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Tchesnokova V, Larson L, Basova I, Sledneva Y, Choudhury D, Solyanik T, Heng J, Bonilla TC, Pasumansky I, Bowers V, Pham S, Madziwa LT, Holden E, Tartof SY, Ralston JD, Sokurenko EV. Gut resident Escherichia coli profile predicts the eighteen-month probability and antimicrobial susceptibility of urinary tract infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305377. [PMID: 38645148 PMCID: PMC11030298 DOI: 10.1101/2024.04.05.24305377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Community-acquired UTI is the most common bacterial infection managed in general medical practice that can lead to life-threatening outcomes. While UTIs are primarily caused by Escherichia coli colonizing the patient's gut, it is unclear whether the gut resident E. coli profiles can predict the person's risks for UTI and optimal antimicrobial treatments. Thus, we conducted an eighteen-month long community-based observational study of fecal E. coli colonization and UTI in women aged 50 years and above. Methods and Findings We enrolled a total of 1,804 women distributed among age groups 50-59 yo (437 participants), 60-69 yo (632), 70-79 yo (532), and above 80 yo (203), lacking antibiotic prescriptions for at least one year. The provided fecal samples were plated for the presence of E. coli and other enterobacteria resistant to trimethoprim/sulfamethoxazole (TMP/STX), ciprofloxacin (CIP) and 3rd generation cephalosporins (3GC). E. coli was also characterized as belonging to the pandemic multi-drug resistant clonal groups ST131 (subclone H30) and ST1193. Following sample collection, the women were monitored for 18 months for occurrence of UTI.E. coli was cultured from 90.8% fecal samples, with 24.1% containing bacteria resistant to TMP/STX, 19.4% to CIP, and 7.9% to 3GC. In 62.5% samples, only all-susceptible E. coli were present. Overall, there were no age-related differences in resistance prevalence. However, while the total E. coli H30 and ST1193 carriage rates were similar (4.3% and 4.2%, respectively), there was a notable increase of H30 carriage with age (P = .001), while carriage decreased with age for ST1193 (P = .057).Within 18 months, 184 women (10.2%) experienced at least one episode of UTI - 10.9% among the gut E. coli carriers and 3.0% among the non-carriers (P=.0013). The UTI risk among carriers of E. coli H30 but not ST1193 was significantly above average (24.3%, P = .0004). The UTI probability increased with age, occurring in 6.4% of 50-59 yo and 19.7% of 80+ yo (P<.001), with the latter group being especially at high risk for UTI, if they were colonized by E. coli H30 (40.0%, P<.001).E. coli was identified in 88.1% of urine samples, with 16.1% resistant to TMP/STX, 16.1% to CIP, 4.2% to 3GC and 73.1% to none of the antibiotics. Among tested urinary E. coli resistant to antibiotics, 86.1% matched the resistance profile of E. coli in the fecal samples, with the clonotyping and whole genome sequencing confirming the matching strains' identity. Positive predictive value (PPV) of using gut resistance profiles to predict UTI pathogens' susceptibility to TMP/STX, CIP, 3GC and all three antibiotics were 98.4%, 98.3%, 96.6% and 95.3%, respectively. Corresponding negative predictive values (NPV) were 63.0%, 54.8%, 44.4% and 75.8%, respectively. The AUC ROC curve values for the accuracy of fecal diagnostic testing for the prediction of UTI resistance ranged .86-.89. The fecal test-guided drug-bug mismatch rate for empirical (pre-culture) prescription of TMP-SXT or CIP is reduced to ≤2% in 89.6% of patients and 94.8% of patients with an optional 3GC prescription. Conclusion The resistance profile and clonal identity of gut colonizing E. coli, along with the carrier's age, can inform personalized prediction of a patients' UTI risk and the UTI pathogen's antibiotic susceptibility within an 18-month period.
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Affiliation(s)
- Veronika Tchesnokova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Lydia Larson
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Irina Basova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Yulia Sledneva
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Debarati Choudhury
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Thalia Solyanik
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Jennifer Heng
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Teresa Cristina Bonilla
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Isaac Pasumansky
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Victoria Bowers
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Sophia Pham
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Lawrence T. Madziwa
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Erika Holden
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Sara Y. Tartof
- Kaiser Permanente Southern California, Department of Research & Evaluation, Pasadena, 100 S Los Robles, Pasadena, CA 91101, USA
- Kaiser Permanente Bernard J. Tyson School of Medicine, Department of Health Systems Science, 100 S Los Robles, Pasadena, CA 91101, USA
| | - James D. Ralston
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Evgeni V. Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
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Lin FC, Ng WV, Wang HP, Hung CH, Chang JT, Yang CC, Liu PY, Cheng MF. Characterization of young infants with fecal carriage of multidrug-resistant Escherichia coli in Southern Taiwan. Pediatr Neonatol 2024; 65:138-144. [PMID: 37718133 DOI: 10.1016/j.pedneo.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/12/2023] [Accepted: 04/20/2023] [Indexed: 09/19/2023] Open
Abstract
BACKGROUND The accelerating prevalence of extended-spectrum β-lactamase (ESBL)-producing and multidrug-resistance (MDR) Escherichia coli(E. coli) become a public health challenge worldwide. This study aimed to discuss the prevalence of drug-resistant E. coli colonization and analyze its risk factors and clinical characteristics among young infants in Southern Taiwan. METHODS Stool samples were collected from young infants, aged less than three months, within three days of their hospitalization from September to December 2019 in a tertiary hospital. A questionnaire was designed for parents to complete. E. coli colonies were selected and analyzed for antimicrobial susceptibility. PCR-based multilocus sequence typing was to detect the presence of sequence type ST131 and blaCTX-M genes. RESULTS Among 100 enrolled infants, 36% had fecal carriage of E. coli isolates, of which twenty nine (80.5%) were MDR, thirteen (36.1%) were ESBL-producing isolates and five (13.8%) and ten (27.7%) were ST131 and strains carrying CTX-M-14 gene, respectively. Compared to non-ST131 and non-CTX-M-14 gene carrier, isolates of ST131 and CTX-M-14 gene carrier showed a significantly higher resistance rate to cefixime, ceftriaxone, and gentamycin, with p value all <0.05. CONCLUSION The prevalence of ESBL-producing and MDR E. coli fecal carriage were both high in young infants. The most common sequence type is ST131, of which all are strains carrying CTX-M-14. Further surveillance and investigation to control for the high prevalence of antimicrobial-resistant E. coli fecal carriage among infants in Taiwan are warranted.
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Affiliation(s)
- Fang-Chih Lin
- Division of Pediatric Neonatology, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Wailap Victor Ng
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiao-Ping Wang
- Division of Pediatric Neonatology, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Hsin Hung
- Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Jenn-Tzong Chang
- Division of Pediatric Neonatology, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Chih-Chieh Yang
- Division of Pediatric Neonatology, Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Po-Yen Liu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ming-Fang Cheng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; School of Nursing, Fooyin University, Kaohsiung, Taiwan.
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3
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Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
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Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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Bianconi I, Spath M, Aschbacher R, Pedron R, Wieser S, Pagani E. Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Escherichia coli Isolates Collected over a 16-Year Period in Bolzano (Northern Italy). Microb Drug Resist 2024; 30:91-100. [PMID: 38150043 DOI: 10.1089/mdr.2023.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Multidrug-resistant Escherichia coli, particularly carbapenemase producers, are a major source of concern. This study aims to investigate the long-term epidemiology of Verona integron-encoded metallo-β-lactamase (VIM)-producing E. coli in the health district of Bolzano, Northern Italy, by examining the phenotypic and genotypic characteristics of 26 isolates obtained during 2005-2020. Isolates were identified with matrix-assisted laser desorption/ionization time-of-flight, susceptibility testing was by Vitek 2, Sensititre, and Etest; carbapenemase activity was confirmed by Etest and Carbapenemase Inactivation Method (CIM) test; and the VIM-antigen was identified by the NG-Test CARBA 5. Genome sequencing was performed on an Illumina MiSeq platform. Carbapenem minimum inhibitory concentrations varied across methodologies, and overall category agreement between phenotypic methods was low. All 23 sequenced isolates contained blaVIM-1. Eleven (47.8%) isolates belonged to the clonal lineage ST131, with fimH30 being the most common subclone. In Bolzano ST131-fimH30 was present as early as 2005. While the ST131 clonal lineage predominated for the first 10 years, various clonal lineages were present, especially in subsequent years, indicating the concurrent circulation of multiple clonal lineages. Future efforts should focus on the implementation of surveillance methods, including genomic analysis, as well as the use of updated infection control strategies and antibiotic stewardship programs to prevent the spread of these carbapenem-resistant strains.
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Affiliation(s)
- Irene Bianconi
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
- CIBIO-Department of Cellular, Computational and Integrative BiologyTrento, University of Trento, Trentino-Alto Adige, Italy
| | - Manuela Spath
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
| | - Richard Aschbacher
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
| | - Renato Pedron
- CIBIO-Department of Cellular, Computational and Integrative BiologyTrento, University of Trento, Trentino-Alto Adige, Italy
| | - Stefanie Wieser
- Claudiana Higher Provincial School of Health Professions Bolzano, Trentino-Alto Adige, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
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5
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Sapula SA, Amsalu A, Whittall JJ, Hart BJ, Siderius NL, Nguyen L, Gerber C, Turnidge J, Venter H. The scope of antimicrobial resistance in residential aged care facilities determined through analysis of Escherichia coli and the total wastewater resistome. Microbiol Spectr 2023; 11:e0073123. [PMID: 37787536 PMCID: PMC10715142 DOI: 10.1128/spectrum.00731-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/07/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates-a worrying trend seen globally despite measures in place aimed at limiting their use.
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Affiliation(s)
- Sylvia A. Sapula
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anteneh Amsalu
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Department of Medical Microbiology, University of Gondar, Gondar, Ethiopia
| | - Jon J. Whittall
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Bradley J. Hart
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Naomi L. Siderius
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Lynn Nguyen
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Cobus Gerber
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - John Turnidge
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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Cho ST, Mills EG, Griffith MP, Nordstrom HR, McElheny CL, Harrison LH, Doi Y, Van Tyne D. Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571174. [PMID: 38168243 PMCID: PMC10760032 DOI: 10.1101/2023.12.11.571174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL genes belonging to the blaCTX-M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.
