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Concurrent transmission of multiple carbapenemases in a long-term acute-care hospital
- Danielle A. Rankin, Maroya Spalding Walters, Luz Caicedo, Paige Gable, Heather A. Moulton-Meissner, Allison Chan, Albert Burks, Kendra Edwards, Gillian McAllister, Alyssa Kent, Alison Laufer Halpin, Christina Moore, Tracy McLemore, Linda Thomas, Nychie Q. Dotson, Alvina K. Chu
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 45 / Issue 3 / March 2024
- Published online by Cambridge University Press:
- 10 January 2024, pp. 292-301
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- March 2024
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Objective:
We investigated concurrent outbreaks of Pseudomonas aeruginosa carrying blaVIM (VIM-CRPA) and Enterobacterales carrying blaKPC (KPC-CRE) at a long-term acute-care hospital (LTACH A).
Methods:We defined an incident case as the first detection of blaKPC or blaVIM from a patient’s clinical cultures or colonization screening test. We reviewed medical records and performed infection control assessments, colonization screening, environmental sampling, and molecular characterization of carbapenemase-producing organisms from clinical and environmental sources by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing.
Results:From July 2017 to December 2018, 76 incident cases were identified from 69 case patients: 51 had blaKPC, 11 had blaVIM, and 7 had blaVIM and blaKPC. Also, blaKPC were identified from 7 Enterobacterales, and all blaVIM were P. aeruginosa. We observed gaps in hand hygiene, and we recovered KPC-CRE and VIM-CRPA from drains and toilets. We identified 4 KPC alleles and 2 VIM alleles; 2 KPC alleles were located on plasmids that were identified across multiple Enterobacterales and in both clinical and environmental isolates.
Conclusions:Our response to a single patient colonized with VIM-CRPA and KPC-CRE identified concurrent CPO outbreaks at LTACH A. Epidemiologic and genomic investigations indicated that the observed diversity was due to a combination of multiple introductions of VIM-CRPA and KPC-CRE and to the transfer of carbapenemase genes across different bacteria species and strains. Improved infection control, including interventions that minimized potential spread from wastewater premise plumbing, stopped transmission.
Outbreak of Stenotrophomonas maltophilia infections in an intensive care unit—Alameda County, California, May–October 2022
- Rebeca Elliott, Jeffrey Silvers, Axel Vazquez Deida, Paige Gable, Gillian McAllister, Alyssa Kent, Thomas Ewing, Janet Glowicz, Matthew Arduino, Heather Moulton-Meissner, Mir Noorbakhsh, Patricia Rodrigues, Munira Shemsu, Amit Chitnis, Hilary Metcalf, Barbara Allen, Suada Abdic, Alison Halpin, Kavita Trivedi, Amelia Keaton, Margarita Elsa Villarino
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- Journal:
- Antimicrobial Stewardship & Healthcare Epidemiology / Volume 3 / Issue S2 / June 2023
- Published online by Cambridge University Press:
- 29 September 2023, p. s89
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Background: Stenotrophomonas maltophilia is a gram-negative, biofilm-producing bacterium that is ubiquitous in water environments and often associated with healthcare-associated infections (HAIs). Outbreaks of S. maltophilia bloodstream infections are a rare event and raise the suspicion of a common source. We used whole-genome sequencing (WGS) for an investigation of a cluster of S. maltophilia HAIs at a single hospital. Methods: A patient was defined as an intensive care unit (ICU) patient with fever and S. maltophilia isolated from a culture and who was treated for an HAI from May to October 2022. The response to the cluster included an epidemiologic investigation, water infection control risk assessments (WICRA), and environmental sampling. We also conducted WGS to characterize and assess relatedness between clinical and environmental S. maltophilia isolates. Results: From May 5 to October 1, 2022, we identified 11 HAIs due to S. maltophilia: 9 bloodstream infections and 2 ventilator-associated pneumonia cases. The initial epidemiological investigation did not identify common medical products, procedures, or personnel as an exposure source. The WICRA identified several breaches that may have exposed patients to contaminated water from sink backsplashes in the ICU, computerized tomography (CT) rooms, and the emergency department. In the CT rooms, saline bags were sometimes used for multiple patients, as were single-use intravenous contrast solution bottles. No additional cases were identified once infection control breaches were mitigated by installing sink splashguards, disinfecting drains, dedicating sink use for handwashing, and adhering to single-patient use of pharmaceutical products in the CT rooms. Of 46 environmental water samples, 19 were culture-positive for S. maltophilia. Isolates available for WGS included 7 clinical isolates (6 blood and 1 respiratory) and 17 environmental isolates. Among the 24 isolates sequenced, 16 unique multilocus sequence types (MLSTs) were identified. The 6 blood isolates sequenced were highly related (ST239, 0–4 high-quality, single-nucleotide variants [hqSNV] over 98.99% core genome), suggesting a common source. Two clusters of related environmental isolates were identified; however, overall MLST and hqSNV analyses suggested no relatedness between clinical and environmental isolates. Conclusions: An ICU cluster of S. maltophilia bloodstream infections was likely associated with water contamination of room surfaces and use of single-use intravenous products for multiple patients in the setting of a national pharmaceutical product shortage. This investigation highlights the importance of strong surveillance and water infection control, including routine assessment of ancillary areas in which intravenous products are administered and interdisciplinary collaboration to properly mitigate nosocomial transmission.
