13 results on '"Alison Laufer Halpin"'
Search Results
2. Aggressive Colonization Screening and Infection Control Measures in Containment of NDM-5 Carbapenemase-Producing CRE
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Heather Moulton-Meissner, Kate Tyner, Tom Safranek, Gillian McAllister, Maroya Spalding Walters, Ishrat Kamal-Ahmed, Maureen Tierney, Teresa Fitzgerald, Alison Laufer Halpin, and Muhammad Salman Ashraf
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Microbiology (medical) ,Containment (computer programming) ,Infectious Diseases ,Epidemiology ,business.industry ,Medicine ,Infection control ,Colonization ,Carbapenemase producing ,business ,Microbiology - Abstract
Background: In April 2019, Nebraska Public Health Laboratory identified an NDM-producing Enterobacter cloacae from a urine sample from a rehabilitation inpatient who had recently received care in a specialized unit (unit A) of an acute-care hospital (ACH-A). After additional infections occurred at ACH-A, we conducted a public health investigation to contain spread. Methods: A case was defined as isolation of NDM-producing carbapenem-resistant Enterobacteriaceae (CRE) from a patient with history of admission to ACH-A in 2019. We conducted clinical culture surveillance, and we offered colonization screening for carbapenemase-producing organisms to all patients admitted to unit A since February 2019. We assessed healthcare facility infection control practices in ACH-A and epidemiologically linked facilities by visits from the ICAP (Infection Control Assessment and Promotion) Program. The recent medical histories of case patients were reviewed. Isolates were evaluated by whole-genome sequencing (WGS). Results: Through June 2019, 7 cases were identified from 6 case patients: 4 from clinical cultures and 3 from 258 colonization screens including 1 prior unit A patient detected as an outpatient (Fig. 1). Organisms isolated were Klebsiella pneumoniae (n = 5), E. cloacae (n = 1), and Citrobacter freundii (n = 1); 1 patient had both NDM-producing K. pneumoniae and C. freundii. Also, 5 case patients had overlapping stays in unit A during February–May 2019 (Fig. 2); common exposures in unit A included rooms in close proximity, inhabiting the same room at different times and shared caregivers. One case-patient was not admitted to unit A but shared caregivers, equipment, and devices (including a colonoscope) with other case patients while admitted to other ACH-A units. No case patients reported travel outside the United States. Screening at epidemiologically linked facilities and clinical culture surveillance showed no evidence of transmission beyond ACH-A. Infection control assessments at ACH-A revealed deficiencies in hand hygiene, contact precautions adherence, and incomplete cleaning of shared equipment within and used to transport to/from a treatment room in unit A. Following implementation of recommended infection control interventions, no further cases were identified. Finally, 5 K. pneumoniae of ST-273 were related by WGS including carriage of NDM-5 and IncX3 plasmid supporting transmission of this strain. Further analysis is required to relate IncX3 plasmid carriage and potential transmission to other organisms and sequence types identified in this study. Conclusions: We identified a multiorganism outbreak of NDM-5–producing CRE in an ACH specialty care unit. Transmission was controlled through improved infection control practices and extensive colonization screening to identify asymptomatic case-patients. Multiple species with NDM-5 were identified, highlighting the potential role of genotype-based surveillance.Funding: NoneDisclosures: Muhammad Salman Ashraf reports that he is the principal investigator for a study funded by an investigator-initiated research grant.
