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Weterings V, van den Bijllaardt W, Bootsma M, Hendriks Y, Kilsdonk L, Mulders A, Kluytmans J. Duration of rectal colonization with extended-spectrum beta-lactamase-producing Escherichia coli: results of an open, dynamic cohort study in Dutch nursing home residents (2013–2019). Antimicrob Resist Infect Control 2022; 11:98. [PMID: 35841002 PMCID: PMC9287922 DOI: 10.1186/s13756-022-01132-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Background In 2016, a study in a Dutch nursing home showed prolonged colonization duration of extended-spectrum β-lactamase-producing (ESBL)-ST131 compared to ESBL-non-ST131. In this study, we assessed the duration of rectal ESBL-producing E. coli (ESBL-EC) colonization in residents in the same nursing home for an extended period of six years. We aimed to estimate the influence of a possible bias when follow up is started during an outbreak. Methods Between 2013 and 2019, repetitive point prevalence surveys were performed by culturing rectal or faecal swabs from all residents. Kaplan–Meier survival analysis was performed to calculate the median time to clearance of ESBL-EC with a log-rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131. Results The study showed a median time to clearance of 13.0 months (95% CI 0.0–27.9) for ESBL-ST131 compared to 11.2 months (95% CI 4.8–17.6) for ESBL-non-ST131 (p = 0.044). In the subgroup analysis of residents who were ESBL-EC positive in their first survey, the median time to clearance for ST131 was 59.7 months (95% CI 23.7–95.6) compared to 16.2 months (95% CI 2.1–30.4) for ESBL-non-ST131 (p = 0.036). In the subgroup analysis of residents who acquired ESBL-EC, the median time to clearance for ST131 was 7.2 months (95% CI 2.1–12.2) compared to 7.9 months (95% CI 0.0–18.3) for ESBL-non-ST131 (p = 0.718). The median time to clearance in the ESBL-ST131 group was significantly longer in residents who were ESBL-ST131 colonised upon entering the study than in residents who acquired ESBL-ST131 during the study (p = 0.001). Conclusion A prolonged colonization with ESBL-ST131 was only found in the subgroup who was ESBL-EC positive upon entering the study. The prolonged duration with ESBL-ST131 in the previous study was probably biased by factors that occured during (the start of) the outbreak. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01132-9.
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Salamanca-Rivera E, López-Cerero L, Rodríguez-Martínez JM, Pascual A, Rodríguez-Baño J. Prevalence, Incidence, and Risk Factors for Intestinal Colonization Due to Fluoroquinolone-Resistant ST131 Escherichia coli: a Longitudinal Study in Highly Dependent, Long-Term Care Facility Residents. Microbiol Spectr 2022; 10:e0167322. [PMID: 35943257 PMCID: PMC9431526 DOI: 10.1128/spectrum.01673-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli ST131 clade C is an important driver for fluoroquinolone resistance (FQ-R). We conducted a prospective observational study in residents from two long-term care facilities (LTCFs) in Seville, Spain, in 2018. Fecal swabs and environmental samples were obtained. E. coli isolates were screened for clade C, FQ-R ST131 by PCR, and molecular typing by PFGE; representatives from pulsotypes were studied by whole-genome-sequencing (WGS) and assigned to lineages (cgSTs). Prevalence of colonization at each time point, incidence density, and risk factors for acquisition were studied. Seventy-six FQ-R ST131 E. coli isolates belonging to 34 cgSTs were obtained; 24 belonging to subclade C1 (116 isolates, 65.9%) and 10 to C2 (60, 34.1%). C1 lineages showed lower virulence scores than C2 (median [IQR], 19 [18 to 20] versus 21 [20 to 21.5], P = 0.001) and higher number of plasmids (4 [3 to 5] versus 2 [2 to 3], P = 0.01). aac(6')-Ib-cr and blaOXA-1 were less frequent in C1 than C2 (2 [8.3%] versus 6 [60%], P = 0.003 for both); ESBL genes were detected in eight (33.3%) C1 (5 blaCTX-M-27) and three (30%) C2 (all blaCTX-M-15). Of the 82 residents studied, 49 were colonized at some point (59.7%), with a pooled prevalence of 38.6%. Incidence density of new lineage acquisition was 2.22 per 100 resident weeks (1.28 and 0.93 C1 and C2 subclades, respectively). Independent risk factors for acquisitions were having a colonized roommate (HR = 4.21; 95% CI = 1.71 to 10.36; P = 0.002) and urinary or fecal incontinence (HR = 2.82; 95% CI = 1.21 to 6.56; P = 0.01). LTCFs are important reservoirs of clade C ST131 E. coli. The risk factors found suggest that cross-transmission is the most relevant transmission mechanisms. IMPORTANCE We aimed at investigating the microbiological and epidemiological features of clade C fluoroquinolone-resistant ST131 E. coli isolates colonizing highly dependent residents in long-term care facilities (LTCFs) during 40 weeks and the risk factors of acquisition. Isolates from C1 and C2 subclades were characterized in this environment. The clonality of the isolates was characterized and they were assigned to lineages (cgSTs), Resistance genes, virulence factors, and plasmids were also described. This study suggests that cross-transmission is the most relevant transmission mechanisms; however, environmental colonization might also play a role. We believe the data provide useful information to depict the epidemiology of these bacteria by merging detailed microbiological and epidemiological information.