Disclosures: None
Mycobacterium chimaera infections among cardiothoracic surgery patients associated with heater-cooler devices—Kansas and California, 2019
- Kerui Xu, Lauren E. Finn, Robert L. Geist, Christopher Prestel, Heather Moulton-Meissner, Moon Kim, Bryna Stacey, Gillian A. McAllister, Paige Gable, Talar Kamali, Annabelle de St Maurice, Shangxin Yang, Kiran M. Perkins, Matthew B. Crist
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 43 / Issue 10 / October 2022
- Published online by Cambridge University Press:
- 06 October 2021, pp. 1333-1338
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- October 2022
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Background:
In 2015, an international outbreak of Mycobacterium chimaera infections among patients undergoing cardiothoracic surgeries was associated with exposure to contaminated LivaNova 3T heater-cooler devices (HCDs). From June 2017 to October 2020, the Centers for Disease Control and Prevention was notified of 18 patients with M. chimaera infections who had undergone cardiothoracic surgeries at 2 hospitals in Kansas (14 patients) and California (4 patients); 17 had exposure to 3T HCDs. Whole-genome sequencing of the clinical and environmental isolates matched the global outbreak strain identified in 2015.
Methods:Investigations were conducted at each hospital to determine the cause of ongoing infections. Investigative methods included query of microbiologic records to identify additional cases, medical chart review, observations of operating room setup, HCD use and maintenance practices, and collection of HCD and environmental samples.
Results:Onsite observations identified deviations in the positioning and maintenance of the 3T HCDs from the US Food and Drug Administration (FDA) recommendations and the manufacturer’s updated cleaning and disinfection protocols. Additionally, most 3T HCDs had not undergone the recommended vacuum and sealing upgrades by the manufacturer to decrease the dispersal of M. chimaera–containing aerosols into the operating room, despite hospital requests to the manufacturer.
Conclusions:These findings highlight the need for continued awareness of the risk of M. chimaera infections associated with 3T HCDs, even if the devices are newly manufactured. Hospitals should maintain vigilance in adhering to FDA recommendations and the manufacturer’s protocols and in identifying patients with potential M. chimaera infections with exposure to these devices.
Verona Integron-Encoded Metallo-Beta-Lactamase (VIM)–Producing Pseudomonas aeruginosa Outbreak Associated with Acute Care
- Allison Chan, Alicia Shugart, Albert Burks, Christina Moore, Paige Gable, Heather Moulton-Meissner, Gillian McAllister, Alison Halpin, Maroya Walters, Amelia Keaton, Kelley Tobey, Katie Thure, Sarah Schmedes, Paige Gable, Henrietta Hardin, Adrian Lawsin
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- Journal:
- Antimicrobial Stewardship & Healthcare Epidemiology / Volume 1 / Issue S1 / July 2021
- Published online by Cambridge University Press:
- 29 July 2021, p. s26
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Background: Contaminated healthcare facility plumbing is increasingly recognized as a source of carbapenemase-producing organisms (CPOs). In August 2019, the Tennessee State Public Health Laboratory identified Tennessee’s twelfth VIM-producing carbapenem-resistant Pseudomonas aeruginosa (VIM-CRPA), from a patient in a long-term acute-care hospital. To determine a potential reservoir, the Tennessee Department of Health (TDH) reviewed healthcare exposures for all cases. Four cases (33%), including the most recent case and earliest from March 2018, had a history of admission to intensive care unit (ICU) room X at acute-care hospital A (ACH A), but the specimens were collected at other facilities. The Public Health Laboratory collaborated with ACH A to assess exposures, perform environmental sampling, and implement control measures. Methods: TDH conducted in-person infection prevention assessments with ACH A, including a review of the water management program. Initial recommendations included placing all patients admitted to room X on contact precautions, screening for CPO on room discharge, daily sink basin and counter cleaning, and other sink hygiene measures. TDH collected environmental and water samples from 5 ICU sinks (ie, the handwashing and bathroom sinks in room X and neighboring room Y [control] and 1 hallway sink) and assessed the presence of VIM-CRPA. Moreover, 5 patients and 4 environmental VIM-CRPA underwent whole-genome sequencing (WGS). Results: From February to June 2020, of 21 patients admitted to room X, 9 (43%) underwent discharge screening and 4 (44%) were colonized with VIM-CRPA. Average room X length of stay was longer for colonized patients (11.3 vs 4.8 days). Drain