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Hyun M, Lee JY, Lim KR, Kim HA. Clinical Characteristics of Uncomplicated Acute Pyelonephritis Caused by Escherichia coli and Klebsiella pneumoniae. Infect Dis Ther 2024; 13:581-595. [PMID: 38460083 DOI: 10.1007/s40121-024-00940-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/09/2024] [Indexed: 03/11/2024] Open
Abstract
INTRODUCTION This study compared the clinical characteristics and antimicrobial susceptibility of uncomplicated acute pyelonephritis (APN) caused by Escherichia coli and Klebsiella pneumoniae. METHODS We retrospectively reviewed the medical records of patients with uncomplicated APNs caused by E. coli and K. pneumoniae admitted to Keimyung University Dongsan Hospital between February 2014 and December 2021. RESULTS We enrolled 497 patients (372 with E. coli infection, 125 with K. pneumoniae infection). Male, healthcare-associated infection, solid tumors, liver cirrhosis, chronic renal disease, solid organ transplantation, and antibiotic usage within the last 3 months were more strongly associated with K. pneumoniae uncomplicated APNs than with E. coli. Bacteremia and fever occurred more frequently in E. coli uncomplicated APNs. Antimicrobial resistance rates to piperacillin/tazobactam and carbapenem were higher in K. pneumoniae. Antimicrobial resistance rates to aztreonam and ciprofloxacin were lower in K. pneumoniae. Thirty-day mortality was more observed in K. pneumoniae group in univariate analysis, but this difference was not observed after adjustment. Male sex, ultimately fatal disease in McCabe, and prior antibiotic use within 3 months were more associated with K. pneumoniae. CONCLUSIONS Male, underlying diseases, and prior antibiotic use was more associated with K. pneumoniae. Further study will be needed that microbiome of each situation and the related with the distribution of the strains.
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Affiliation(s)
- Miri Hyun
- Department of Infectious Diseases, Keimyung University Dongsan Hospital, School of Medicine & Institute for Medical Science, Keimyung University, Keimyung University, 1035 Dalgubeol-daero, Dalseogu, Daegu, 42601, South Korea
| | - Ji Yeon Lee
- Department of Infectious Diseases, Keimyung University Dongsan Hospital, School of Medicine & Institute for Medical Science, Keimyung University, Keimyung University, 1035 Dalgubeol-daero, Dalseogu, Daegu, 42601, South Korea
| | - Kyong Ree Lim
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, 892 Dongnam-ro, Gangdonggu, Seoul, 05278, South Korea
| | - Hyun Ah Kim
- Department of Infectious Diseases, Keimyung University Dongsan Hospital, School of Medicine & Institute for Medical Science, Keimyung University, Keimyung University, 1035 Dalgubeol-daero, Dalseogu, Daegu, 42601, South Korea.
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Park DE, Aziz M, Koch BJ, Roach K, Clabots C, Johnson JR, Price LB, Liu CM. Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss. EBioMedicine 2024; 99:104909. [PMID: 38096689 PMCID: PMC10758731 DOI: 10.1016/j.ebiom.2023.104909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R clade (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. METHODS Veterans and their household members underwent longitudinal fecal swab surveillance for ST131 in 2014-2018. The fecal microbiome was characterized by 16S rRNA qPCR and sequencing. We evaluated associations between ST131-H30R carriage and gut microbiome at baseline by random forest models to identify the most informative gut bacterial phyla and genera attributes for ST131 and ST131-H30R carriage status. Next, we assessed longitudinal associations between fecal microbiome and ST131-H30R carriage using a mixed-effects logistic regression with longitudinal measures. FINDINGS Of the 519 participants, 78 were carriers of ST131, among whom 49 had ST131-H30R. At the baseline timepoint, H30R-positive participants had higher proportional abundances of Actinobacteria phylum (mean: 4.9% vs. 3.1%) than ST131-negative participants. H30R-positive participants also had higher abundances of Collinsella (mean: 2.3% vs. 1.1%) and lower abundances of Alistipes (mean: 2.1% vs. 2.6%) than ST131-negative participants. In the longitudinal analysis, Collinsella abundance correlated positively with ST131-H30R carriage status and negatively with the loss of ST131-H30R. Conversely, Alistipes corresponded with the loss and persistent absence of ST131-H30R even in the presence of a household exposure. INTERPRETATION Abundances of specific fecal bacteria correlated with ST131-H30R carriage, persistence, and loss, suggesting their potential as targets for microbiome-based strategies to reduce carriage of ST131-H30R, a significant risk factor for invasive infections. FUNDING This work was supported in part by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R21AI117654 and UM1AI104681 and the Office of Research and Development, Department of Veterans Affairs. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Department of Veterans Affairs.
