCP on 38 units were interviewed to identify healthcare personnel (HCP)–resident care patterns. All unit staff were eligible for interviews, including certified nursing assistants (CNAs), nurses, physical or occupational therapists, physicians, midlevel practitioners, and respiratory therapists. HCP were asked to list which residents they had cared for (within resident rooms or common areas) since the prior interview. Respondents selected from 14 care tasks. We classified units into 1 of 4 types: long-term, mixed, short stay or rehabilitation, or ventilator or skilled nursing. Interactions were classified based on the risk of HCP contamination after task performance. We compared proportions of interactions associated with each HCP role and performed clustered linear regression to determine the effect of unit type and HCP role on the number of unique task types performed per interaction. Results: Intercept-interviews described 7,050 interactions and 13,843 care tasks. Except in ventilator or skilled nursing units, CNAs have the greatest proportion of care interactions (interfacility range, 50%–60%) (Fig. 1). In ventilator and skilled nursing units, interactions are evenly shared between CNAs and nurses (43% and 47%, respectively). On average, CNAs in ventilator and skilled nursing units perform the most unique task types (2.5 task types per interaction, Fig. 2) compared to other unit types (P < .05). Compared to CNAs, most other HCP types had significantly fewer task types (0.6–1.4 task types per interaction, P < .001). Across all facilities, 45.6% of interactions included tasks that were higher-risk for HCP contamination (eg, transferring, wound and device care, Fig. 3). Conclusions: Focusing infection prevention education efforts on CNAs may be most efficient for preventing MDRO transmission within NH because CNAs have the most HCP–resident interactions and complete more tasks per visit. Studies of HCP-resident interactions are critical to improving understanding of transmission mechanisms as well as target MDRO prevention interventions.
Funding: Centers for Disease Control and Prevention (grant no. U01CK000555-01-00)
Disclosures: Scott Fridkin, consulting fee, vaccine industry (spouse)
Background: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a frequent cause of healthcare-associated infections (HAIs). The CDC Emerging Infections Program (EIP) conducted population and laboratory-based surveillance of CRPA in selected areas in 8 states from August 1, 2016, through July 31, 2018. We aimed to describe the molecular epidemiology and mechanisms of resistance of CRPA isolates collected through this surveillance. Methods: We defined a case as the first isolate of P. aeruginosa resistant to imipenem, meropenem, or doripenem from the lower respiratory tract, urine, wounds, or normally sterile sites identified from a resident of the EIP catchment area in a 30-day period; EIP sites submitted a systematic random sample of isolates to CDC for further characterization. Of 1,021 CRPA clinical isolates submitted, 707 have been sequenced to date using an Illumina MiSeq. Sequenced genomes were classified using the 7-gene multilocus sequence typing (MLST) scheme, and a core genome MLST (cgMLST) scheme was used to determine phylogeny. Antimicrobial resistance genes were identified using publicly available databases, and chromosomal mechanisms of carbapenem resistance were determined using previously validated genetic markers. Results: There were 189 sequence types (STs) among the 707 sequenced genomes (Fig. 1). The most frequently occurring were high-risk clones ST235 (8.5%) and ST298 (4.7%), which were found across all EIP sites. Carbapenemase genes were identified in 5 (<1%) isolates. Overall, 95.6% of the isolates had chromosomal mutations associated with carbapenem resistance: 93.2% had porinD-associated mutations that decrease membrane permeability to the drugs; 24.8% had mutations associated with overexpression of the multidrug efflux pump MexAB-OprM; and 22.9% had mutations associated with overexpression of the endogenous β-lactamase ampC. More than 1 such chromosomal resistance mutation type was present in 37.8% of the isolates. Conclusions: The diversity of the sequence types demonstrates that HAIs caused by CRPA can arise from a variety of strains and that high-risk clones are broadly disseminated across the EIP sites but are a minority of CRPA strains overall. Carbapenem resistance in P. aeruginosa was predominantly driven by chromosomal mutations rather than acquired mechanisms (ie, carbapenemases). The diversity of the CRPA isolates and the lack of carbapenemase genes suggest that this ubiquitous pathogen can readily evolve chromosomal resistance mechanisms, but unlike carbapenemases, these cannot be easily spread through horizontal transfer.