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Affiliation(s)
- Shu-Ting Cho
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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7
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Grey B, Upton M, Joshi LT. Urinary tract infections: a review of the current diagnostics landscape. J Med Microbiol 2023; 72. [PMID: 37966174 DOI: 10.1099/jmm.0.001780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Urinary tract infections are the most common bacterial infections worldwide. Infections can range from mild, recurrent (rUTI) to complicated (cUTIs), and are predominantly caused by uropathogenic Escherichia coli (UPEC). Antibiotic therapy is important to tackle infection; however, with the continued emergence of antibiotic resistance there is an urgent need to monitor the use of effective antibiotics through better stewardship measures. Currently, clinical diagnosis of UTIs relies on empiric methods supported by laboratory testing including cellular analysis (of both human and bacterial cells), dipstick analysis and phenotypic culture. Therefore, development of novel, sensitive and specific diagnostics is an important means to rationalise antibiotic therapy in patients. This review discusses the current diagnostic landscape and highlights promising novel diagnostic technologies in development that could aid in treatment and management of antibiotic-resistant UTIs.
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Affiliation(s)
- Braith Grey
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
| | - Mathew Upton
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
| | - Lovleen Tina Joshi
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
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8
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Hamilton WL, Coscione S, Maes M, Warne B, Pike LJ, Khokhar FA, Blane B, Brown NM, Gouliouris T, Dougan G, Török ME, Baker S. The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom. Microb Genom 2023; 9:001122. [PMID: 37902454 PMCID: PMC10634454 DOI: 10.1099/mgen.0.001122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023] Open
Abstract
Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300 E. coli isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of E. coli bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR E. coli populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.
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Affiliation(s)
- William L. Hamilton
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Suny Coscione
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Mailis Maes
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Ben Warne
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lindsay J. Pike
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Fahad A. Khokhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UK
| | - Beth Blane
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
| | - Nicholas M. Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Gordon Dougan
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - M. Estée Török
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Stephen Baker
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
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Ballash GA, Diaz-Campos D, van Balen JC, Mollenkopf DF, Wittum TE. Previous Antibiotic Exposure Reshapes the Population Structure of Infecting Uropathogenic Escherichia coli Strains by Selecting for Antibiotic Resistance over Urovirulence. Microbiol Spectr 2023; 11:e0524222. [PMID: 37338386 PMCID: PMC10433818 DOI: 10.1128/spectrum.05242-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
Antibiotic therapy is the standard of care for urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC). However, previous antibiotic therapy may impart a selective pressure that influences the population structure and pathogenic potential of infecting UPEC strains. Here, we conducted a 3-year study using whole-genome-sequencing analysis and retrospective medical record review to characterize how antibiotic exposure influenced the phenotypic antibiotic resistance, acquired resistome, virulome, and population structure of 88 UTI-causing E. coli strains from dogs. A majority of UTI-associated E. coli strains were from phylogroup B2 and clustered within sequence type 372. Previous antibiotic exposure was associated with a population shift toward UPEC from phylogroups other than the typical urovirulent phylogroup B2. The specific virulence profiles within the accessory virulome that were associated with antibiotic use were elicited by the effect of antibiotics on UPEC phylogenetic structure. Among phylogroup B2, antibiotic exposure increased the quantity of genes within the resistome and the odds of developing reduced susceptibility to at least one antibiotic. Non-B2 UPEC strains harbored a more diverse and greater resistome that conferred reduced susceptibility to multiple antibiotic classes following antibiotic exposure. Collectively, these data suggest that previous antibiotic exposure establishes an environment that provides a selective edge to non-B2 UPEC strains through their diverse and abundant antibiotic resistance genes, despite their lack of urovirulence genes. Our findings highlight the necessity for judicious use of antibiotics as we uncover another mechanism by which antibiotic exposure and resistance can influence the dynamics of bacterial infectious disease. IMPORTANCE Urinary tract infections (UTIs) are one of the most common infections of dogs and humans. While antibiotic therapy is the standard of care for UTIs and other infections, antibiotic exposure may influence the pathogenic profile of subsequent infections. We used whole-genome sequencing and retrospective medical record review to characterize the effect of systemic antibiotic therapy on the resistance, virulence, and population structure of 88 UTI-causing UPEC strains isolated from dogs. Our results indicate that antibiotic exposure alters the population structure of infecting UPEC strains, providing a selective edge for non-B2 phylogroups that harbor diverse and abundant resistance gene catalogues but fewer urovirulence genes. These findings highlight how antibiotic resistance can influence pathogen infection dynamics and have clinical implications for the judicious use of antibiotics for bacterial infections.
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Affiliation(s)
- Gregory A. Ballash
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Dubraska Diaz-Campos
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Joany C. van Balen
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Dixie F. Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Thomas E. Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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10
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Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F. The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLoS Genet 2023; 19:e1010842. [PMID: 37531401 PMCID: PMC10395866 DOI: 10.1371/journal.pgen.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Affiliation(s)
- Judit Burgaya
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, UMR CNRS 6047, Université Paris-Cité, Paris, France
| | | | | | | | | | | | - Agnès Lefort
- Université Paris Cité, INSERM, IAME, Paris, France
| | | | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR7241 / INSERM U1050, PSL Research University, Paris, France
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11
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Brumwell A, Sutton G, Lantos PM, Hoffman K, Ruffin F, Brinkac L, Clarke TH, Adams MD, Fowler VG, Fouts DE, Thaden JT. Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source. J Clin Microbiol 2023; 61:e0019923. [PMID: 37338371 PMCID: PMC10358158 DOI: 10.1128/jcm.00199-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/18/2023] [Indexed: 06/21/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone, although its clinical impact on patients with bloodstream infection (BSI) is incompletely understood. This study aims to further define the risk factors, clinical outcomes, and bacterial genetics associated with ST131 BSI. A prospectively enrolled cohort study of adult inpatients with E. coli BSI was conducted from 2002 to 2015. Whole-genome sequencing was performed with the E. coli isolates. Of the 227 patients with E. coli BSI in this study, 88 (39%) were infected with ST131. Patients with E. coli ST131 BSI and those with non-ST131 BSI did not differ with respect to in-hospital mortality (17/82 [20%] versus 26/145 [18%]; P = 0.73). However, in patients with BSI from a urinary tract source, ST131 was associated with a numerically higher in-hospital mortality than patients with non-ST131 BSI (8/42 [19%] versus 4/63 [6%]; P = 0.06) and increased mortality in an adjusted analysis (odds ratio of 5.85; 95% confidence interval of 1.44 to 29.49; P = 0.02). Genomic analyses showed that ST131 isolates primarily had an H4:O25 serotype, had a higher number of prophages, and were associated with 11 flexible genomic islands as well as virulence genes involved in adhesion (papA, kpsM, yfcV, and iha), iron acquisition (iucC and iutA), and toxin production (usp and sat). In patients with E. coli BSI from a urinary tract source, ST131 was associated with increased mortality in an adjusted analysis and contained a distinct repertoire of genes influencing pathogenesis. These genes could contribute to the higher mortality observed in patients with ST131 BSI.
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Affiliation(s)
- Amanda Brumwell
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, USA
- Noblis, Inc., Washington, DC, USA
| | - Paul M. Lantos
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kate Hoffman
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | - Mark D. Adams
- J. Craig Venter Institute, Rockville, Maryland, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Clinical Research Institute, Durham, North Carolina, USA
| | | | - Joshua T. Thaden
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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12
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Jespersen ML, Munk P, Johansen J, Kaas RS, Webel H, Vigre H, Nielsen HB, Rasmussen S, Aarestrup FM. Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering. Commun Biol 2023; 6:700. [PMID: 37422584 PMCID: PMC10329687 DOI: 10.1038/s42003-023-05083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.
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Affiliation(s)
- Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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13
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Celebi D, Aydın E, Rakici E, Baser S, Celebi O, Taghizadehghalehjoughi A. Evaluation of presence of clone ST131 and biofilm formation in ESBL producing and non-producing Escherichia coli strains. Mol Biol Rep 2023:10.1007/s11033-023-08532-z. [PMID: 37256442 DOI: 10.1007/s11033-023-08532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Escherichia coli ST131 is a pandemic clone associated with multidrug resistance, starting with beta-lactamase production and fluoroquinolone resistance in the first place, leading to significant systemic infections. Clones that develop due to the frequency of antimicrobial resistance and the rate of spread in our country are important issues that need to be investigated. This study aims to investigate the incidence of ST131which is a "high-risk pandemic clone E. coli" in ESBL-producing and non-ESBL-producing strains, as well as their biofilm-forming abilities and antibiotic resistance rates. MATERIALS AND METHODS A total of 86 E. coli isolates were used in the study. Bacterial identifications were performed by conventional and automated methods. The double disc synergy method was used to demonstrate the presence of ESBL. Molecular studies in all E. coli strains were performed by real-time PCR method. FINDINGS 86 strains were studied, of which 83.72% were urine, 6.98% were wound, 4.65% were blood, and 2.33% were tracheal aspirate and sputum. 79.07% of these strains were ESBL-positive. 58.1% of the strains were female, whereas 41.9% were male patients, and the average age was 46.2. Out of 86 strains, 38.72% were ST131 positive, the H30 subclone was detected in 27.27% of them, and the H30-Rx subclone was detected in all of the H30 subclone positive strains. The presence of the ESBL resistance gene was detected at the rate of TEM 41.86%, SHV 37.21%, CTX-M 36.04%, and OXA 4.65%. Most commonly SHV gene (54.54%) was seen in ST131 clone-positive samples. Finally, while it was found that 48.83% of the strains formed biofilm by any method, biofilm formation was detected in 69.7% of the samples that were positive for the ST131 clone. RESULT Our study can reveal the dramatic prevalence of the ESBL-producing E. coli strains along with the high-risk ST131 clone, the dominance of the H30Rx subclone of this risky clone, as well as the importance of the influence of resistance mechanisms along with resistance and biofilm.
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Affiliation(s)
- Demet Celebi
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, 25240, Erzurum, Turkey.