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Affiliation(s)
- Daniel E Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, 617 S Beaver St., Flagstaff, AZ, 86011, USA
| | - Kelsey Roach
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA
| | - James R Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA; Department of Medicine, University of Minnesota, 401 East River Parkway, VCRC 1st, UK Floor, Suite 131, Minneapolis, MN, 55455, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
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Singh SR, Tang CY, Mao B, Soeng S, Ling CL, Teo JQM, Vonthanak S, Turner P, Hsu LY, Ong RTH. Whole genome sequencing of multidrug resistant Enterobacterales identified in children and their household members within Siem Reap, Cambodia. JAC Antimicrob Resist 2023; 5:dlad067. [PMID: 37325250 PMCID: PMC10265595 DOI: 10.1093/jacamr/dlad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Objectives To explore the association of recent hospitalization and asymptomatic carriage of multidrug-resistant Enterobacterales (MDRE) and determine the prevailing strains and antibiotic resistance genes in Siem Reap, Cambodia using WGS. Methods In this cross-sectional study, faecal samples were collected from two arms: a hospital-associated arm consisted of recently hospitalized children (2-14 years), with their family members; and a community-associated arm comprising children in the matching age group and their family members with no recent hospitalization. Forty-two families in each study arm were recruited, with 376 enrolled participants (169 adults and 207 children) and 290 stool specimens collected from participants. The DNA of ESBL- and carbapenemase-producing Enterobacterales cultured from the faecal samples was subject to WGS on the Illumina NovaSeq platform. Results Of the 290 stool specimens, 277 Escherichia coli isolates and 130 Klebsiella spp. were identified on CHROMagar ESBL and KPC plates. The DNA of 276 E. coli (one isolate failed quality control test), 89 Klebsiella pneumoniae, 40 Klebsiella quasipneumoniae and 1 Klebsiella variicola was sequenced. CTX-M-15 was the most common ESBL gene found in E. coli (n = 104, 38%), K. pneumoniae (n = 50, 56%) and K. quasipneumoniae (n = 16, 40%). The prevalence of bacterial lineages and ESBL genes was not associated with any specific arm. Conclusions Our results demonstrate that MDRE is likely to be endemic within the Siem Reap community. ESBL genes, specifically blaCTX-M, can be found in almost all E. coli commensals, indicating that these genes are continuously propagated in the community through various unknown channels at present.
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Affiliation(s)
- Shweta R Singh
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Bunsoth Mao
- University of Health Sciences, Phnom Penh, Cambodia
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | | | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, NUHS Tower Block, National University of Singapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
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Toombs-Ruane LJ, Marshall JC, Benschop J, Drinković D, Midwinter AC, Biggs PJ, Grange Z, Baker MG, Douwes J, Roberts MG, French NP, Burgess SA. Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study. Int J Infect Dis 2023; 128:325-334. [PMID: 36529370 DOI: 10.1016/j.ijid.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.
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Affiliation(s)
- Leah J Toombs-Ruane
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Jonathan C Marshall
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | - Jackie Benschop
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Dragana Drinković
- Microbiology Department, North Shore Hospital, Auckland, New Zealand
| | - Anne C Midwinter
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J Biggs
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; School of Natural Sciences, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Zoë Grange
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael G Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Jeroen Douwes
- Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Mick G Roberts
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Nigel P French
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand; Research Centre for Hauora and Health, Massey University, Wellington, New Zealand
| | - Sara A Burgess
- (m)EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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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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Godijk NG, Bootsma MCJ, Bonten MJM. Transmission routes of antibiotic resistant bacteria: a systematic review. BMC Infect Dis 2022; 22:482. [PMID: 35596134 PMCID: PMC9123679 DOI: 10.1186/s12879-022-07360-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Background Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes. Methods PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included. Results We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled. Conclusion Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07360-z.