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Affiliation(s)
- Elena Salamanca-Rivera
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jose Manuel Rodríguez-Martínez
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Alvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Johnson JR, Clabots C, Porter SB, Bender T, Johnston BD, Thuras P. Intestinal Persistence of Colonizing Escherichia coli Strains, Especially ST131-H30, in Relation to Bacterial and Host Factors. J Infect Dis 2022; 225:2197-2207. [PMID: 34979558 PMCID: PMC9200155 DOI: 10.1093/infdis/jiab638] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/30/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Superior gut colonization may underlie the pandemic emergence of the resistance-associated H30 subclone of Escherichia coli sequence type 131 (ST131-H30). Little is known about the associated host and bacterial characteristics, or the comparative persistence of non-ST131 intestinal E. coli. METHODS Generic and fluoroquinolone-resistant E. coli isolates from volunteers' serial fecal samples underwent clonal analysis and extensive polymerase chain reaction (PCR)-based characterization (phylogroup, selected sequence types, virulence genes). Kaplan-Meier survival analysis and Cox proportional hazards survival analysis using penalized regression (a machine-learning method) were used to identify correlates of strain persistence. RESULTS Screening of 2005 subjects at the Minneapolis VA Medical Center identified 222 subjects (117 veterans, 105 human and animal household members) for longitudinal fecal surveillance. Analysis of their 585 unique-by-subject fecal E. coli strains identified multiple epidemiological, ecological, and bacterial correlates of strain persistence. ST131-H30, a strong univariable correlate of persistence, was superseded in multivariable analysis by outpatient status, fluoroquinolone resistance, and diverse (predominantly iron uptake-related) virulence genes. CONCLUSIONS ST131-H30 exhibits exceptional intestinal persistence, possibly due to a combination of fluoroquinolone resistance and virulence factors, which may be primarily colonization factors. This identifies both likely contributors to the ST131-H30 pandemic and potential targets for interventions against it.
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Affiliation(s)
- James R Johnson
- Correspondence: James R. Johnson, MD, Infectious Diseases (111F), VA Medical Center, 1 Veterans Drive, Minneapolis, MN 55417 ()
| | - Connie Clabots
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Stephen B Porter
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Tricia Bender
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Brian D Johnston
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA,University of Minnesota, Minneapolis, Minnesota, USA
| | - Paul Thuras
- Minneapolis Veterans Affairs Medical Center, Minneapolis, Minnesota, USA,University of Minnesota, Minneapolis, Minnesota, USA
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Tchesnokova VL, Rechkina E, Chan D, Haile HG, Larson L, Ferrier K, Schroeder DW, Solyanik T, Shibuya S, Hansen K, Ralston JD, Riddell K, Scholes D, Sokurenko EV. Pandemic Uropathogenic Fluoroquinolone-resistant Escherichia coli Have Enhanced Ability to Persist in the Gut and Cause Bacteriuria in Healthy Women. Clin Infect Dis 2021; 70:937-939. [PMID: 31271206 DOI: 10.1093/cid/ciz547] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
We report that fluoroquinolone-resistant Escherichia coli are found in feces of 8.8% of healthy women, with most bacteria belonging to pandemic multidrug-resistant ST131-H30R or ST1193 clonal groups. Moreover, these highly uropathogenic clonal groups demonstrate an especially prolonged gut persistence and high rate of bacteriuria without documented urinary tract infection.