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- 2020
3. Epidemiologic Characteristics of ESBL-Producing ST131 E. coli Identified Through the Emerging Infections Program, 2017
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Elizabeth Basiliere, Hannah E. Reses, Daniel Muleta, Jonathan Daniels, Davina Campbell, Marion A. Kainer, Joseph D. Lutgring, Chris Bower, Richard A. Stanton, Isaac See, Nadezhda Duffy, Alison Laufer Halpin, Benji Byrd-Warner, and Ghinwa Dumyati
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Microbiology (medical) ,Infectious Diseases ,Epidemiology ,Emerging infections ,Esbl production ,Biology ,Microbiology - Abstract
Background: Extended-spectrum β-lactamase–producing (ESBL) Escherichia coli infection incidence is increasing in the United States. This increase may be due to the rapid expansion of ST131, which is now the predominant ESBL strain globally, often multidrug resistant, and has been shown to establish longer-term human colonization than other E. coli strains. We assessed potential risk factors that distinguish ST131 from other ESBL E. coli. Methods: From October 1 through December 31, 2017, 5 CDC Emerging Infections Program (EIP) sites pilot tested active, laboratory-based surveillance in selected counties in Colorado, Georgia, New Mexico, New York, and Tennessee. An E. coli case was defined as the first isolation from a normally sterile body site or urine in a surveillance area resident in a 30-day period resistant to 1 extended-spectrum cephalosporin antibiotic and susceptible or intermediate to all carbapenem antibiotics tested. Epidemiologic data were collected from case patients’ medical records. A convenience sample of 117 E. coli isolates from case patients was collected. All isolates underwent whole-genome sequencing to determine sequence type and the presence of ESBL genes. We compared ST131 E. coli epidemiology to other ESBL E. coli. Results: Among 117 E. coli isolates, 97 (83%) were ESBL producers. Of the 97 ESBL E. coli, 52 (54%) were ST131 (range, for 4 EIP sites submitting >10 isolates: 25%–88%; P < .001). Other common STs were ST38 (12%) and ST10 (5%). ST131 infections were more likely to be healthcare-associated than non-ST131 (56% vs 36%; P = .05) (Table 1). Among specific prior healthcare exposures, only residence in long-term care facilities (LTCFs) in the year before culture was more common among ST131 case patients (29% vs 11%; P = .03). Notably, 85% of ESBL E. coli collected from LTCF residents were ST131. ST131 E. coli were more common among patients with underlying medical conditions (81% vs 60%; P = .02). No statistically significant difference by sex, race, age, culture source, location of culture collection, and frequency of antibiotic use in the prior 30 days was observed. Conclusions:The prevalence of ST131 E. coli varies regionally. The association between ST131 and LTCFs suggests that these may be particularly important settings for ST131 acquisition. Improving infection control measures that limit ESBL transmission in these settings and preventing dissemination in facilities receiving patients from LTCFs may be necessary to contain ST131 spread.Funding: NoneDisclosures: None
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- 2020
4. Transmission of Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae in Georgia, 2018–2019
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Richard A. Stanton, Alison Laufer Halpin, David C. Ham, Gillian McAllister, Jacobs Slifka Kara, Tonia Parrott, Patricia Kopp, Gebre Tiga, Maroya Spalding Walters, Mary Connelly, Elizabeth Smith, Jeanne Negley, and Cherie Drenzek
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Microbiology (medical) ,Infectious Diseases ,Transmission (mechanics) ,Epidemiology ,law ,Klebsiella pneumoniae ,Carbapenemase producing ,Biology ,biology.organism_classification ,Microbiology ,law.invention - Abstract
Background: In April 2019, the Georgia Department of Public Health (DPH) initiated whole-genome sequencing (WGS) on NDM-producing Enterobacteriaceae identified since January 2018. The WGS data analyzed at CDC identified related Klebsiella pneumoniae isolates with hypervirulence markers from 2 patients. Carbapenemase-producing hypervirulent K. pneumoniae (CP-hvKP) are rarely reported in the United States, but they can to cause serious, highly resistant, invasive infections. We conducted an investigation to identify cases and prevent spread. Methods: We defined a case as NDM-producing K. pneumoniae with ≥4 hypervirulence markers identified by WGS, isolated from any specimen source from a Georgia patient. We reviewed the case patient’s