- Ataturk University Vaccine Application, and Development Center, Ataturk University, 25240, Erzurum, Turkey.
| | - Elif Aydın
- Tavsanli Vocational School of Health Services, Kutahya Health Sciences University, 430200, Kutahya, Turkey
| | - Erva Rakici
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey
| | - Sumeyye Baser
- Department of Medical Microbiology, Faculty of Medicine, Ataturk University, 25240, Erzurum, Turkey
| | - Ozgur Celebi
- Department of Medical Microbiology, Faculty of Medicine, Ataturk University, 25240, Erzurum, Turkey
| | - Ali Taghizadehghalehjoughi
- Department of Medical Pharmacology, Faculty of Medicine, Şeyh Edebali University, 11000, Bilecik, Turkey
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14
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Sajeev S, Hamza M, Rajan V, Vijayan A, Sivaraman GK, Shome BR, Holmes MA. Resistance profiles and genotyping of extended-spectrum beta-lactamase (ESBL) -producing and non-ESBL-producing E. coli and Klebsiella from retail market fishes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105446. [PMID: 37245778 DOI: 10.1016/j.meegid.2023.105446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/13/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
Studies on antimicrobial resistance (AMR) profiles and epidemiological affirmation for AMR transmission are limited in fisheries and aquaculture settings. Since 2015, based on Global Action Plan on AMR by World Health Organization (WHO) and World Organization for Animal Health (OIE), several initiatives have been under taken to enhance the knowledge, skills and capacity to establish AMR trends through surveillance and strengthening of epidemiological evidence. The focus of this study was to determine the prevalence of antimicrobial resistance (AMR), its resistance profiles and molecular characterization with respect to phylogroups, antimicrobial resistance genes (ARGs), virulence genes (VGs), quaternary ammonium compounds resistance (QAC) genes and plasmid typing in retail market fishes. Pulse field gel electrophoresis (PFGE) to understand the genetic lineage of the two most important Enterobacteriaceae members, E. coli and Klebsiella sp. was performed. 94 fish samples were collected from three different sites viz., Silagrant (S1), Garchuk (S2) and North Guwahati Town Committee (NGTC) Region (S3) in Guwahati, Assam. Out of the 113 microbial isolates from the fish samples, 45 (39.82%) were E. coli; 23 (20.35%) belonged to Klebsiella genus. Among E. coli, 48.88% (n = 22) of the isolates were alerted by the BD Phoenix M50 instrument as ESBL, 15.55% (n = 7) as PCP and 35.55% (n = 16) as non-ESBL. E. coli (39.82%) was the most prevalent pathogen among the Enterobacteriaceae members screened and showed resistance to ampicillin (69%) followed by cefazoline (64%), cefotaxime (49%) and piperacillin (49%). In the present study, 66.66% of E. coli and 30.43% of Klebsiella sp. were categorized as multi drug resistance (MDR) bacteria. CTX-M-gp-1, with CTX-M-15 variant (47%), was the most widely circulating beta-lactamase gene, while other ESBL genes blaTEM (7%), blaSHV (2%) and blaOXA-1-like (2%) were also identified in E. coli. Out of the 23 isolates of Klebsiella, 14(60.86%) were ampicillin (AM)-resistant (11(47.82%) K. oxytoca, 3(13.04%) K. aerogenes), whereas 8(34.78%) isolates of K. oxytoca showed intermediate resistance to AM. All Klebsiella isolates were susceptible to AN, SCP, MEM and TZP, although two K. aerogenes were resistant to imipenem. DHA and LAT genes were detected, respectively, in 7(16%) and 1(2%) of the E. coli strains while a single K. oxytoca (4.34%) isolate carried MOX, DHA and blaCMY-2 genes. The fluoroquinolone resistance genes identified in E. coli included qnrB (71%), qnrS (84%), oqxB (73%) and aac(6)-Ib-cr (27%); however, in Klebsiella, these genes, respectively, had a prevalence of 87%, 26%, 74% and 9%. The E. coli isolates belonged to phylogroup A(47%), B1(33%) and D(14%). All of the 22(100%) ESBL E. coli had chromosome-mediated disinfectant resistance genes viz., ydgE, ydgF, sugE(c), mdfA while 82% of ESBL E. coli had emrE. Among the non-ESBL E. coli isolates, 87% of them showed the presence of ydgE, ydgF and sugE(c) genes, while 78% of the isolates had mdfA and 39% had emrE genes respectively. 59% of the ESBL and 26% of the non-ESBL E. coli had showed the presence of qacEΔ1. The sugE(p) was present in 27% of the ESBL-producing E. coli and in 9% of non-ESBL isolates. Out of the 3 ESBL-producing Klebsiella isolates, 2(66.66%) K. oxytoca isolates were found harboring plasmid-mediated qacEΔ1 gene while one (33.33%) K. oxytoca isolate had sugE(p) gene. IncFI was the most prevalent plasmid type detected in the isolates studied, with A/C (18%), P (14%), X, Y (9% each) and I1-Iγ (14%, 4%). 50% (n = 11) of the ESBL and 17% (n = 4) of the non-ESBL E. coli isolates harboured IncFIB and 45% (n = 10) ESBL and one (4.34%) non-ESBL E. coli isolates harboured IncFIA. Dominance of E. coli over other Enterobacterales and diverse phylogenetic profiles of E. coli and Klebsiella sp. suggests the possibility of contamination and this may be due to compromised hygienic practices along the supply chain and contamination of aquatic ecosystem. Continuous surveillance in domestic markets must be a priority in addressing antimicrobial resistance in fishery settings and to identify any unwarranted epidemic clones of E. coli and Klebsiella that can challenge public health sector.
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Affiliation(s)
- Sudha Sajeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Muneeb Hamza
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Vineeth Rajan
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Ardhra Vijayan
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, India.
| | - Bibek R Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, UK
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15
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Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
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Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
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16
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Pitout JDD, Chen L. The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli. Infect Dis Ther 2023; 12:1029-1041. [PMID: 36947392 PMCID: PMC10147871 DOI: 10.1007/s40121-023-00791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.
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Affiliation(s)
- Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.
- Dynacare Laboratories, Alberta, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
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17
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Shahbazi R, Salmanzadeh-Ahrabi S, Aslani MM, Alebouyeh M, Falahi J, Nikbin VS. The genotypic and phenotypic characteristics contributing to high virulence and antibiotics resistance in Escherichia coli O25-B2-ST131 in comparison to non- O25-B2-ST131. BMC Pediatr 2023; 23:59. [PMID: 36737722 PMCID: PMC9895973 DOI: 10.1186/s12887-023-03866-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Escherichia coli serogroup O25b-sequence type 131 (E. coli O25-B2-ST131) is considered as multidrug-resistant and hypervirulent organism. There is lack of data about involvement of this pathogen in the children's infection. In this study, the prevalence, and clonality, virulence capacity, and antibiotic resistance phenotype and genotype of E. coli O25-B2-ST131 compared with non-O25-B2-ST131 isolates were investigated in children with urinary tract infection in Tehran, Iran. METHODS The E. coli isolates from urine samples were identified using conventional microbiological methods. Characterization of E. coli O25-B2-ST131 clone, antibiotic susceptibility, biofilm formation, ESBLs phenotype and genotype, serum resistance, hemolysis, hydrophobicity, and formation of curli fimbriae were done using conventional microbiological and molecular methods. Clonality of the isolates was done by rep-PCR typing. RESULTS Among 120 E. coli isolates, the highest and lowest antibiotic resistance was detected against ampicillin (92, 76.6%) and imipenem 5, (4.1%), respectively. Sixty-eight (56.6%) isolates were ESBL-producing and 58 (48.3%) isolates were considered as multi-drug resistance (MDR). The prevalence of ESBL-producing and MDR isolates in O25-B2-ST131 strains was higher compared with the non-O25-B2-ST131 strains (p value < 0.05). O25-B2-ST131 strains showed significant correlation with serum resistance and biofilm formation. Amongst the resistance and virulence genes, the prevalence of iucD, kpsMTII, cnf1, vat, blaCTX-M-15, and blaSHV were significantly higher among O25-B2-ST131 isolates in comparison with non-O25-B2-ST131 isolates (p value < 0.05). Considering a ≥ 80% homology cut-off, fifteen different clusters of the isolates were shown with the same rep-PCR pattern. CONCLUSIONS Our results confirmed the involvement of MDR-ESBLs producing E. coli strain O25-B2-ST131 in the occurrence of UTIs among children. Source tracking and control measures seem to be necessary for containment of the spread of hypervirulent and resistance variants in children.
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Affiliation(s)
- Razieh Shahbazi
- grid.411354.60000 0001 0097 6984Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Deh Vank Ave., Tehran, 1993891176 Iran
| | - Siavosh Salmanzadeh-Ahrabi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Deh Vank Ave., Tehran, 1993891176, Iran.
| | - Mohammad Mehdi Aslani
- grid.420169.80000 0000 9562 2611Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Masoud Alebouyeh
- grid.411600.2Pediatric Infections Research Center, Research for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Falahi
- Health Clinical Science Research Center, Zahedan Branch, Islamic Azad University, Zahedan, Iran
| | - Vajihe Sadat Nikbin
- grid.420169.80000 0000 9562 2611Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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18
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Obeng-Nkrumah N, Hansen DS, Awuah-Mensah G, Blankson NK, Frimodt-Møller N, Newman MJ, Opintan JA, Krogfelt KA. High level of colonization with 3rd-generation cephalosporin-resistant Enterobacterales in African community settings, Ghana. Diagn Microbiol Infect Dis 2023; 106:115918. [PMID: 37058979 DOI: 10.1016/j.diagmicrobio.2023.115918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
A cross-sectional survey was conducted in eight Ghanaian communities to investigate the extent of intestinal colonization with 3rd-generation cephalosporin-resistant Enterobacterales. The study collected faecal samples and corresponding lifestyle data from 736 healthy residents to assess the occurrence of cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae, with a focus on genotypes of plasmid-mediated ESBLs, AmpCs, and carbapenemases. The results showed that 371 participants (50.4%) carried 3rd-generation cephalosporin-resistant E. coli (n=362) and K. pneumoniae (n=9). Most of these were ESBL-producing E. coli (n=352, 94.9%), carrying CTX-M genes (96.0%, n=338/352), mostly for CTX-M-15 (98.9%, n=334/338). Nine participants (1.2%) carried AmpC-producing E. coli that harboured blaDHA-1 or blaCMY-2 genes, and two participants (0.3%) each carried a carbapenem-resistant E. coli that harboured both blaNDM-1 and blaCMY-2. Quinolone-resistant O25b: ST131 E. coli were recovered from six participants (0.8%) and were all CTX-M-15 ESBL-producers. Having a household toilet facility was significantly associated with a reduced risk of intestinal colonization (adjusted odds ratio, 0.71; 95% CI, 0.48-0.99; P-value=0.0095) in multivariate analysis. These findings raise serious public health concerns, and effective control of the spread of antibiotic-resistant bacteria is possible by providing better sanitary conditions for communities.