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Affiliation(s)
- Noortje G Godijk
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Mathematics, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Nobrega D, Peirano G, Lynch T, Finn TJ, Devinney R, Pitout JDD. Spatial distribution of Escherichia coli ST131 C subclades in a centralized Canadian urban region. J Antimicrob Chemother 2021; 76:1135-1139. [PMID: 33547472 DOI: 10.1093/jac/dkab020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/11/2021] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Escherichia coli ST131 is the most common multidrug-resistant (MDR) E. coli clone causing bloodstream infections (BSIs) in Calgary. This study describes patient characteristics and spatial distribution of ST131 subclades C1 and C2 causing BSIs in Calgary. METHODS E. coli from blood (n = 685) obtained in Calgary, Canada, (2016) were PCR screened for ST131 and positives (n = 141) underwent whole genome sequencing. Patient characteristics were analysed using Fisher's Exact/t-tests and spatial analysis was used to identify clusters. RESULTS Overall, 21% of E. coli was identified as ST131 and clade C dominated the population. ST131-C2 was associated with blaCTX-M-15 and significantly more MDR than ST131-C1. The spatial distribution in Calgary showed that ST131-C1 was mainly present in long-term care (LTC) residents whereas ST131-C2 clustered in a specific North East (NE) Calgary sector comprising of six neighbourhoods without LTC centres. This NE sector has high immigration and travel rates from the Indian subcontinent. CONCLUSIONS This study showed that ST131 C subclades have different geographical distribution patterns in Calgary. We believe that recent travel to and immigration from certain high-risk regions for antimicrobial resistance are responsible for the ST131-C2 NE Calgary clustering pattern.
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Affiliation(s)
- Diego Nobrega
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Gisele Peirano
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Tarah Lynch
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Thomas J Finn
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Rebekah Devinney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Johann D D Pitout
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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9
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The evolutionary puzzle of Escherichia coli ST131. INFECTION GENETICS AND EVOLUTION 2020; 81:104265. [PMID: 32112974 DOI: 10.1016/j.meegid.2020.104265] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/22/2020] [Accepted: 02/26/2020] [Indexed: 01/02/2023]
Abstract
The abrupt expansion of Escherichia coli sequence type (ST) 131 is unmatched among Gram negative bacteria. In many ways, ST131 can be considered a real-world model for the complexities involved in the evolution of a multidrug resistant pathogen. While much progress has been made on our insights into the organism's population structure, pathogenicity and drug resistance profile, significant gaps in our knowledge remain. Whole genome studies have shed light on key mutations and genes that have been selected against the background of antibiotics, but in most cases such events are inferred and not supported by experimental data. Notable examples include the unknown fitness contribution made by specific plasmids, genomic islands and compensatory mutations. Furthermore, questions remain like why this organism in particular achieved such considerable success in such a short time span, compared to other more pathogenic and resistant clones. Herein, we document what is known regarding the genetics of this organism since its first description in 2008, but also highlight where work remains to be done for a truly comprehensive understanding of the biology of ST131, in order to account for its dramatic rise to prominence.
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Ripabelli G, Sammarco ML, Scutellà M, Felice V, Tamburro M. Carbapenem-Resistant KPC- and TEM-Producing Escherichia coli ST131 Isolated from a Hospitalized Patient with Urinary Tract Infection: First Isolation in Molise Region, Central Italy, July 2018. Microb Drug Resist 2019; 26:38-45. [PMID: 31386590 DOI: 10.1089/mdr.2019.0085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In July 2018, a Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli ST131 was isolated from a patient admitted to the Vascular Surgery Unit of the main hospital of Molise region, Central Italy. Sequencing and alignment with the available sequences revealed that the isolate harbored the KPC-2 variant and TEM-1 beta-lactamase. This observation raises great concerns about the spread of carbapenem resistance in national and local settings with high endemicity level of KPC in K. pneumoniae, and underlines the importance of strengthening a proactive surveillance.