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Affiliation(s)
- Veronika L Tchesnokova
- Department of Microbiology, University of Washington School of Medicine.,ID Genomics, Inc
| | | | - Diana Chan
- Department of Microbiology, University of Washington School of Medicine
| | | | - Lydia Larson
- Department of Microbiology, University of Washington School of Medicine
| | - Kendra Ferrier
- Department of Microbiology, University of Washington School of Medicine
| | - David W Schroeder
- Department of Microbiology, University of Washington School of Medicine
| | - Thalia Solyanik
- Department of Microbiology, University of Washington School of Medicine
| | - Spencer Shibuya
- Department of Microbiology, University of Washington School of Medicine
| | - Kelly Hansen
- Kaiser Permanente Washington Health Research Institute.,Kaiser Permanente Washington, Seattle
| | - James D Ralston
- Kaiser Permanente Washington Health Research Institute.,Kaiser Permanente Washington, Seattle
| | | | - Delia Scholes
- Kaiser Permanente Washington Health Research Institute.,Kaiser Permanente Washington, Seattle
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Davis E, Hicks L, Ali I, Salzman E, Wang J, Snitkin E, Gibson K, Cassone M, Mody L, Foxman B. Epidemiology of Vancomycin-Resistant Enterococcus faecium and Enterococcus faecalis Colonization in Nursing Facilities. Open Forum Infect Dis 2020; 7:ofz553. [PMID: 31993459 PMCID: PMC6979485 DOI: 10.1093/ofid/ofz553] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/01/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Vancomycin-resistant Enterococcus faecium and Enterococcus faecalis frequently colonize nursing facility (NF) residents, creating opportunities for vancomycin-resistant Enterococcus (VRE) transmission and dissemination of mobile genetic elements conferring antimicrobial resistance. Most VRE studies do not speciate; our study addresses this lack and compares the epidemiology of E faecium and E faecalis. METHODS We enrolled 651 newly admitted patients from 6 different NFs and collected swabs from several body sites at enrollment, 14 days, 30 days, and monthly thereafter for up to 6 months. The VRE were speciated using a duplex polymerase chain reaction. We used multinomial logistic regression models to compare risk factors associated with colonization of E faecium and E faecalis. RESULTS Overall, 40.7% were colonized with E faecium, E faecalis, or both. At enrollment, more participants were colonized with E faecium (17.8%) than E faecalis (8.4%); 3.2% carried both species. Enterococcus faecium was carried twice as long as E faecalis (69 days and 32 days, respectively), but incidence rates were similar (E faecium, 3.9/1000 person-days vs E faecalis, 4.1/1000 person-days). Length of stay did not differ by species among incident cases. Residents who used antibiotics within the past 30 days had a greater incidence of both E faecium (odds ratio [OR] = 2.89; 95% confidence interval [CI], 1.82-4.60) and E faecalis (OR = 1.80; 95% CI, 1.16-2.80); device use was most strongly associated with the incidence of E faecium colonization (OR = 2.01; 95% CI, 1.15-3.50). CONCLUSIONS Recent increases in vancomycin-resistant E faecium prevalence may reflect increased device use and longer duration of carriage.
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Affiliation(s)
- Elyse Davis
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Liam Hicks
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Ihsan Ali
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Faculty of Basic and Applied Sciences, Department of Medical Laboratory Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Elizabeth Salzman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Joyce Wang
- Faculty of Basic and Applied Sciences, Department of Medical Laboratory Technology, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Evan Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Departmental of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kristen Gibson
- Departmental of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Marco Cassone
- Departmental of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lona Mody
- Departmental of Internal Medicine, Division of Geriatric and Palliative Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Geriatrics Research Education and Clinical Center, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, USA
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms. Proc Natl Acad Sci U S A 2017; 114:10467-10472. [PMID: 28900004 DOI: 10.1073/pnas.1710235114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of multidrug-resistant organisms (MDROs) across global healthcare networks poses a serious threat to hospitalized individuals. Strategies to limit the emergence and spread of MDROs include oversight to decrease selective pressure for MDROs by promoting appropriate antibiotic use via antibiotic stewardship programs. However, restricting the use of one antibiotic often requires a compensatory increase in the use of other antibiotics, which in turn selects for the emergence of different MDRO species. Further, the downstream effects of antibiotic treatment decisions may also be influenced by functional interactions among different MDRO species, with the potential clinical implications of such interactions remaining largely unexplored. Here, we attempt to decipher the influence network between antibiotic treatment, MDRO colonization, and infection by leveraging active surveillance and antibiotic treatment data for 234 nursing home residents. Our analysis revealed a complex network of interactions: antibiotic use was a risk factor for primary MDRO colonization, which in turn increased the likelihood of colonization and infection by other MDROs. When we focused on the risk of catheter-associated urinary tract infections (CAUTI) caused by Escherichia coli, Enterococcus, and Staphylococcus aureus we observed that cocolonization with specific pairs of MDROs increased the risk of CAUTI, signifying the involvement of microbial interactions in CAUTI pathogenesis. In summary, our work demonstrates the existence of an underappreciated healthcare-associated ecosystem and strongly suggests that effective control of overall MDRO burden will require stewardship interventions that take into account both primary and secondary impacts of antibiotic treatments.