medical history to identify potentially affected facilities. We also performed PCR-based colonization screening and retrospective and prospective laboratory-based surveillance. Finally, we assessed facility infection control practices. Results: Overall, 7 cases from 3 case patients (A, B, and C) were identified (Fig. 1). The index case specimen was collected from case-patient A at ventilator-capable skilled nursing facility 1 (vSNF1) in May 2018. Case-patient A had been hospitalized for 1 month in India before transfer to the United States. Case-patient B’s initial isolate was collected in January 2019 on admission to vSNF2 from a critical access hospital (CAH). The CAH laboratory retrospectively identified case-patient C, who overlapped with case-patient B at the CAH in October 2018. The CAH and the vSNF2 are geographically distant from vSNF1. Case-patients B and C had no known epidemiologic links to case-patient A. Colonization screening occurred at vSNF1 in May 2018, following detection of NDM-producing K. pneumoniae from case-patient A ∼1 year before determining that the isolate carried hypervirulence markers. Among 30 residents screened, 1 had NDM and several had other carbapenemases. Subsequent screening did not identify additional NDM. Colonization screening of 112 vSNF2 residents and 13 CAH patients in 2019 did not reveal additional case patients; case-patient B resided at vSNF2 at the time of screening and remained colonized. At all 3 facilities, the DPH assessed infection control practices, issued recommendations to resolve lapses, and monitored implementation. The DPH sequenced all 27 Georgia NDM–K. pneumoniae isolates identified since January 2018; all were different multilocus sequence types from the CP-hvKP isolates, and none possessed hypervirulence markers. Conclusions: We hypothesize that CP-hvKP was imported by a patient hospitalized in India and spread to 3 Georgia facilities in 2 distinct geographic regions through indirect patient transfers. Although a response to contain NDM at vSNF1 in 2018 likely limited CP-hvKP transmission, WGS identified hvKP and established the relatedness of isolates from distinct regions, thereby directing the DPH’s additional containment activities to halt transmission.Funding: NoneDisclosures: None
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- 2020
5. Improving Confirmatory Testing for the Antimicrobial Resistance Surveillance Network in Ethiopia
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Michele Parsons, Degefu Beyene, Susan Bollinger, Matthew Westercamp, Aynalem Mohamed, Dawit Assefa, Elizabeth Thomas, Michael Omondi, Ashutosh Wadhwa, Gebrie Alebachew, Kathleen Gallagher, Mequanit Mitiku, Kibra Hailu, Surafel Fentaw Dinku, Amare Berhanu, Carmen Hazim, Theresa Kanter, and Alison Laufer Halpin
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Microbiology (medical) ,Medical education ,medicine.medical_specialty ,Infectious Diseases ,Workflow ,Surveillance data ,Epidemiology ,Computer science ,Public health ,medicine ,Monitoring and evaluation ,Laboratory testing - Abstract
Background: In July 2017, the Ethiopian Public Health Institute (EPHI) launched an antimicrobial resistance (AMR) surveillance network at 4 sentinel laboratories. The National Clinical Bacteriology and Mycology Laboratory (NRL) at EPHI performs monthly confirmatory testing on a subset of isolates submitted by these sites. We assessed the existing confirmatory testing program to identify gaps and develop solutions, including a monitoring and evaluation (M&E) system. Methods: We assembled a technical working group (TWG) of key stakeholders. Laboratory site visits included workflow observation, process mapping, document review, and technologist interviews. Proposed solutions to observed gaps were drafted in formats consistent with their intended application. Feedback from the TWG was incorporated into final drafts. Available AMR network staff members were trained remotely, and they will train remaining staff. Results: Table 1 describes major gaps and solutions identified. Conclusions: Confirmatory testing provides a mechanism to evaluate laboratory testing proficiency, target improvements, and estimate surveillance data quality, yet standardized methods were lacking. Our efforts highlight key components of confirmatory testing programs and provide a model for use in laboratories with similar needs.Funding: NoneDisclosures: None
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- 2020
6. Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected Through the Emerging Infections Program