We used all 167 typhoon warnings issued by the Taiwanese Central Weather Bureau from 1958–2006 to assess the long-term effect of cyclone disturbance on vascular epiphytes. Tracks and eyes of past typhoons were plotted as circles with radii of Beaufort scale 7 and 10, and the frequency of each cohort in 1-km2 grid cells was calculated. The presence of vascular epiphytes in the same grid cells was predicted using species distribution models (SDMs). First, we used herbarium specimens and other sources to compile a comprehensive georeferenced vascular epiphyte database that contained 39084 records in 331 species. Next, we assigned each epiphyte record to a cell in the same 1-km2 grid as above. Finally, we used SDMs (MaXent), based on 30 environmental variables except typhoon frequency, to predict the potential presence of each species in the grid cells. For our analysis we only considered cells east of the central mountain ridge where typhoons hit with full force. After elimination of rare species and species that could not be validated in the SDMs, we were left with 156 epiphyte species in 10725 1-km2 cells. The number of projected species in the cells was 36.5 on average, varying between two and 82 species. Correlation analyses showed that, over time, typhoons led to a decrease in epiphyte richness at Beaufort scale 7 and 10 (Pearson's r = −0.07 and −0.08 respectively). Ferns, orchids, hemiepiphytes and dicotyledons generally showed the same pattern, except hemiepiphytes that showed a positive correlation at B7 (Pearson's r = 0.15). A partial canonical correspondence ordination analysis showed that, independent of temperature- and rainfall-related variables, Beaufort scale 7 and 10 typhoons also had significant influence on the species composition of the vascular epiphyte communities in the landscape. We recommend in situ monitoring of epiphytes over a long period to corroborate the suggestion from this indirect study that typhoons have a long-term effect on the distribution of epiphytes in Taiwan.
Long-term care facility (LTCF) residents are at increased risk of Clostridium difficile infection (CDI). However, little is known about the incidence, recurrence, and severity of CDI in LTCFs or the extent to which acute care exposure contributes to CDI in LTCFs. We describe the epidemiology of CDI in a cohort of LTCF residents in Monroe County, New York, where recent estimates suggest a CDI incidence in hospitals of 9.2 cases per 10,000 patient-days.
Population-based surveillance study.
Monroe County, New York.
LTCF residents with onset of CDI while in the LTCF or less than 4 calendar-days after hospital admission from the LTCF from January 1 through December 31, 2010.
We conducted surveillance for CDI in residents of 33 LTCFs. A CDI case was defined as a stool specimen positive for C. difficile obtained from a patient without a C. difficile-positive specimen in the previous 8 weeks; recurrence was defined as a stool specimen positive for C. difficile obtained between 2 and 8 weeks after the last C. difficile-positive stool specimen.
There were 425 LTCF-onset cases and 184 recurrences, which yielded an incidence of 2.3 cases per 10,000 resident-days (interquartile range [IQR], 1.2–3.3) and a recurrence rate of 1.0 case per 10,000 resident-days (IQR, 0.3–1.4). The cases occurred in 394 LTCF residents, and 52% of these residents developed CDI within 4 weeks after hospital discharge. Hospitalization for CDI occurred in 70 cases (16%). Of those cases that involved hospitalization for CDI, 70% were severe CDI, and 23% ended in death within 30 days after hospital admission.
CDI incidence in Monroe County LTCFs is one-fourth the incidence among hospitalized patients. Approximately 50% of LTCF-onset cases occurred more than 4 weeks after hospital discharge, which emphasizes that prevention of CDI transmission should go beyond acute care settings.
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