swabs from room X’s bathroom and handwashing sinks grew VIM-CRPA; VIM-CRPA was not detected in tap water or other swab samples. VIM-CRPA from the environment and patients were sequence type 253 and varied by 0–13 single-nucleotide variants. ACH A replaced room X’s sinks and external plumbing in July. Discharge screening and contact precautions for all patients were discontinued in November, 5 months following the last case and 12 consecutive negative patient discharge screens. Improved sink hygiene and mechanism testing for CRPA from clinical cultures continued, with no new cases identified. Conclusions: An ICU room with a persistently contaminated sink drain was a persistent reservoir of VIM-CRPA. The room X attack rate was high, with VIM-CRPA acquisition occurring in >40% of patients screened. The use of contaminated plumbing fixtures in ACH have the potential to facilitate transmission to patients but may be challenging to identify and remediate. All healthcare facilities should follow sink hygiene best practices.
Funding: No
Disclosures: None
Aggressive Colonization Screening and Infection Control Measures in Containment of NDM-5 Carbapenemase-Producing CRE
- Ishrat Kamal-Ahmed, Kate Tyner, Teresa Fitzgerald, Heather Adele Moulton-Meissner, Gillian McAllister, Alison Halpin, Muhammad Salman Ashraf, Tom Safranek, Maroya Walters, Maureen Tierney
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s458-s459
- Print publication:
- October 2020
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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: None
Disclosures: Muhammad Salman Ashraf reports that he is the principal investigator for a study funded by an investigator-initiated research grant.
Carbapenemase-Producing, Carbapenem-Resistant Acinetobacter baumannii: Summary of CDC Consultations, 2017–2019
- Lauren Epstein, Alicia Shugart, David Ham, Snigdha Vallabhaneni, Richard Brooks, Gillian McAllister, Alison Halpin, Sarah Gilbert, Maroya Walters
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s151-s152
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- October 2020
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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: None
Disclosures: None
Changing US Epidemiology of NDM-Producing Carbapenem-Resistant Enterobacteriaceae, 2017–2019
- Alicia Shugart, Garrett Mahon, Lauren Epstein, Jennifer Y. Huang, Gillian McAllister, Adrian Lawsin, Erisa Sula, Alison Laufer Halpin, Amanda Smith, Rebekah Carman, P. Maureen Cassidy, Karim Morey, Anu Paranandi, Randy Downing, Diane Noel, , Alexander J. Kallen, Maroya Spalding Walters
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- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s25-s26
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- October 2020
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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: None
Funding: None
Transmission of Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae in Georgia, 2018–2019
- Jeanne Negley, Elizabeth Smith, Maroya Walters, Tonia Parrott, Richard Stanton, David Ham, Jacobs Slifka Kara, Patricia Kopp, Mary Connelly, Gebre Tiga, Gillian McAllister, Alison Halpin, Cherie Drenzek
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s414-s415
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- October 2020
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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: None
Disclosures: None
Molecular Landscape of Carbapenemase-Producing Acinetobacter baumanii in the United States
- Kellan Burrell, Jennifer Huang, Maria Karlsson, Gillian McAllister, Allison Brown
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- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s320-s321
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- October 2020
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Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) are an urgent public health threat because they cause healthcare-associated infections that are difficult to treat and can spread in healthcare environments. Acinetobacter spp may develop resistance to carbapenems through various mechanisms, including decreased permeability, overexpression of efflux pumps, and production of carbapenemases. Carbapenemases found in CRAB commonly belong to the group of carbapenem-hydrolyzing class D β-lactamases, which can be either intrinsic or acquired. The most clinically relevant class D enzymes are the OXA-23-like, OXA-24/40–like, and OXA-58–like because they are commonly plasmid mediated and thereby have the potential for rapid dissemination. We describe the molecular epidemiology of CRAB in the United States using a convenience sample of isolates collected from reference submissions, an isolate-based surveillance system, and the Antibiotic Resistance