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Maroya Spalding Walters, Ghinwa Dumyati, P. Maureen Cassidy, Jonathan Daniels, Linda Li, Jesse T. Jacob, Jacquelyn Mounsey, Elisabeth Vaeth, Erin C Phipps, Julian E. Grass, Lucy E. Wilson, Joseph D. Lutgring, Kyle Schutz, Rebecca Tsay, Maria Karlsson, Richard A. Stanton, Ruth Lynfield, Alison Laufer Halpin, Emily B. Hancock, Davina Campbell, and Erin Breaker
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Microbiology (medical) ,Whole genome sequencing ,Infectious Diseases ,Epidemiology ,Emerging infections ,Carbapenem resistant Pseudomonas aeruginosa ,Biology ,Microbiology - Abstract
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 (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.Funding: NoneDisclosures: None
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- 2020
7. Molecular Epidemiology and Outcomes of Patients with Carbapenem-Resistant Enterobacteriaceae Bacteriuria, Atlanta 2012–2015
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Gillian Smith, Sarah W. Satola, Maria Karlsson, Uzma Ansari, Jesse T. Jacob, Alison Laufer Halpin, Robert A. Petit, Adrian Lawson, Chris Bower, Jessica Howard-Anderson, Monica M. Farley, Gillian McAllister, and Joseph D. Lutgring
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Microbiology (medical) ,medicine.medical_specialty ,Infectious Diseases ,Molecular epidemiology ,Epidemiology ,business.industry ,Internal medicine ,medicine ,Bacteriuria ,Carbapenem-resistant enterobacteriaceae ,medicine.disease ,business - Abstract
Background: Carbapenem-resistant Enterobacteriaceae (CRE) represent a significant antibiotic resistance threat, in part because carbapenemase genes can spread on mobile genetic elements. Here, we describe the molecular epidemiology and outcomes of patients with CRE bacteriuria from the same city in a nonoutbreak setting. Methods: The Georgia Emerging Infections Program performs active, population-based CRE surveillance in Atlanta. We studied a cohort of patients with CRE (resistant to all tested third-generation cephalosporins and ≥1 carbapenem, excluding ertapenem) first identified in urine, and not in a prior or simultaneous sterile site, between 2012 and 2015. Whole-genome sequencing (WGS) was performed on a convenience sample. We obtained epidemiologic and outcome data through chart review and Georgia Vital Statistics records (90-day mortality). Using WGS, we created a core-genome alignment-based phylogenetic tree of the Klebsiella pneumoniae isolates and calculated the SNP difference between each sample. Using SAS version 9.4 software, we performed the Fisher exact test and univariable odds ratios (OR) with 95% CI to compare patient isolates with and without a carbapenemase gene. Results: Among 81 patients included, the median age was 68 (IQR, 57–74) years, and most were female (58%), black (60%), and resided in a long-term care facility 4 days prior to culture isolation (53%). Organisms isolated were K. pneumoniae (84%), Escherichia coli (7%), Enterobacter cloacae (7%), and Klebsiella oxytoca (1%). WGS identified at least 1 β-lactamase gene in 91% of the isolates; 85% contained a carbapenemase gene, the most frequent of which was blaKPC-3 (94%). Patients with CRE containing a carbapenemase gene were more likely to be black (OR, 3.7; 95% CI, 1.0–13.8) and to have K. pneumoniae (OR, 8.9; 95% CI, 2.2–35.0). Using a core-genome alignment of 3,708 genes (~63% of the complete genome), we identified a median of 67 (IQR, 23–3,881) SNP differences between each K. pneumoniae isolate. A phylogenetic tree identified clustering around carbapenemase gene and multilocus sequence type (84% were ST 258) but not based on referring laboratory or county of residence (Fig. 1). Although 7% of patients developed an invasive CRE infection within 1 year and 21% died within 90 days, having a carbapenemase gene was not associated with these outcomes. Conclusions: Molecular sequencing of a convenience sample of CRE bacteriuria support K. pneumoniae ST258 harboring blaKPC-3 being distributed throughout the Atlanta area, across the healthcare continuum. Overall mortality was high in this population, but the presence of carbapenemase genes was not associated with worse outcomes.Funding: NoneDisclosures: NoneDisclosures: NoneFunding: None
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- 2020
8. Carbapenemase-Producing, Carbapenem-Resistant Acinetobacter baumannii: Summary of CDC Consultations, 2017–2019
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Gillian McAllister, David C. Ham, Alicia Shugart, Richard Brooks, Maroya Spalding Walters, Lauren Epstein, Alison Laufer Halpin, Snigdha Vallabhaneni, and Sarah E Gilbert