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Affiliation(s)
- Noah Obeng-Nkrumah
- Department of Medical Laboratory Sciences, University of Ghana School of Biomedical and Allied Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | | | - Georgina Awuah-Mensah
- School of Life Sciences Medical School, Queen's Medical Centre, University of Nottingham, Nottingham England
| | - Nana Kweiba Blankson
- Department of Microbiological diagnostics, Statens Serum Institut, Copenhagen Denmark
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Mercy Jemima Newman
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Legon, Accra, Ghana
| | - Japheth Awuletey Opintan
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Legon, Accra, Ghana
| | - Karen Angeliki Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark.
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19
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Seo KW, Do KH, Shin MK, Lee WK, Lee WK. Comparative genetic characterization of CMY-2-type beta-lactamase producing pathogenic Escherichia coli isolated from humans and pigs suffering from diarrhea in Korea. Ann Clin Microbiol Antimicrob 2023; 22:7. [PMID: 36658572 PMCID: PMC9854124 DOI: 10.1186/s12941-023-00559-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pathogenic Escherichia coli are an important cause of bacterial infections in both humans and pigs and many of antimicrobials are used for the treatment of E. coli infection. The objective of this study was to investigate the characteristics and relationship between humans and pigs regarding third-generation cephalosporin resistance and CMY-2-producing E. coli in Korea. RESULTS All 103 third-generation cephalosporin-resistant E. coli isolates showed multidrug resistance. Also, except for β-lactam/β-lactamase inhibitor combinations, all antimicrobials resistant rates were higher in pigs than in humans. A total of 36 isolates (humans: five isolates; pigs: 31 isolates) were positive for the CMY-2-encoding genes and thirty-two (88.9%) isolates detected class 1 integrons with 10 different gene cassette arrangements, and only 1 isolate detected a class 2 integron. The most common virulence genes in pigs were LT (71.0%), F18 (51.6%), and STb (51.6%), while stx2 (80.0%) was the most frequently detected gene in humans. Stx2 gene was also detected in pigs (6.5%). Interestingly, 36 CMY-2-producing E. coli isolates showed a high diversity of sequence types (ST), and ST88 was present in E. coli from both pigs (11 isolates) and humans (one isolate). CONCLUSION Our findings suggest that a critical need for comprehensive surveillance of third-generation cephalosporin resistance is necessary to preserve the usefulness of third-generation cephalosporins in both humans and pigs.
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Affiliation(s)
- Kwang-Won Seo
- College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Kyung-Hyo Do
- Laboratory of Veterinary Bacteriology and Infectious Diseases, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Wan-Kyu Lee
- Laboratory of Veterinary Bacteriology and Infectious Diseases, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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20
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Li C, Chen X, Ju Z, Li C, Xu Y, Ding J, Wang Y, Ma P, Gu K, Lei C, Tang Y, Wang H. Comparative Analysis of Phylogenetic Relationships and Virulence Factor Characteristics between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Derived from Clinical Sites and Chicken Farms. Microbiol Spectr 2022; 10:e0255722. [PMID: 36374015 PMCID: PMC9769871 DOI: 10.1128/spectrum.02557-22] [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: 07/15/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance in bacteria is the most urgent global threat to public health, with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) being one of the most documented examples. Nonetheless, the ESBL-E. coli transmission relationship among clinical sites and chicken farms remains unclear. Here, 408 ESBL-E. coli strains were isolated from hospitals and chicken farms in Sichuan Province and Yunnan Province in 2021. We detected blaCTX-M genes in 337 (82.62%) ESBL-E. coli strains. Although the isolation rate, prevalent sequence type (ST) subtypes, and blaCTX-M gene subtypes of ESBL-E. coli varied based on regions and sources, a few strains of CTX-ESBL-E. coli derived from clinical sites and chicken farms in Sichuan Province displayed high genetic similarity. This indicates a risk of ESBL-E. coli transmission from chickens to humans. Moreover, we found that the high-risk clonal strains ST131 and ST1193 primarily carried blaCTX-M-27. This indicates that drug-resistant E. coli from animal and human sources should be monitored. As well, the overuse of β-lactam antibiotics should be avoided in poultry farms to ensure public health and build an effective regulatory mechanism of "farm to fork" under a One Health perspective. IMPORTANCE Bacterial drug resistance has become one of the most significant threats to human health worldwide, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-E. coli). Timely and accurate epidemiological surveys can provide scientific guidance for the adoption of treatments in different regions and also reduce the formation of drug-resistant bacteria. Our study showed that the subtypes of ESBL-E. coli strains prevalent in different provinces are somewhat different, so it is necessary to individualize treatment regimens in different regions, and it is especially important to limit and reduce antibiotic use in poultry farming since chicken-derived ESBL-E. coli serves as an important reservoir of drug resistance genes and has the potential to spread to humans, thus posing a threat to human health. The use of antibiotics in poultry farming should be particularly limited and reduced.
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Affiliation(s)
- Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zijing Ju
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ying Xu
- The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiawei Ding
- Clinical Laboratory Department, Yan’an Hospital Affiliated with Kunming Medical University, Kunming, Yunnan, China
| | - Yuting Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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21
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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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22
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Munk P, Brinch C, Møller FD, Petersen TN, Hendriksen RS, Seyfarth AM, Kjeldgaard JS, Svendsen CA, van Bunnik B, Berglund F, Larsson DGJ, Koopmans M, Woolhouse M, Aarestrup FM. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nat Commun 2022; 13:7251. [PMID: 36456547 PMCID: PMC9715550 DOI: 10.1038/s41467-022-34312-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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Affiliation(s)
- Patrick Munk
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Christian Brinch
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Frederik Duus Møller
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Thomas N Petersen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Anne Mette Seyfarth
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Jette S Kjeldgaard
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Christina Aaby Svendsen
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bram van Bunnik
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
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23
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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: 25] [Impact Index Per Article: 12.5] [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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24
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Gelalcha BD, Kerro Dego O. Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health. Antibiotics (Basel) 2022; 11:antibiotics11101313. [PMID: 36289970 PMCID: PMC9598938 DOI: 10.3390/antibiotics11101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.
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25
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Naini A, Bartetzko MP, Sanapala SR, Broecker F, Wirtz V, Lisboa MP, Parameswarappa SG, Knopp D, Przygodda J, Hakelberg M, Pan R, Patel A, Chorro L, Illenberger A, Ponce C, Kodali S, Lypowy J, Anderson AS, Donald RGK, von Bonin A, Pereira CL. Semisynthetic Glycoconjugate Vaccine Candidates against Escherichia coli O25B Induce Functional IgG Antibodies in Mice. JACS AU 2022; 2:2135-2151. [PMID: 36186572 PMCID: PMC9516715 DOI: 10.1021/jacsau.2c00401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 06/01/2023]
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a major health concern due to emerging antibiotic resistance. Along with O1A, O2, and O6A, E. coli O25B is a major serotype within the ExPEC group, which expresses a unique O-antigen. Clinical studies with a glycoconjugate vaccine of the above-mentioned O-types revealed O25B as the least immunogenic component, inducing relatively weak IgG titers. To evaluate the immunological properties of semisynthetic glycoconjugate vaccine candidates against E. coli O25B, we here report the chemical synthesis of an initial set of five O25B glycan antigens differing in length, from one to three repeat units, and frameshifts of the repeat unit. The oligosaccharide antigens were conjugated to the carrier protein CRM197. The resulting semisynthetic glycoconjugates induced functional IgG antibodies in mice with opsonophagocytic activity against E. coli O25B. Three of the oligosaccharide-CRM197 conjugates elicited functional IgGs in the same order of magnitude as a conventional CRM197 glycoconjugate prepared with native O25B O-antigen and therefore represent promising vaccine candidates for further investigation. Binding studies with two monoclonal antibodies (mAbs) revealed nanomolar anti-O25B IgG responses with nanomolar K D values and with varying binding epitopes. The immunogenicity and mAb binding data now allow for the rational design of additional synthetic antigens for future preclinical studies, with expected further improvements in the functional antibody responses. Moreover, acetylation of a rhamnose residue was shown to be likely dispensable for immunogenicity, as a deacylated antigen was able to elicit strong functional IgG responses. Our findings strongly support the feasibility of a semisynthetic glycoconjugate vaccine against E. coli O25B.
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Affiliation(s)
- Arun Naini
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Max Peter Bartetzko
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Someswara Rao Sanapala
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Felix Broecker
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Victoria Wirtz
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Marilda P. Lisboa
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | | | - Daniel Knopp
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Jessica Przygodda
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Matthias Hakelberg
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Rosalind Pan
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Axay Patel
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Laurent Chorro
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Arthur Illenberger
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Christopher Ponce
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Srinivas Kodali
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Jacqueline Lypowy
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | | | - Robert G. K. Donald
- Pfizer
Vaccine Research and Development, Pearl River, New York 10965, United States
| | - Arne von Bonin
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
| | - Claney L. Pereira
- Vaxxilon
Deutschland GmbH, Part of Idorsia Pharmaceuticals Ltd., Magnusstr. 11, 12489 Berlin, Germany
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26
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Mechesso AF, Na SH, Moon DC, Kim SJ, Choi JH, Song HJ, Yoon SS, Lim SK. Antibiotic Resistance Profiles and Molecular Characteristics of blaCTX-M-15-Carrying Salmonella enterica Serovar Enteritidis Isolates from Healthy and Diseased Chickens in Korea. Foodborne Pathog Dis 2022; 19:663-674. [PMID: 36125409 DOI: 10.1089/fpd.2022.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Enteritidis has emerged as a public health concern. The main objectives of this study were therefore to determine the antimicrobial susceptibility profiles of Salmonella Enteritidis and to investigate the molecular characteristics of identified ESBL-producing isolates. In the study, 237 Salmonella Enteritidis isolates (232 isolates from chickens, 4 from cattle, and 1 from a pig) were recovered from carcasses and fecal samples of healthy and diseased food animals between 2010 and 2017. Ceftiofur resistance was noted only in chicken isolates (43%, 102/237), with the highest in healthy chickens and their carcasses (48.3%, 83/172) compared with that in diseased chickens (31.7%, 19/60). All of the ceftiofur-resistant isolates exhibited resistance to multiple antimicrobials. Indeed, a relatively higher percentage of ceftiofur-resistant isolates demonstrated resistance to the tested aminoglycosides and tetracycline compared with the ceftiofur-susceptible strains. In this study, blaCTX-M-15 was the only ESBL gene detected in all of the ceftiofur-resistant isolates. The blaCTX-M-15-carrying isolates belonged to 11 different pulsotypes. The blaCTX-M-15 gene was transferred from 20.6% (21/102) of the blaCTX-M-15-harboring isolates to a recipient Escherichia coli J53. The coexistence of IncHI2/ST2 and IncFIIs/ST1 plasmids was noted in the majority (81.8%, 18/22) of the transconjugants. E. coli J53 transconjugants carrying blaCTX-M-15 gene showed distinct genetic environments, predominantly ISEcp1-blaCTX-M-15-orf477 (15/21, 71.4%). This study demonstrated that healthy chickens and their carcasses act as reservoirs of blaCTX-M-15-carrying Salmonella Enteritidis that can potentially be transmitted to humans.