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Affiliation(s)
- Giancarlo Ripabelli
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
| | - Massimiliano Scutellà
- Laboratory Medicine Unit, "Antonio Cardarelli" Hospital, Azienda Sanitaria Regionale del Molise, Campobasso, Italy
| | - Valentina Felice
- Laboratory Medicine Unit, "Antonio Cardarelli" Hospital, Azienda Sanitaria Regionale del Molise, Campobasso, Italy
| | - Manuela Tamburro
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
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11
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Wu PC, Wang JL, Hsueh PR, Lin PH, Cheng MF, Huang IF, Chen YS, Lee SSJ, Guang-Yuan M, Yu HC, Hsu CL, Wang FW, Chen CS, Hung CH, Ko WC. Prevalence and risk factors for colonization by extended-spectrum β-lactamase-producing or ST 131 Escherichia coli among asymptomatic adults in community settings in Southern Taiwan. Infect Drug Resist 2019; 12:1063-1071. [PMID: 31118712 PMCID: PMC6506006 DOI: 10.2147/idr.s201086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/29/2019] [Indexed: 12/22/2022] Open
Abstract
Purpose: Fecal carriage of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) is common in Asia, especially in China and Southeast Asia. There are no data about fecal carriage of ESBL-EC and mcr-1-positive E. coli in Taiwan, and few studies focusing on the risk factors of asymptomatic fecal carriage of epidemic ST131 E. coli have been published. Patients and methods: From healthy inhabitants attending health examinations at a medical center in southern Taiwan in 2017, we collected 724 stool samples, which were examined for ESBL-EC fecal carriage using chromogenic medium. ST131 and mcr1-positive E. coli were also investigated using multiplex PCR. Clinical data from all participating adults were collected to analyze the risk factors for fecal ESBL-EC or ST131 E. coli carriage. Results: The prevalence rate of asymptomatic ESBL-EC fecal carriage in adults was 1.9% (14/724). ST131 was found in 22 (3.0%) adults and mcr-1-positive E. coli was found in three (0.4%) adults. A multivariate analysis showed that the risk factors associated with ESBL-EC carriage were diabetes mellitus (adjusted odds ratio [aOR]: 5.5, 95% confidence interval [CI]: 1.3–22.7), a history of colonic polyps (aOR: 6.4, 95% CI: 1.6–24.9), and chronic renal insufficiency (aOR: 20.7, 95% CI: 1.4–305.7). Underlying cancer (aOR: 4.8, 95% CI: 1.0–22.5) and stroke (aOR: 18.0, 95% CI: 1.6–207.5) were associated with ST131 E. coli fecal carriage. In our cohort, travel to Asian countries and food habit were not associated with ST131 or ESBL-EC fecal carriage. Conclusions: The ESBL-EC or ST131 E. coli fecal carriage rate is low among asymptomatic adults in Taiwan. Certain underlying medical conditions were associated with their fecal carriage.
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Affiliation(s)
- Pin-Chieh Wu
- Department of Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Nursing, Meiho University, Pingtung, Taiwan
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Hsiang Lin
- Department of Emergency Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ming-Fang Cheng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.,Department of Nursing, Fooyin University, Kaohsiung, Taiwan
| | - I-Fei Huang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yao-Shen Chen
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Susan Shin-Jung Lee
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Mar Guang-Yuan
- Department of Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hsien-Chung Yu
- Department of Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Health Care Management, Department of Business Management, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chiao-Lin Hsu
- Department of Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Nursing, Meiho University, Pingtung, Taiwan
| | - Fu-Wei Wang
- Department of Nursing, Meiho University, Pingtung, Taiwan.,Department of Family Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chi-Shen Chen
- Department of Physical Examination Center, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Hsin Hung
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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12
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钟 一, 张 晓, 刘 文, 杨 芳, 晏 群, 刘 清, 李 艳, 李 虹, 邹 明. [Bloodstream infections with Escherichia coli O16-ST131 and O25b-ST131: molecular epidemiology, phylogenetic analysis and antimicrobial resistance]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:1521-1526. [PMID: 30613024 PMCID: PMC6744214 DOI: 10.12122/j.issn.1673-4254.2018.12.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To investigate the phylogenetics and prevalence of bloodstream infections with Escherichia coli ST131, the antimicrobial resistance profiles of the pathogens, and the clinical features. METHODS Non-duplicate Escherichia coli isolates were collected from 144 patients with bloodstream infections in our hospital between January and December, 2016.The phylogenetic groups of the isolates were analyzed using multiplex PCR, and O serotyping of ST131 strains was performed by allele-specific PCR.The clinical characteristics of the 144 patients were analyzed to define the differences in the clinical features between patients with ST131 infection and those with non-ST131 infection.Antibiotic susceptibility of the isolates was determined using the Vitek 2 compact system. RESULTS The phylogenetic group analysis showed a domination by group B2 (41.0%[59/144]), followed by group F, group B1 and group E, which accounted for 16.7%(24/144), 13.9%(20/144), and 13.2% (19/144), respectively.Nine strains (6.3%) of Escherichia coli were identified to be ST131 strains, among which 8 were O25b-B2-ST131 strains and 1 was O16-B2-ST131 strain.Of the 9 cases of ST131 infection, 7(77.8%) were found to occur in a nosocomial setting.The demographic characteristics and clinical features of the ST131-infected patients were similar to those of non-ST131-infected patients.ST131 strains were sensitive to piperacillin/tazobactam, imipenem, ertapenem, and amikacin, but showed high resistance rates to cefazolin, ceftriaxone, ciprofloxacin, levofloxacin, gentamicin, and trimethoprim/ sulfamethoxazole (all over 50%).The positivity rate of ESBLs in the ST131 strains was 77.8%, and the multidrug resistance rate reached 88.9%, which was higher than that of non-ST131 isolates, but the difference was not statistically significant. CONCLUSIONS The most common phylogenetic groups of Escherichia coli isolates from patients with bloodstream infections are group B2 and F, and the positivity rate of ST131 is low.We for the first time detected O16-ST131 in patients with blood-borne infections in China.The clinical features of ST131-infected patients are similar to those of non-ST131-infected patients.The positivity rate of ESBLs and the multidrug resistance rate are high in ST131 strains, which may raise concerns in the future.