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Microbiology (medical) ,medicine.medical_specialty ,biology ,Epidemiology ,business.industry ,Public health ,Carbapenemase producing ,Burn units ,medicine.disease ,biology.organism_classification ,Acinetobacter baumannii ,Nursing Stations ,Infectious Diseases ,Health care ,Medicine ,Infection control ,Medical emergency ,business ,Carbapenem resistant Acinetobacter baumannii - Abstract
Background: Carbapenemase-producing carbapenem-resistant Acinetobacter baumannii (CP-CRAB) are a public health threat due to potential for widespread dissemination and limited treatment options. We describe CDC consultations for CP-CRAB to better understand transmission and identify prevention opportunities. Methods: We defined CP-CRAB as CRAB isolates with a molecular test detecting KPC, NDM, VIM, or IMP carbapenemases or a plasmid-mediated oxacillinase (OXA-23, OXA-24/40, OXA-48, OXA-58, OXA-235/237). We reviewed the CDC database of CP-CRAB consultations with health departments from January 1, 2017, through June 1, 2019. Consultations were grouped into 3 categories: multifacility clusters, single-facility clusters, and single cases. We reviewed the size, setting, environmental culturing results, and identified infection control gaps for each consultation. Results: We identified 29 consultations involving 294 patients across 19 states. Among 9 multifacility clusters, the median number of patients was 12 (range, 2–87) and the median number of facilities was 2 (range, 2–6). Among 9 single-facility clusters, the median number of patients was 5 (range, 2–50). The most common carbapenemase was OXA-23 (Table 1). Moreover, 16 consultations involved short-stay acute-care hospitals, and 6 clusters involved ICUs and/or burn units. Also, 8 consultations involved skilled nursing facilities. Environmental sampling was performed in 3 consultations; CP-CRAB was recovered from surfaces of portable, shared equipment (3 consultations), inside patient rooms (3 consultations) and nursing stations (2 consultations). Lapses in environmental cleaning and interfacility communication were common across consultations. Among 11 consultations for single CP-CRAB cases, contact screening was performed in 7 consultations and no additional CP-CRAB was identified. All 4 patients with NDM-producing CRAB reported recent international travel. Conclusions: Consultations for clusters of oxacillinase-producing CP-CRAB were most often requested in hospitals and skilled nursing facilities. Healthcare facilities and public health authorities should be vigilant for possible spread of CP-CRAB via shared equipment and the potential for CP-CRAB spread to connected healthcare facilities.Funding: NoneDisclosures: None
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- 2020
9. Changing US Epidemiology of NDM-Producing Carbapenem-Resistant Enterobacteriaceae, 2017–2019
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Gillian McAllister, Maroya Spalding Walters, Alison Laufer Halpin, Lauren Epstein, Alicia Shugart, Karim E. Morey, Anu Paranandi, Erisa Sula, Alexander J. Kallen, Amanda R Smith, Randy Downing, Jennifer Y Huang, Rebekah Carman, Diane Noel, P. Maureen Cassidy, Adrian Lawsin, and Garrett Mahon
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Microbiology (medical) ,medicine.medical_specialty ,Veterinary medicine ,biology ,Epidemiology ,Public health ,Enterobacter ,Carbapenem-resistant enterobacteriaceae ,biology.organism_classification ,Enterobacteriaceae ,Klebsiella spp ,Single strain ,Infectious Diseases ,Antibiotic resistance ,medicine - Abstract
Background: Due to limited therapeutic options and potential for spread, carbapenem-resistant Enterobacteriaceae (CRE)-producing New Delhi metallo-β-lactamases (NDMs) are a public health priority. We investigated the epidemiology of NDM-producing CRE reported to the CDC to clarify its distribution and relative prevalence. Methods: The CDC’s Antibiotic Resistance Laboratory Network supports molecular testing of CRE for 5 carbapenemases nationally. Although KPC is the most common carbapenemase in the United States, non-KPC carbapenemases are a growing concern. We analyzed CRE with any of 4 non-KPC plasmid-mediated carbapenemases (NDM, VIM, IMP, or OXA-48 type) isolated from specimens collected from January 1, 2017, through June 30, 2019; only a patient’s first isolate per organism–carbapenemase combination was included. We excluded isolates from specimen sources associated with colonization screening (eg, perirectal). We compared the proportion of NDM-producing CRE to all non-KPC–producing CP-CRE between period A (January to June 