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Affiliation(s)
- Abraham Fikru Mechesso
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea.,Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Seok-Hyeon Na
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
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Do KH, Seo K, Lee WK. Antimicrobial resistance, virulence genes, and phylogenetic characteristics of pathogenic Escherichia coli isolated from patients and swine suffering from diarrhea. BMC Microbiol 2022; 22:199. [PMID: 35974313 PMCID: PMC9380393 DOI: 10.1186/s12866-022-02604-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Escherichia (E.) coli causes colibacillosis in swine and humans, and is frequently associated with antimicrobial resistance. In this study we aimed to compare antimicrobial resistance, O-serogroups, virulence genes, and multi-locus sequence type of E. coli between isolates from pigs and patients suffering from diarrhea, and the most prevalent pathogenic E. coli strain from swine isolates in Korea. Methods We tested 64 and 50 E. coli strains from pigs and patients suffering from diarrhea for antimicrobial susceptibility test, virulence genes, O-serogroups, and multi-locus sequence typing. Results We confirmed that isolates from swine showed significantly higher resistance than from those from patients, especially to fluoroquinolone (ciprofloxacin: 37.5 and 10.0%; norfloxacin: 29.7 and 8.0%, respectively). Stx1 (46.0%) was most frequently detected in patients followed by stx2 (38.0%). There was no significant difference in stx2 (swine: 23.4%, patients: 38.0%). In isolates from patients, O157 (12.0%) was the most prevalent O-serogroup, and two isolates (3.1%) from pigs were confirmed to have O157. Additionally, sequence type (ST) 10 (swine: 6 isolates, patients: 2 isolates) and ST 88 (swine: 2 isolates, patients: 1 isolate) were simultaneously detected. Conclusions We found that both isolates from swine and human had the stx2 gene, which could cause severe disease. Moreover, antimicrobial resistance was significantly higher in pigs than in patients. These results suggest that pig could act as a reservoir in human infection and antimicrobial resistance could be transferred to human from pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02604-z.
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Affiliation(s)
- Kyung-Hyo Do
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Kwangwon Seo
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Wan-Kyu Lee
- Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Kim B, Kim J, Jo HU, Kwon KT, Ryu SY, Wie SH, Kim J, Park SY, Hong KW, Kim HI, Kim HA, Kim MH, Bae MH, Sohn YH, Kim J, Lee Y, Pai H. Changes in the characteristics of community-onset fluoroquinolone-resistant Escherichia coli isolates causing community-acquired acute pyelonephritis in South Korea. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:678-685. [PMID: 35140038 DOI: 10.1016/j.jmii.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/16/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
PURPOSE This study aimed to examine the changes in the characteristics of community-onset fluoroquinolone-resistant (FQ-R) Escherichia coli isolates causing community-acquired acute pyelonephritis (APN) in South Korea. METHODS Blood or urine samples were prospectively collected from patients aged ≥15 years with community-acquired APN who were admitted to one of the eight Korean hospitals included in this study between September 2017 and August 2018. Phylogenetic typing, multilocus sequence typing, and molecular characterization of β-lactamase resistance and plasmid-mediated quinolone resistance (PMQR) determinants were performed. The data were compared with those from a previous study with the same design conducted in 2010-2011. RESULTS A total of 300 and 346 isolates were identified in 2010-2011 and 2017-2018, respectively. Among them, 76 (22.0%) and 77 (25.7%) FQ-R isolates were identified in 2010-2011 and 2017-2018, respectively. A significantly higher antimicrobial resistance against third-to fourth-generation cephalosporins, including cefotaxime (23.9% vs. 77.9%, P < 0.001), were observed among FQ-R isolates in 2017-2018 than among those in 2010-2011. A higher proportion of ST131 isolates (27.6% vs. 66.2%, P < 0.001), as well as isolates that had extended-spectrum β-lactamase (ESBL)/plasmid-mediated AmpC β-lactamase (PABL) (23.7% vs. 79.2%, P < 0.001), was observed in 2017-2018 than in 2010-2011. Further, more PMQR determinants (11.8% vs. 40.8%, P < 0.001) were observed in 2017-2018 than in 2010-2011. CONCLUSIONS Among uropathogenic FQ-R E. coli isolates in South Korea, the prevalence of ST131 and the proportion of isolates containing ESBL and/or PMQR determinants have increased.
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Affiliation(s)
- Bongyoung Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea.
| | - Jeoungyeon Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyun-Uk Jo
- Department of Urology, Good Moonhwa Hospital, Busan, South Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Seong-Yeol Ryu
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Seong-Heon Wie
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Se Yoon Park
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University, Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, South Korea
| | - Kyung-Wook Hong
- Division of Infectious Diseases, Department of Internal Medicine, Gyeongsang National University Hospital, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Hye In Kim
- Department of Internal Medicine, Daegu Fatima Hospital, Daegu, South Korea
| | - Hyun Ah Kim
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Mi-Hee Kim
- Division of Infectious Diseases, Department of Internal Medicine, St. Vincent Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Mi Hyun Bae
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | | | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, South Korea
| | - Yangsoon Lee
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea.
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Sola M, Mani Y, Saras E, Drapeau A, Grami R, Aouni M, Madec JY, Haenni M, Mansour W. Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacterales from Tunisian Seafood. Microorganisms 2022; 10:microorganisms10071364. [PMID: 35889085 PMCID: PMC9323973 DOI: 10.3390/microorganisms10071364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/01/2023] Open
Abstract
Aquaculture is a rapidly expanding sector in which it is important to monitor the occurrence of multi-drug resistant (MDR) bacteria. The presence of extended-spectrum β-lactamase (ESBL-) or carbapenemase-producing Enterobacterales is a commonly used indicator of the resistance burden in a given sector. In this study, 641 pieces of farmed fish (sea bream and sea bass), as well as 1075 Mediterranean clams, were analyzed. All ESBL- and carbapenemase-producing Enterobacterales collected were whole-genome sequenced. The proportion of ESBL-producing Enterobacterales was 1.4% in fish and 1.6% in clams, carried by Escherichia coli (n = 23) and Klebsiella pneumoniae (n = 4). The ESBL phenotype was exclusively due to the presence of blaCTX-M genes, the most frequent one being blaCTX-M-15. The blaCTX-M-1 gene was also identified in six E. coli, among which four were carried by IncI1/pST3 plasmids, possibly betraying an animal origin. Carbapenemases were absent in fish but identified in two K. pneumoniae isolates from clams (blaNDM-1 and blaOXA-48). Several sequence types (STs) identified were associated with human MDR clones such as E. coli ST131 and ST617, or K. pneumoniae ST307 and ST147. Our results might indicate that bacteria from hospital or farm effluents can reach the open sea and contaminate seafood and fish that are living or raised nearby. Therefore, monitoring the quality of water discharged to the sea and the presence of MDR bacteria in seafood is mandatory to ensure the quality of fishery products.
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Affiliation(s)
- Mehdi Sola
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Yosra Mani
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Raoudha Grami
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Mahjoub Aouni
- Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculté de Pharmacie de Monastir, Université de Monastir, Monastir 5000, Tunisia;
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
- Correspondence:
| | - Wejdene Mansour
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
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Johnston BD, Gordon DM, Burn S, Johnson TJ, Weber BP, Miller EA, Johnson JR. Novel Multiplex PCR Method and Genome Sequence-Based Analog for High-Resolution Subclonal Assignment and Characterization of Escherichia coli Sequence Type 131 Isolates. Microbiol Spectr 2022; 10:e0106422. [PMID: 35604132 PMCID: PMC9241916 DOI: 10.1128/spectrum.01064-22] [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: 03/29/2022] [Accepted: 04/30/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a pandemic, multidrug-resistant extraintestinal pathogen. The multiple distinctive ST131 subclones differ for rfb and fliC alleles (O and H antigens), fimH allele (type-1 fimbriae adhesin), resistance phenotype and genotype, clinical correlates, and host predilection. Current PCR assays for detecting ST131 and its main subclones offer limited sub-ST characterization. Here we combined 22 novel and 14 published primers for a multiplex PCR assay to detect and extensively characterize ST131 isolates. The primers target mdh36, gyrB47, trpA72, sbmA, plsB, nupC, rmuC, kefC, ybbW, the O16 and O25b rfb variants, five fimH alleles (fimH22, fimH27, fimH30, fimH35, and fimH41), two fliC alleles (H4 and H5), a (subclone-specific) fluoroquinolone resistance-associated parC allele, and a (subclone-specific) prophage marker. The resulting amplicons resolve 15 molecular subsets within ST131, including 3 within clade A (H41 subclone), 5 within clade B (H22 subclone), and 7 within clade C (H30 subclone), which includes subclones C0 (H30S: 2 subsets), C1 and C1-M27 (H30R1: 2 subsets), and C2 (H30Rx: 3 subsets). Validation in three laboratories showed that this assay provides a rapid, accurate, and portable method for rapidly detecting and characterizing E. coli ST131 and its key subsets. Additionally, for users with whole genome sequencing (WGS) capability, we developed a command-line executable called ST131Typer, an in silico version of the extended multiplex PCR assay. Its accuracy was 87.8%, with most issues due to incomplete or fragmented input genome assemblies. These two novel assays should facilitate detailed ST131 subtyping using either endpoint PCR or WGS. IMPORTANCE These novel assays provide greater subclonal resolution and characterization of E. coli ST131 isolates than do the available comparable PCR assays, plus offer a novel sequence-based alternative to PCR. They may prove useful for molecular epidemiological studies, surveillance, and, potentially, clinical management.