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Affiliation(s)
- 一鸣 钟
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 晓荷 张
- 中南大学湘雅医学院医学检验系,湖南 长沙 410013Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - 文恩 刘
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 芳 杨
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 群 晏
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 清霞 刘
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 艳明 李
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 虹玲 李
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - 明祥 邹
- 中南大学湘雅医院检验科,湖南 长沙 410008Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
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13
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Morales Barroso I, López-Cerero L, Navarro MD, Gutiérrez-Gutiérrez B, Pascual A, Rodríguez-Baño J. Intestinal colonization due to Escherichia coli ST131: risk factors and prevalence. Antimicrob Resist Infect Control 2018; 7:135. [PMID: 30473785 PMCID: PMC6238289 DOI: 10.1186/s13756-018-0427-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia coli sequence type 131 (ST131) is a successful clonal group that has dramatically spread during the last decades and is considered an important driver for the rapid increase of quinolone resistance in E. coli. Methods Risk factors for rectal colonization by ST131 Escherichia coli (irrespective of ESBL production) were investigated in 64 household members (18 were colonized) and 54 hospital contacts (HC; 10 colonized) of 34 and 30 index patients with community and nosocomial infection due to these organisms, respectively, using multilevel analysis with a p limit of < 0.1. Result Colonization among household members was associated with the use of proton-pump inhibitors (PPI) by the household member (OR = 3.08; 95% CI: 0.88–10.8) and higher age of index patients (OR = 1.05; 95% CI; 1.01–1.10), and among HC, with being bed-ridden (OR = 21.1; 95% CI: 3.61–160.0) and having a urinary catheter (OR = 8.4; 95% CI: 0.87–76.9). Conclusion Use of PPI and variables associated with higher need of person-to-person contact are associated with increased risk of rectal colonization by ST131. These results should be considered for infection control purposes.
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Affiliation(s)
- Isabel Morales Barroso
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain.,3Unidad Clínica de Urgencias, Hospital Universitario Virgen Macarena, Seville, Spain
| | - Lorena López-Cerero
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain
| | - María Dolores Navarro
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain
| | - Belén Gutiérrez-Gutiérrez
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain
| | - Alvaro Pascual
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain
| | - Jesús Rodríguez-Baño
- 1Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain.,2Departamentos de Medicina y Microbiología, Universidad de Sevilla / CSIC/ Instituto de Biomedicina de Sevilla, Seville, Spain
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14
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An ounce of prevention. Clin Microbiol Infect 2018; 24:1037-1038. [DOI: 10.1016/j.cmi.2018.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/19/2018] [Accepted: 08/19/2018] [Indexed: 11/22/2022]
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15
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Clinical and Molecular Correlates of Escherichia coli Bloodstream Infection from Two Geographically Diverse Centers in Rochester, Minnesota, and Singapore. Antimicrob Agents Chemother 2018; 62:AAC.00937-18. [PMID: 30082285 DOI: 10.1128/aac.00937-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/26/2018] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated H30 subclone, H30R1 and H30Rx. We examined clinical and molecular correlates of E. coli bacteremia in two geographically distinct centers. We retrospectively studied 251 unique E. coli bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, blaCTX-M type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all E. coli bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated H30Rx clade was more prominent in SG than in MN (15% versus 4%; P = 0.04). In SG only, patients with STc131 (versus other E. coli STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; P = 0.005); this was true specifically for patients with H30Rx (odds ratio, 7.0; P = 0.005). H30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for H30Rx than for H30R1, non-H30 STc131, and non-STc131 isolates (P < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated H30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for H30/H30Rx might facilitate earlier prescribing of active therapy.
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