2018) and period B (January to June 2019). Health departments and the CDC collected additional exposure and molecular information in selected states to better describe current NDM-producing CRE epidemiology. Results: Overall, 47 states reported 1,013 non–KPC-producing CP-CRE (range/state, 1–109 isolates; median, 11 isolates); 46 states reported 631 NDM-producing CRE (range/state, 1–84; median, 6). NDM-producing CRE increased quarterly from the third quarter of 2018 through the second quarter of 2019; CP-CRE isolates with other non-KPC carbapenemases remained stable (Fig. 1). In period A, 124 of 216 emerging CP-CRE had NDM (57.1%), compared with 255 of 359 emerging CP-CRE (71.0%) during period B (P = .1179). Among NDM-producing CRE, the proportion of Enterobacter spp increased from 10.5% in 2018 to 18.4% in 2019 (P = .0467) (Fig. 2). In total, 18 states reported more NDM-producing CRE in the first 6 months of 2019 than in all of 2018. Connecticut, Ohio, and Oregon were among states that conducted detailed investigations; these 3 states identified 24 NDM-producing CRE isolates from 23 patients in period B. Overall, 5 (21.7%) of 22 patients with history available traveled internationally ≤12 months prior to culture; 17 (73.9%) acquired NDM-producing CRE domestically. Among 15 isolates sequenced, 8 (53.3%) carried NDM-5 (6 E. coli, 1 Enterobacter spp and 1 Klebsiella spp) and 7 (46.7%) carried NDM-1 (6 Enterobacter spp and 1 Klebsiella spp). Species were diverse; no single strain type was shared by >2 isolates. Conclusions: Detection of NDM-producing CRE has increased across the AR Lab Network. Among states with detailed information available, domestic acquisition was common, and no single variant or strain predominated. Aggressive public health response and further understanding of current US NDM-CRE epidemiology are needed to prevent further spread.Disclosures: NoneFunding: None
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- 2020
10. Molecular Typing of Invasive Staphylococcus aureus from the Emerging Infections Program (EIP) Using Whole-Genome Sequencing
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Kelly A. Jackson, Susan Petit, Erin Epson, Davina Campbell, Susan M. Ray, Amy S. Gargis, Gillian McAllister, Thomas O. Ewing, Ghinwa Dumyati, Alison Laufer Halpin, Michelle Adamczyk, Isaac See, William Schaffner, and Joseph D. Lutgring
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Microbiology (medical) ,Sanger sequencing ,Whole genome sequencing ,Genetics ,Epidemiology ,SCCmec ,Biology ,Genome ,Subtyping ,symbols.namesake ,Infectious Diseases ,Arginine catabolic mobile element ,symbols ,Multilocus sequence typing ,Typing - Abstract
Background: The CDC has performed surveillance for invasive Staphylococcus aureus (iSA) infections through the Emerging Infections Program (EIP) since 2004. SCCmec and spa typing for clonal complex (CC) assignment and genomic markers have been used to characterize isolates. In 2019, whole-genome sequencing (WGS) of isolates began, allowing for high-resolution assessment of genomic diversity. Here, we evaluate the reliability of SCCmec typing, spa typing, and CC assignment using WGS data compared to traditional methods to ensure that backwards compatibility is maintained. Methods:S. aureus isolates were obtained from a convenience sample of iSA cases reported through the EIP surveillance system. Overall, 78 iSA isolates with diverse spa repeat patterns, CCs, SCCmec types, and antimicrobial susceptibility profiles were sequenced (MiSeq, Illumina). Real-time PCR and Sanger sequencing were used as the SCCmec and spa typing reference methods, respectively. spa-MLST mapping (Ridom SpaServer) served as the reference method for CC assignment. WGS assembly and multilocus sequence typing (MLST) were performed using the CDC QuAISAR-H pipeline. WGS-based MLST CCs were assigned using eBURST and SCCmec types using SCCmecFinder. spa types were assigned from WGS assemblies using BioNumerics. For isolate subtyping, previously published and validated canonical single-nucleotide polymorphisms (canSNPs) as well as the presence of the Panton-Valentine leukocidin (PVL) toxin and arginine catabolic mobile element (ACME) virulence factor were assessed for all genome assemblies. Results: All isolates were assigned WGS-based spa types, which were 100% concordant (78 of 78) with Sanger-based spa typing. SCCmecFinder assigned 91% of isolates (71 of 78) SCCmec types, which were 100% concordant with reference method results. Also, 7 isolates had multiple cassettes predicted or an incomplete SCCmec region assembly. Using WGS data, 96% (75 of 78) of isolates were