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Affiliation(s)
- Brian D. Johnston
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
| | - David M. Gordon
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Samantha Burn
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Bonnie P. Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Elizabeth A. Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - James R. Johnson
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
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Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
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Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
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Genomic insights of high-risk clones of ESBL-producing Escherichia coli isolated from community infections and commercial meat in southern Brazil. Sci Rep 2022; 12:9354. [PMID: 35672430 PMCID: PMC9174282 DOI: 10.1038/s41598-022-13197-y] [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: 08/13/2021] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
During a microbiological and genomic surveillance study conducted to investigate the molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from community-acquired urinary tract infections (UTI) and commercial meat samples, in a Brazilian city with a high occurrence of infections by ESBL-producing bacteria, we have identified the presence of CTX-M (-2, -14, -15, -24, -27 and -55)-producing E. coli of international clones ST38, ST117, ST131 and ST354. The ST131 was more prevalent in human samples, and worryingly the high-risk ST131-C1-M27 was identified in human infections for the first time. We also detected CTX-M-55-producing E. coli ST117 from meat samples (i.e., chicken and pork) and human infections. Moreover, the clinically relevant CTX-M-24-positive E. coli ST354 clone was detected for the first time in human samples. In summary, our results highlight a potential of commercialized meat as a reservoir of high-priority E. coli lineages in the community, whereas the identification of E. coli ST131-C1-M27 indicates that novel pandemic clones have emerged in Brazil, constituting a public health issue.
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Bidet P, Birgy A, Ouldali N, Béchet S, Levy C, Madhi F, Sobral E, Cohen R, Bonacorsi S. Comparative genomic analysis of ESBL-producing Escherichia coli from faecal carriage and febrile urinary tract infection in children: a prospective multicentre study. JAC Antimicrob Resist 2022; 4:dlac056. [PMID: 35611261 PMCID: PMC9123598 DOI: 10.1093/jacamr/dlac056] [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: 11/15/2021] [Accepted: 05/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background The reliability of ESBL-producing Escherichia coli (ESBL-Ec) faecal carriage monitoring to guide probabilistic treatment of febrile urinary tract infection (FUTI) in children remains unclear. Objectives To compare the genomic characteristics of ESBL-Ec isolates from faecal carriage and FUTI to assess their correlation and identify a FUTI-associated virulence profile. Methods We conducted a prospective multicentre hospital and ambulatory-based study. We analysed the genotypes and virulence factors of both faecal and FUTI ESBL-Ec by whole genome sequencing. Correlations were assessed by non-parametric Spearman coefficient and virulence factors were assessed by chi-squared tests with Bonferroni correction. Results We included 218 ESBL-Ec causing FUTI and 154 ESBL-Ec faecal carriage isolates. The most frequent ST was ST131 (44%) in both collections. We found high correlation between carriage and ESBL-Ec FUTI regarding genes/alleles (rho = 0.88, P < 0.0001) and combinations of virulence genes, MLST and serotypes (rho = 0.90, P < 0.0001, rho = 0.99, P = 0.0003, rho = 0.97, P = 0.005 respectively). Beside this strong correlation, we found five genes that were significantly associated with FUTI (papC, papGII, hlyC, hek and traJ). The strongest association with FUTI was found with adhesin gene allele papGII (54% in FUTI versus 16% in carriage) and for papGII and gene traJ alone or in combination (63% versus 24%). Conclusions The genomic profile of ESBL-Ec causing FUTI in children strongly correlates with faecal carriage isolates except for a few genes. The presence of papGII and/or traJ in a previously identified carriage strain could be used as a marker of uropathogenicity and may guide the empirical antimicrobial choice in subsequent FUTI.
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Affiliation(s)
- Philippe Bidet
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - André Birgy
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Naim Ouldali
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Service de Pédiatrie Générale, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Stéphane Béchet
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
| | - Corinne Levy
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
| | - Fouad Madhi
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Elsa Sobral
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
| | - Robert Cohen
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
| | - Stéphane Bonacorsi
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
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Mahoney MT, Brigman HV, Johnston BD, Johnson JR, Hirsch EB. Prevalence and characteristics of multidrug-resistant Escherichia coli sequence type ST131 at two academic centers in Boston and Minneapolis, USA. Am J Infect Control 2022; 51:434-439. [PMID: 35764181 DOI: 10.1016/j.ajic.2022.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Escherichia coli sequence type (ST) ST131, with its emergent resistance-associated H30Rx, H30R1, and C1-M27 clonal subsets, accounts for the greatest share of extraintestinal E. coli infections and most extended-spectrum β-lactamase (ESBL)-producing E. coli. METHODS We characterized and compared consecutive E. coli urine isolates from two geographically distinct medical centers in Minneapolis, Minnesota (n = 172) and Boston, Massachusetts (n = 143) for ESBL phenotype, CTX-M-type ESBL genes, phylogenetic groups, selected ST131 subclones, and 40 extraintestinal virulence genes. RESULTS Whereas the Boston vs. Minneapolis isolates had a similar prevalence of phylogenetic groups (mainly B2: 79% vs 73%), ST131 (34% vs 28%), H30 (28% vs 21%), and H30Rx (6% vs 5%), the emerging C1-M27 subclone occurred uniquely among Boston (6%) isolates. ESBL production was more prevalent among Boston isolates (15% vs 8%) and among ST131 isolates. Identified ESBL genes included blaCTX-M-27 (Boston only) and blaCTX-M-15. Ciprofloxacin resistance was ST131-associated and similarly prevalent across centers. Boston isolates had higher virulence gene scores. CONCLUSIONS Despite numerous similarities to Minneapolis isolates, Boston ST131 isolates demonstrated more prevalent ESBL production, higher virulence gene scores, and, uniquely, the C1-M27 subclone and blaCTX-M-27. Broader surveillance is needed to define the prevalence of ST131's globally successful C1-M27 subclone across the U.S.
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Comparative Metabolic Characterization of Extraintestinal Pathogenic Escherichia coli Blood Isolates from Saudi Arabia. J Trop Med 2022; 2022:1745835. [PMID: 35677619 PMCID: PMC9170502 DOI: 10.1155/2022/1745835] [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: 04/03/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
Background The prevalence of bloodstream infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) has increased substantially. E. coli ST131 is one of the dominant ExPEC clones among E. coli bacteremia population. Metabolism can trigger the pathogenesis of some bacterial isolates, and here we evaluated and compared the metabolic traits of E. coli bacteremia isolates including β-lactamase (BL)/extended-spectrum β-lactamase (ESBL)-positive and ESBL-negative isolates and ST131 and non-ST131 isolates. Methods The metabolic profiles of thirty E. coli isolates, obtained from blood samples for hospitalized individuals at a tertiary healthcare facility in Riyadh, were determined using HiMedia carbohydrate test strips. The difference in the utilization ability between isolate groups was then statistically assessed. Results Our data found that non-BL/ESBL producers were of low metabolic capacity compared with ESBL-positive isolates although the difference remained insignificant. Higher levels of utilization for some carbohydrates, such as fructose and trehalose, were detected among ST131 isolates when compared with non-ST131, and ST131 was also significantly associated with metabolizing rhamnose. The mean bio-score of both isolate groups was insignificant. We showed no link between metabolism and antimicrobial susceptibility profiles among tested blood isolates. Conclusion ST131 blood isolates were slightly higher in their carbohydrate utilization activity than non-ST131. More importantly, ST131 isolates were significantly capable of metabolizing rhamnose. Future research should focus on the factors that might drive the success of major ExPEC clones such as ST131.
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Ghenea AE, Zlatian OM, Cristea OM, Ungureanu A, Mititelu RR, Balasoiu AT, Vasile CM, Salan AI, Iliuta D, Popescu M, Udriștoiu AL, Balasoiu M. TEM,CTX-M,SHV Genes in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a County Clinical Emergency Hospital Romania-Predominance of CTX-M-15. Antibiotics (Basel) 2022; 11:antibiotics11040503. [PMID: 35453254 PMCID: PMC9028254 DOI: 10.3390/antibiotics11040503] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Background: CTX-M betalactamases have shown a rapid spread in the recent years among Enterobacteriaceae and have become the most prevalent Extended Spectrum Beta-Lactamases (ESBLs) in many parts of the world. The introduction and dissemination of antibiotic-resistant genes limits options for treatment, increases mortality and morbidity in patients, and leads to longer hospitalization and expensive costs. We aimed to identify the beta-lactamases circulating encoded by the genes blaCTX-M-15, blaSHV-1 and blaTEM-1 in Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) strains. Furthermore, we established the associated resistance phenotypes among patients hospitalized in the Intensive Care Unit (ICU) from County Clinical Emergency Hospital of Craiova, Romania. Methods: A total of 46 non-duplicated bacterial strains (14 strains of E. coli and 32 strains of K. pneumoniae), which were resistant to ceftazidime (CAZ) and cefotaxime (CTX) by Kirby–Bauer disk diffusion method, were identified using the automated VITEK2 system. Detection of ESBL-encoding genes and other resistance genes was carried out by PCR. Results. E. coli strains were resistant to 3rd generation cephalosporins and moderately resistant to quinolones, whereas K. pneumoniae strains were resistant to penicillins, cephalosporins, and sulfamides, and moderately resistant to quinolones and carbapenems. Most E. coli strains harbored blaCTX-M-15 gene (13/14 strains), a single strain had the blaSHV-1 gene, but 11 strains harbored blaTEM-1 gene. The mcr-1 gene was not detected. We detected tet(A) gene in six strains and tet(B) in one strain. In K. pneumoniae strains we detected blaCTX-M-15 in 23 strains, blaSHV-1 in all strains and blaTEM-1 in 14 strains. The colistin resistance gene mcr-1 was not detected. The tetracycline gene tet(A) was detected in 11 strains, but the gene tet(B) was not detected in any strains. Conclusions. The development in antibiotic resistance highlights the importance of establishing policies to reduce antibiotic use and improving the national resistance surveillance system in order to create local antibiotic therapy guidelines.