Laboratory Network (ARLN). Methods: Beginning in August 2017, 7 public health laboratories in the ARLN began testing CRAB isolates submitted by participating sentinel clinical laboratories across their region. Carbapenem-resistant isolates were identified by resistance to imipenem, meropenem, or doripenem. Testing included molecular detection of 4 targeted carbapenemase genes: blaKPC, blaNDM, blaVIM, and blaIMP. Participating labs reported testing results to CDC at least monthly. A separate collection of isolates from CDC reference and surveillance activities between 2013 and 2015 underwent whole-genome sequencing (WGS) to evaluate the presence of acquired carbapenemase genes, including class D OXA-variants. Results: From August 2017 through July 2019, the ARLN tested 2,368 CRAB isolates across 44 states. Only 12 (0.5%) of these harbored a bla- gene: blaKPC (n = 5), blaNDM (n = 5), blaIMP (n = 1), and blaVIM (n = 1). Of 95 reference and surveillance isolates sequenced, none harbored these targeted carbapenemases. However, 69 (73%) harbored at least 1 acquired class D OXA gene; OXA-23 was the most commonly acquired OXA variant (n = 46, 48.4%). Conclusions: Using a multipronged approach, our studies indicate that the presence of class D β-lactamases of the OXA type are common in CRAB among surveillance and reference samples that underwent WGS analysis. Other acquired carbapenemases appear to be rare. To prevent the spread of highly resistant CRAB, particularly those carrying the targeted, emerging carbapenemase genes, continued testing, and rapid infection control are necessary to improve patient safety and maintain situational awareness.
Funding: None
Disclosures: None
Harnessing Next-Generation Sequence Technology to Elucidate Healthcare-Associated Infection Transmission Pathways
- Paige Gable, Gillian McAllister, Erisa Sula, Danielle A. Rankin, Erin Breaker, Jonathan Daniels, Monica Y. Chan, Nychie Dotson, Maroya Walters, Alison Laufer Halpin
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- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, p. s66
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- October 2020
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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: None
Disclosures: None
Molecular Typing of Invasive Staphylococcus aureus from the Emerging Infections Program (EIP) Using Whole-Genome Sequencing
- Davina Campbell, Gillian McAllister, Kelly Jackson, Isaac See, Alison Halpin, Joseph Lutgring, Erin Epson, Susan Petit, Susan Ray, William Schaffner, Ghinwa Dumyati, Thomas Ewing, Michelle Adamczyk, Amy Gargis
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- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s71-s72
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- October 2020
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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: None
Disclosures: None
Molecular Epidemiology and Outcomes of Patients with Carbapenem-Resistant Enterobacteriaceae Bacteriuria, Atlanta 2012–2015
- Jessica Howard-Anderson, Robert Petit, Chris Bower, Gillian Smith, Uzma Ansari, Alison Halpin, Maria Karlsson, Adrian Lawson, Joseph Lutgring, Gillian McAllister, Monica Farley, Jesse Jacob, Sarah Satola
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 41 / Issue S1 / October 2020
- Published online by Cambridge University Press:
- 02 November 2020, pp. s489-s490
- Print publication:
- October 2020
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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: None
Disclosures: None
Disclosures: None
Funding: None
Transmission of novel Klebsiella pneumoniae carbapenemase-producing Escherichia coli sequence type 1193 among residents and caregivers in a community-based, residential care setting—Nevada, 2018
- Danica J. Gomes, Ana C. Bardossy, Lei Chen, Adrian Forero, Andrew Gorzalski, Heather Holmstadt, Kimisha Causey, Chidinma Njoku, Nimalie D. Stone, Abimbola Ogundimu, Heather Moulton-Meissner, Gillian McAllister, Alison L. Halpin, Paige Gable, Nicholas Vlachos, Sandra Larson, Maroya Spalding Walters, Lauren Epstein
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- Journal:
- Infection Control & Hospital Epidemiology / Volume 41 / Issue 11 / November 2020
- Published online by Cambridge University Press:
- 29 June 2020, pp. 1341-1343
- Print publication:
- November 2020
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We describe transmission of Klebsiella pneumoniae carbapenemase-producing Escherichia coli sequence type (ST) 1193 in a group home. E. coli ST1193 is an emerging multidrug-resistant clone not previously shown to carry carbapenemases in the United States. Our investigation illustrates the potential of residential group homes to amplify rare combinations of pathogens and resistance mechanisms.