assigned CCs; 3 isolates had unknown sequence types that were single-locus variants of established sequence types. Overall, 70 isolates had CCs assigned by the reference method; 100% (70 of 70) concordance was observed with WGS-based CCs. Analysis of canSNPs placed 42% (33 of 78) of isolates into CC8, with 17 (52%) of these isolates classified as USA300. PVL and ACME were not accurate markers for inferring the USA300 subtype as 24% (4 of 17) of isolates did not contain these markers. Conclusions:S. aureus CCs, SCCmec, and spa types can be reliably determined using WGS. Incorporation of canSNP analysis represents a more efficient method for CC8 assignment than the use of genomic markers alone. WGS allows for the replacement of multiple typing methods for increased laboratory efficiency, while maintaining backward compatibility with historical typing nomenclature.Funding: NoneDisclosures: None
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- 2020
11. Pseudomonas aeruginosa Outbreak in a Neonatal Intensive Care Unit Attributed to Hospital Tap Water
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Jon Rosenberg, Carolyn V. Gould, Alison Laufer Halpin, Matthew J. Arduino, Judith Noble-Wang, Samir Koirala, Antonio Neri, Benjamin L. Solomon, Nora Chea, Byron F. Robinson, Heather Moulton-Meissner, and Cara Bicking Kinsey
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Male ,0301 basic medicine ,Microbiology (medical) ,Catheterization, Central Venous ,medicine.medical_specialty ,Pediatrics ,Neonatal intensive care unit ,Epidemiology ,030106 microbiology ,Colony Count, Microbial ,medicine.disease_cause ,Disease Outbreaks ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Intensive Care Units, Neonatal ,Health care ,medicine ,Humans ,Infection control ,Pseudomonas Infections ,030212 general & internal medicine ,business.industry ,Pseudomonas aeruginosa ,Drinking Water ,Micropore Filters ,Infant, Newborn ,Case-control study ,Infant ,Outbreak ,Gestational age ,Odds ratio ,Respiration, Artificial ,Electrophoresis, Gel, Pulsed-Field ,Infectious Diseases ,Case-Control Studies ,Emergency medicine ,Female ,Sanitary Engineering ,business - Abstract
OBJECTIVETo investigate an outbreak of Pseudomonas aeruginosa infections and colonization in a neonatal intensive care unit.DESIGNInfection control assessment, environmental evaluation, and case-control study.SETTINGNewly built community-based hospital, 28-bed neonatal intensive care unit.PATIENTSNeonatal intensive care unit patients receiving care between June 1, 2013, and September 30, 2014.METHODSCase finding was performed through microbiology record review. Infection control observations, interviews, and environmental assessment were performed. A matched case-control study was conducted to identify risk factors for P. aeruginosa infection. Patient and environmental isolates were collected for pulsed-field gel electrophoresis to determine strain relatedness.RESULTSIn total, 31 cases were identified. Case clusters were temporally associated with absence of point-of-use filters on faucets in patient rooms. After adjusting for gestational age, case patients were more likely to have been in a room without a point-of-use filter (odds ratio [OR], 37.55; 95% confidence interval [CI], 7.16–∞). Case patients had higher odds of exposure to peripherally inserted central catheters (OR, 7.20; 95% CI, 1.75–37.30) and invasive ventilation (OR, 5.79; 95% CI, 1.39–30.62). Of 42 environmental samples, 28 (67%) grew P. aeruginosa. Isolates from the 2 most recent case patients were indistinguishable by pulsed-field gel electrophoresis from water-related samples obtained from these case-patient rooms.CONCLUSIONSThis outbreak was attributed to contaminated water. Interruption of the outbreak with point-of-use filters provided a short-term solution; however, eradication of P. aeruginosa in water and fixtures was necessary to protect patients. This outbreak highlights the importance of understanding the risks of stagnant water in healthcare facilities.Infect Control Hosp Epidemiol 2017;38:801–808
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- 2017
12. Harnessing Next-Generation Sequence Technology to Elucidate Healthcare-Associated Infection Transmission Pathways
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Monica Y. Chan, Jonathan Daniels, Maroya Spalding Walters, Erisa Sula, Alison Laufer Halpin, Nychie Dotson, Erin Breaker, Paige Gable, Gillian McAllister, and Danielle A Rankin
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Microbiology (medical) ,Healthcare associated infections ,Infectious Diseases ,Transmission (mechanics) ,Epidemiology ,Computer science ,law ,Computational biology ,Next generation sequence ,law.invention - Abstract