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Affiliation(s)
- Alice Elena Ghenea
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Ovidiu Mircea Zlatian
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Oana Mariana Cristea
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
- Correspondence: (O.M.C.); (C.M.V.)
| | - Anca Ungureanu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Radu Razvan Mititelu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Andrei Theodor Balasoiu
- Department of Ophthalmology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Corina Maria Vasile
- Department of Paediatrics, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Correspondence: (O.M.C.); (C.M.V.)
| | - Alex-Ioan Salan
- Department of Oral and Maxillofacial Surgery, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Daniel Iliuta
- Department of Psychiatry, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Mihaela Popescu
- Department of Endocrinology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Anca-Loredana Udriștoiu
- Faculty of Automation, Computers and Electronics, University of Craiova, 200776 Craiova, Romania;
| | - Maria Balasoiu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
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Sarwar F, Rasool MH, Khurshid M, Qamar MU, Aslam B. Escherichia coli Isolates Harboring blaNDM Variants and 16S Methylases Belonging to Clonal Complex 131 in Southern Punjab, Pakistan. Microb Drug Resist 2022; 28:623-635. [PMID: 35363080 DOI: 10.1089/mdr.2021.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence of carbapenem-resistant Escherichia coli (CREC) especially harboring the New Delhi Metallo-β-lactamase (blaNDM) variants are increasingly being reported from many countries, however, the data from Pakistan is limited. In the present study, 109 CREC isolates were obtained from 4,091 E. coli isolates in five tertiary care hospitals in southern Punjab, Pakistan. The antimicrobial susceptibility profiling and screening for the resistance determinants were performed followed by blaNDM typing and multilocus sequence typing (MLST) to characterize the CREC strains. Among the carbapenemases, 57 CREC isolates were found to harbor blaNDM. The blaNDM-1, blaNDM-5, blaNDM-7, and blaNDM-4 variants were identified in 30 (52.6%), 18 (31.6%), (12.3%), 2 (3.5%) isolates, respectively. The ESBL genes, such as blaCTX-M and blaTEM, were also found in different combinations, whereas the 16S methylases that is, rmtB and armA were found in 69 (63.3%) and 55 (50.5%) CREC isolates, respectively. The MLST of blaNDM carrying E. coli revealed eight different sequence types (STs) with ST131 belonging to 21 isolates being the most prevalent. The clonal complex 131 was the predominant complex corresponding to 47 (82.5%) of blaNDM-positive strains. Large-scale surveillance studies coupled with active infection control policies are suggested on an urgent basis to avoid an epidemic in the future.
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Affiliation(s)
- Faiza Sarwar
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Usman Qamar
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
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The effect of nickel ions on the susceptibility of bacteria to ciprofloxacin and ampicillin. Folia Microbiol (Praha) 2022; 67:649-657. [PMID: 35353362 DOI: 10.1007/s12223-022-00960-x] [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: 05/27/2021] [Accepted: 02/19/2022] [Indexed: 11/04/2022]
Abstract
To explore the interaction effects of ciprofloxacin and ampicillin with nickel on the growth of bacteria, Staphylococcus aureus strain ATCC 29213, Enterococcus faecalis ATCC 29212 and Escherichia coli ATCC 25922 were used. Minimum inhibitory concentrations (MICs) were determined for nickel, ciprofloxacin and ampicillin, and the checkerboard method was used to assess their cumulative effects on bacterial growth. The interactions between the metal and antibiotics were assessed by the fractional inhibitory concentration (FIC). The MICs for ciprofloxacin and ampicillin were 0.31 and 1 mg/L for E. faecalis, 0.62 and 1 mg/L for S. aureus and 0.005 and 2.5 for E. coli, respectively. The MIC for nickel was 1000 mg/L for all bacteria. The FIC results for ciprofloxacin and nickel demonstrated an antagonistic effect of the two agents on the growth of E. coli and E. faecalis and an additive effect on S. aureus. The FICs for ampicillin and nickel demonstrated a synergistic effect on the growth of E. faecalis and E. coli. Different interactions of metals and antibiotics were observed depending on the bacteria and the type of antibiotic.
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Abstract
Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.
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Plasmid Replicon Diversity of Clinical Uropathogenic Escherichia coli Isolates from Riyadh, Saudi Arabia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to identify and compare the plasmid replicons of clinical uropathogenic Escherichia coli (UPEC) isolates, involving extended spectrum β-lactamase (ESBL)-positive and ESBL-negative, E. coli ST131 and non-ST131 and various ST131 subclones. Plasmid replicon typing on 24 clinical UPEC isolates was carried out using polymerase chain reaction-based replicon typing. A statistical analysis was performed to assess the associations between plasmid replicon types and ESBL carriage, and to evaluate the link between ST131 isolates and high replicon carriage. Eight replicons, I1α, N2, Iγ, X1, FIIS, K, FIA, and FII were detected. The FII was the most common replicon identified here. ESBL-positive E. coli isolates were highly associated with I1α, N2, Iγ, X1, and FIIS replicons, while FIA was present only in ESBL-negative group. ST131 isolates were highly associated with I1α and N2 replicons compared to non-ST131. No link was found between replicon carriage and the number or type of ESBLs in E. coli isolates. The diversity observed in replicon patterns of our clinical E. coli isolates indicates that they might be originated from different sources. The presence of replicons reported previously in animal sources suggests a possible transfer of antimicrobial resistance between animal and human bacterial isolates.
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Karlsson M, Lutgring JD, Ansari U, Lawsin A, Albrecht V, McAllister G, Daniels J, Lonsway D, McKay S, Beldavs Z, Bower C, Dumyati G, Gross A, Jacob J, Janelle S, Kainer MA, Lynfield R, Phipps EC, Schutz K, Wilson L, Witwer ML, Bulens SN, Walters MS, Duffy N, Kallen AJ, Elkins CA, Rasheed JK. Molecular Characterization of Carbapenem-Resistant Enterobacterales Collected in the United States. Microb Drug Resist 2022; 28:389-397. [PMID: 35172110 DOI: 10.1089/mdr.2021.0106] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are a growing public health concern due to resistance to multiple antibiotics and potential to cause health care-associated infections with high mortality. Carbapenemase-producing CRE are of particular concern given that carbapenemase-encoding genes often are located on mobile genetic elements that may spread between different organisms and species. In this study, we performed phenotypic and genotypic characterization of CRE collected at eight U.S. sites participating in active population- and laboratory-based surveillance of carbapenem-resistant organisms. Among 421 CRE tested, the majority were isolated from urine (n = 349, 83%). Klebsiella pneumoniae was the most common organism (n = 265, 63%), followed by Enterobacter cloacae complex (n = 77, 18%) and Escherichia coli (n = 50, 12%). Of 419 isolates analyzed by whole genome sequencing, 307 (73%) harbored a carbapenemase gene; variants of blaKPC predominated (n = 299, 97%). The occurrence of carbapenemase-producing K. pneumoniae, E. cloacae complex, and E. coli varied by region; the predominant sequence type within each genus was ST258, ST171, and ST131, respectively. None of the carbapenemase-producing CRE isolates displayed resistance to all antimicrobials tested; susceptibility to amikacin and tigecycline was generally retained.
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Affiliation(s)
- Maria Karlsson
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joseph D Lutgring
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Uzma Ansari
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrian Lawsin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonathan Daniels
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Lonsway
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susannah McKay
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Chris Bower
- Georgia Emerging Infections Program, Atlanta, Georgia, USA
| | - Ghinwa Dumyati
- New York Emerging Infections Program at the University of Rochester Medical Center, Rochester, New York, USA
| | | | - Jesse Jacob
- Georgia Emerging Infections Program, Atlanta, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sarah Janelle
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Marion A Kainer
- Tennessee Department of Public Health, Nashville, Tennessee, USA
| | - Ruth Lynfield
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Erin C Phipps
- New Mexico Emerging Infections Program, Santa Fe, New Mexico, USA
| | - Kyle Schutz
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Lucy Wilson
- Maryland Department of Health, Baltimore, Maryland, USA
| | | | - Sandra N Bulens
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maroya Spalding Walters
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nadezhda Duffy
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alexander J Kallen
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Persistence of Antibiotic-Resistant Escherichia coli Strains Belonging to the B2 Phylogroup in Municipal Wastewater under Aerobic Conditions. Antibiotics (Basel) 2022; 11:antibiotics11020202. [PMID: 35203805 PMCID: PMC8868233 DOI: 10.3390/antibiotics11020202] [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: 01/05/2022] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 02/05/2023] Open
Abstract
Escherichia coli is classified into four major phylogenetic groups (A, B1, B2, and D) that are associated with antibiotic resistance genes. Although antibiotic-resistant E. coli is commonly detected in municipal wastewater, little is known about the relationship between the phylogenetic groups and antibiotic-resistant E. coli in wastewater. In this study, the survival of E. coli in wastewater and the changes to the relationships between each phylogroup and the antibiotic-resistant profiles of E. coli isolates from wastewater were investigated under aerobic conditions for 14 days. The isolates were classified into the phylogroups A, B1, B2, and D or others by multiplex PCR. In addition, the susceptibility of the isolates to 11 antibiotics was assessed with the minimum inhibitory concentration (MIC) assay. While E. coli counts decreased in the wastewater with time under aerobic conditions, the prevalence of phylogroup B2 had increased to 73% on day 14. Furthermore, the MIC assay revealed that the abundance of antibiotic-resistant E. coli also increased on day 14. After batch-mixing the experiments under aerobic conditions, the surviving antibiotic-resistant E. coli included mainly multidrug-resistant and beta-lactamase-producing isolates belonging to phylogroup B2. These results suggest that the phylogroup B2 isolates that have acquired antibiotic resistance had a high survivability in the treated wastewater.
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Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana. Sci Rep 2022; 12:1843. [PMID: 35115628 PMCID: PMC8813988 DOI: 10.1038/s41598-022-05869-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 12/18/2022] Open
Abstract
Recently, the emergence and rapid dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria, particularly of the family Enterobacteriaceae, has posed serious healthcare challenges. Here, we determined the antimicrobial susceptibility and genetic characteristics of 164 Escherichia coli strains isolated from infected patients in two hospitals in Ghana. In total, 102 cefotaxime-resistant isolates (62.2%) were identified as ESBL-producers. Multilocus sequence typing of the ESBL-producers identified 20 different sequence types (STs) with ST131 (n = 25, 24.5%) as the dominant group. Other detected STs included ST410 (n = 21, 20.6%) and ST617 (n = 19, 18.6%). All identified ESBL-producers harbored blaCTX-M-14, blaCTX-M-15, or blaCTX-M-27, with blaCTX-M-15 (n = 96, 94.1%) being the most predominant ESBL allele. Further analysis showed that the immediate genetic environment around blaCTX-M-15 is conserved within blaCTX-M-15 containing strains. Five of the 25 ST131 isolates were clustered with clade A, one with sub-clade C1, and 19 with the dominant sub-clade C2. The results show that fluoroquinolone-resistant, blaCTX-M-14- and blaCTX- M-15-producing ESBL E. coli ST131 strains belonging to clade A and sub-clades C1 and C2 are disseminating in Ghanaian hospitals. To the best of our knowledge, this is the first report of the ST131 phylogeny in Ghana.