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Focus on optimization of early antimicrobial therapy in ICU-acquired infections. Intensive Care Med 2016; 42:1658-1660. [DOI: 10.1007/s00134-016-4485-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/01/2016] [Indexed: 10/21/2022]
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Hebbelstrup Jensen B, Stensvold CR, Struve C, Olsen KEP, Scheutz F, Boisen N, Röser D, Andreassen BU, Nielsen HV, Schønning K, Petersen AM, Krogfelt KA. Enteroaggregative Escherichia coli in Daycare-A 1-Year Dynamic Cohort Study. Front Cell Infect Microbiol 2016; 6:75. [PMID: 27468409 PMCID: PMC4942469 DOI: 10.3389/fcimb.2016.00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/29/2016] [Indexed: 12/24/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) has been associated with persistent diarrhea, reduced growth acceleration, and failure to thrive in children living in developing countries and with childhood diarrhea in general in industrialized countries. The clinical implications of an EAEC carrier-status in children in industrialized countries warrants clarification. To investigate the pathological significance of an EAEC carrier-state in the industrialized countries, we designed a 1-year dynamic cohort study and performed follow-up every second month, where the study participants submitted a stool sample and answered a questionnaire regarding gastrointestinal symptoms and exposures. Exposures included foreign travel, consumption of antibiotics, and contact with a diseased animal. In the capital area of Denmark, a total of 179 children aged 0–6 years were followed in a cohort study, in the period between 2009 and 2013. This is the first investigation of the incidence and pathological significance of EAEC in Danish children attending daycare facilities. Conventional microbiological detection of enteric pathogens was performed at Statens Serum Institute, Copenhagen, Denmark, and at Hvidovre Hospital, Copenhagen, Denmark. Parents completed questionnaires regarding gastrointestinal symptoms. The EAEC strains were further characterized by serotyping, phylogenetic analysis, and susceptibility testing. EAEC was detected in 25 (14%) of the children during the observational period of 1 year. One or more gastrointestinal symptoms were reported from 56% of the EAEC-positive children. Diarrhea was reported in six (24%) of the EAEC positive children, but no cases of weight loss, and general failure to thrive were observed. The EAEC strains detected comprised a large number of different serotypes, confirming the genetic heterogeneity of this pathotype. EAEC was highly prevalent (n = 25, 14%) in Danish children in daycare centers and was accompanied by gastrointestinal symptoms in 56% of the infected children. No serotype or phylogenetic group was specifically linked to children with disease.
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Affiliation(s)
| | - Christen R Stensvold
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Carsten Struve
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Katharina E P Olsen
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Flemming Scheutz
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Nadia Boisen
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Dennis Röser
- Department of Microbiology and Infection Control, Statens Serum InstituteCopenhagen, Denmark; Department of Pediatrics, Copenhagen University Hospital HvidovreCopenhagen, Denmark
| | - Bente U Andreassen
- Department of Pediatrics, H.C. Andersen's Hospital, University of Odense Odense, Denmark
| | - Henrik V Nielsen
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre Copenhagen, Denmark
| | - Andreas M Petersen
- Department of Microbiology and Infection Control, Statens Serum InstituteCopenhagen, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital HvidovreCopenhagen, Denmark; Department of Gastroenterology, Copenhagen University Hospital HvidovreCopenhagen, Denmark
| | - Karen A Krogfelt
- Department of Microbiology and Infection Control, Statens Serum Institute Copenhagen, Denmark
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