Background: Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug-resistant bacteria that persist in healthcare environments, particularly in wastewater reservoirs where they can pose risks for patients. Healthcare-associated outbreaks of carbapenemase-producing (CP) CRE can be propagated via a single bacterial strain and/or mobile genetic element (MGEs) harboring a carbapenemase gene. Unlike chromosomally encoded carbapenemases, CP-MGEs can rapidly facilitate the spread of these carbapenemase genes across bacterial strains. From July 2017 to December 2018, the Florida Department of Health in Orange County investigated an outbreak of patients colonized with various bacterial genera of CP-CRE carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC), indicating a potential MGE reservoir. WGS was performed to identify transmission pathways and linked cases, beyond what traditional testing provides. Methods: We selected a subset of blaKPC-harboring isolates for WGS on short- and long-read platforms (MiSeq, PacBio, MinION) to achieve high quality, complete genome and plasmid assemblies. Laboratory, clinical, and epidemiological data were combined to identify possible transmission events, common sources, and common MGEs. Results: Eleven clinical isolates from 5 genera (Citrobacter, Enterobacter, Klebsiella, Morganella, Providencia, and Serratia), and 10 environmental isolates collected from the pharmacy and medication room, ICU, and patient rooms and comprising 4 genera (Citrobacter, Enterobacter, Klebsiella, and Serratia) underwent WGS. Although short-read WGS elucidated additional subsets of closely related strains, high genomic diversity was also observed within some species: Citrobacter freundii: 13,483 single-nucleotide variants (SNVs), 67% core genome; Enterobacter spp: 3–18,563 SNVs; 34%; and K. pneumoniae: 8–18,460 SNVs, 80%. Further analysis using long-read hybrid assemblies revealed 2 unique blaKPC-harboring plasmids. The first plasmid, pDHQP20145-KPC3 (50 kb), contained the blaKPC-3 gene and was detected in both patient and environmental isolates across 3 of the 5 sequenced genera. The second plasmid, pDHQP201745-KPC2 (180 kb), contained the blaKPC-2 gene, and was found across 2 CP-CRE genera isolated from both patients and the environment, including isolates from the medication room sink drain and a patient who received compounded oral medications. Conclusion: WGS identified 2 blaKPC-harboring plasmids, including pDHQP20145-KPC3, which was found across 3 genera of CP-CRE isolated from patients and the environment, supporting prolonged transmission of KPC-producing CRE in this facility, and a CP-MGE driving transmission. The rapid spread of emerging, potentially mobile, antimicrobial resistance has increased our need to further explore the genomic environment of promiscuous MGEs. WGS can contribute to infection control beyond traditional subtyping methods, such as pulsed-field gel electrophoresis (PFGE), as MGEs increasingly represent an important driver of transmission.Funding: NoneDisclosures: None
- Published
- 2020
13. Evaluation of a Novel Intervention to Reduce Unnecessary Urine Cultures in Intensive Care Units at a Tertiary Care Hospital in Maryland, 2011–2014
- Author
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Jonathan R. Edwards, Michael Anne Preas, Mala Filippell, Anthony D. Harris, J. Kristie Johnson, David Blythe, Surbhi Leekha, Carolyn V. Gould, David Hunt, Alison Laufer Halpin, and Lauren Epstein
- Subjects
Microbiology (medical) ,medicine.medical_specialty ,Epidemiology ,Urinary system ,Urine ,Unnecessary Procedures ,Urinalysis ,030501 epidemiology ,Article ,Tertiary Care Centers ,03 medical and health sciences ,0302 clinical medicine ,Intensive care ,Intervention (counseling) ,Unnecessary Procedure ,medicine ,Humans ,030212 general & internal medicine ,Intensive care medicine ,Infection Control ,Maryland ,business.industry ,Tertiary care hospital ,Intensive Care Units ,Infectious Diseases ,Catheter-Related Infections ,Urinary Tract Infections ,Emergency medicine ,0305 other medical science ,business - Abstract
We assessed the impact of a reflex urine culture protocol, an intervention aimed to reduce unnecessary urine culturing, in intensive care units at a tertiary care hospital. Significant decreases in urine culturing rates and reported rates of catheter-associated urinary tract infection followed implementation of the protocol.Infect Control Hosp Epidemiol 2016;37:606–609
- Published
- 2016
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