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Das S, Shaikh O, Gaur NK, Vijayakumar C, Kumbhar U. Fulminant Necrotizing Pyomyositis Tropicans. Cureus 2022; 14:e21767. [PMID: 35251837 PMCID: PMC8890598 DOI: 10.7759/cureus.21767] [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] [Accepted: 01/30/2022] [Indexed: 11/06/2022] Open
Abstract
Pyomyositis tropicans is a purulent invasive infection of the striated muscle tissues, usually caused by Gram-positive bacteria Staphylococcus aureus and Streptococcus in immunocompromised patients. We hereby report a case of fulminant necrotizing pyomyositis that occurred in a 16-year-old immunocompetent patient, and it is the first one of its kind to the best of our knowledge. The patient underwent imaging which suggested extensive intramuscular abdominal wall abscess formation, for which the patient underwent multiple surgical debridements of the lateral thoracic wall. Subsequent cultures grew Escherichia coli as the causative organism. Postoperatively, the patient went into catastrophic, irreversible septic shock ending in an eventual fatality.
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Proton motive force underpins respiration-mediated potentiation of aminoglycoside lethality in pathogenic Escherichia coli. Arch Microbiol 2022; 204:120. [PMID: 34989857 PMCID: PMC8739286 DOI: 10.1007/s00203-021-02710-y] [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: 07/19/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
Abstract
It is well known that loss of aerobic respiration in Gram-negative bacteria can diminish the efficacy of a variety of bactericidal antibiotics, which has lead to subsequent demonstrations that the formation of reactive oxygen species (ROS) and the proton motive force (PMF) can both play a role in antibiotic toxicity. The susceptibility of Gram-negative bacteria to aminoglycoside antibiotics, particularly gentamicin, has previously been linked to both the production of ROS and the rate of antibiotic uptake that is mediated by the PMF, although the relative contributions of ROS and PMF to aminoglycoside toxicity has remained poorly understood. Herein, gentamicin was shown to elicit a very modest increase in ROS levels in an aerobically grown Escherichia coli clinical isolate. The well-characterised uncoupler 2,4-dinitrophenol (DNP) was used to disrupt the PMF, which resulted in a significant decrease in gentamicin lethality towards E. coli. DNP did not significantly alter respiratory oxygen consumption, supporting the hypothesis that this uncoupler does not increase ROS production via elevated respiratory oxidase activity. These observations support the hypothesis that maintenance of PMF rather than induction of ROS production underpins the mechanism for how the respiratory chain potentiates the toxicity of aminoglycosides. This was further supported by the demonstration that the uncoupler DNP elicits a dramatic decrease in gentamicin lethality under anaerobic conditions. Together, these data strongly suggest that maintenance of the PMF is the dominant mechanism for the respiratory chain in potentiating the toxic effects of aminoglycosides.
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Li D, Wyrsch ER, Elankumaran P, Dolejska M, Marenda MS, Browning GF, Bushell RN, McKinnon J, Chowdhury PR, Hitchick N, Miller N, Donner E, Drigo B, Baker D, Charles IG, Kudinha T, Jarocki VM, Djordjevic SP. Genomic comparisons of Escherichia coli ST131 from Australia. Microb Genom 2021; 7:000721. [PMID: 34910614 PMCID: PMC8767332 DOI: 10.1099/mgen.0.000721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically blaCTX-M-15 and blaCTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
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Affiliation(s)
- Dmitriy Li
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ethan R. Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic,Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic,Biomedical Center, Charles University, Czech Republic,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
| | - Marc S. Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Glenn F. Browning
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Rhys N. Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Jessica McKinnon
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Nola Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Natalie Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | | | | | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Veronica M. Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Veronica M. Jarocki,
| | - Steven Philip Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Steven Philip Djordjevic,
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Jain P, Bepari AK, Sen PK, Rafe T, Imtiaz R, Hossain M, Reza HM. High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate. Sci Rep 2021; 11:22859. [PMID: 34819576 PMCID: PMC8613203 DOI: 10.1038/s41598-021-02251-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/08/2021] [Indexed: 12/04/2022] Open
Abstract
Multi-drug-resistance (MDR) is a severe public health concern worldwide, and its containment is more challenging in developing countries due to poor antimicrobial resistance (AMR) surveillance and irrational use of antibiotics. The current study investigated 100 clinical E. coli isolates and revealed that 98% of them were MDR. PCR analysis using 25 selected isolates showed the predominance of metallo-β-lactamase gene blaNDM (80%) and ESBL genes blaOXA (48%) and blaCTX-M-15 (32%). The AmpC gene was detected in 68% of the isolates, while 32% was tetC positive. Notably, 34% of the isolates were resistant to carbapenem. Whole genome sequence (WGS) analysis of an extensively drug-resistant (XDR) isolate (L16) revealed the presence of the notorious sequence type 131 responsible for multi-drug-resistant infections, multiple antibiotic resistance genes (ARGs), virulence genes, and mobile genetic elements that pose risks to environmental transmission. Our results indicate that MDR is alarmingly increasing in Bangladesh that critically limits the treatment option against infections and contributes to further aggravation to the prevailing situation of MDR worldwide. The findings of this study will be valuable in designing sustainable strategies to contain MDR in the region.
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Affiliation(s)
- Preeti Jain
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Asim Kumar Bepari
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Prosengit Kumer Sen
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Tanzir Rafe
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Rashed Imtiaz
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Hasan Mahmud Reza
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh.
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Cummins EA, Snaith AE, McNally A, Hall RJ. The role of potentiating mutations in the evolution of pandemic Escherichia coli clones. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04359-3. [PMID: 34787747 DOI: 10.1007/s10096-021-04359-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/30/2021] [Indexed: 12/16/2022]
Abstract
The Escherichia coli species exhibits a vast array of variable lifestyles, including environmental, commensal, and pathogenic organisms. Many of these E. coli contribute significantly to the global threat of antimicrobial resistance (AMR). Multidrug-resistant (MDR) clones of E. coli have arisen multiple times over varying timescales. The repeated emergence of successful pandemic clones, including the notorious ST131 lineage, highlights a desperate need to further study the evolutionary processes underlying their emergence and success. Here, we review the evolutionary emergence of E. coli ST131 pandemic clones and draw parallels between their evolutionary trajectories and those of other lineages. From colonization and expansion to the acquisition of multidrug resistance plasmids, potentiating mutations are present at each stage, leading to a proposed sequence of events that may result in the formation of an antimicrobial-resistant pandemic clone.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Molecular Epidemiology of Multidrug-Resistant Uropathogenic Escherichia coli O25b Strains Associated with Complicated Urinary Tract Infection in Children. Microorganisms 2021; 9:microorganisms9112299. [PMID: 34835425 PMCID: PMC8623209 DOI: 10.3390/microorganisms9112299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Uropathogenic Escherichia coli (UPEC) has increased the incidence of urinary tract infection (UTI). It is the cause of more than 80% of community-acquired cystitis cases and more than 70% of uncomplicated acute pyelonephritis cases. Aim: The present study describes the molecular epidemiology of UPEC O25b clinical strains based on their resistance profiles, virulence genes, and genetic diversity. Methods: Resistance profiles were identified using the Kirby–Bauer method, including the phenotypic production of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). The UPEC serogroups, phylogenetic groups, virulence genes, and integrons were determined via multiplex PCR. Genetic diversity was established using pulsed-field gel electrophoresis (PFGE), and sequence type (ST) was determined via multilocus sequence typing (MLST). Results: UPEC strains (n = 126) from hospitalized children with complicated UTIs (cUTIs) were identified as O25b, of which 41.27% were multidrug resistant (MDR) and 15.87% were extensively drug resistant (XDR). The O25b strains harbored the fimH (95.23%), csgA (91.26%), papGII (80.95%), chuA (95.23%), iutD (88.09%), satA (84.92%), and intl1 (47.61%) genes. Moreover, 64.28% were producers of ESBLs and had high genetic diversity. ST131 (63.63%) was associated primarily with phylogenetic group B2, and ST69 (100%) was associated primarily with phylogenetic group D. Conclusion: UPEC O25b/ST131 harbors a wide genetic diversity of virulence and resistance genes, which contribute to cUTIs in pediatrics.
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50
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Mazumder R, Hussain A, Abdullah A, Islam MN, Sadique MT, Muniruzzaman SM, Tabassum A, Halim F, Akter N, Ahmed D, Mondal D. International High-Risk Clones Among Extended-Spectrum β-Lactamase-Producing Escherichia coli in Dhaka, Bangladesh. Front Microbiol 2021; 12:736464. [PMID: 34671331 PMCID: PMC8521144 DOI: 10.3389/fmicb.2021.736464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023] Open
Abstract
Background:Escherichia coli is a major extended-spectrum β-lactamase (ESBL)–producing organism responsible for the rapid spread of antimicrobial resistance (AMR) that has compromised our ability to treat infections. Baseline data on population structure, virulence, and resistance mechanisms in E. coli lineages from developing countries such as Bangladesh are lacking. Methods: Whole-genome sequencing was performed for 46 ESBL–E. coli isolates cultured from patient samples at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b)-Dhaka. Sequence data were analyzed to glean details of AMR, virulence, and phylogenetic and molecular markers of E. coli lineages. Results: Genome comparison revealed presence of all major high-risk clones including sequence type 131 (ST131) (46%), ST405 (13%), ST648 (7%), ST410 (4.3%), ST38 (2%), ST73 (2%), and ST1193 (2%). The predominant ESBL gene and plasmid combination were blaCTX–M–15 and FII-FIA-FIB detected in diverse E. coli phylogroups and STs. The blaNDM–5 (9%) gene was present in prominent E. coli STs. One (2%) mcr-1–positive ST1011 E. coli, coharboring blaCTXM–55 gene, was detected. The extraintestinal pathogenic E. coli genotype was associated with specific E. coli lineages. The single nucleotide polymorphism (SNP)-based genome phylogeny largely showed correlation with phylogroups, serogroups, and fimH types. Majority of these isolates were susceptible to amikacin (93%), imipenem (93%), and nitrofurantoin (83%). Conclusion: Our study reveals a high diversity of E. coli lineages among ESBL-producing E. coli from Dhaka. This study suggests ongoing circulation of ST131 and all major non-ST131 high-risk clones that are strongly associated with cephalosporin resistance and virulence genes. These findings warrant prospective monitoring of high-risk clones, which would otherwise worsen the AMR crises.
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Affiliation(s)
- Razib Mazumder
- Genomics Center, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Arif Hussain
- Genomics Center, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ahmed Abdullah
- Genomics Center, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Nazrul Islam
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Tuhin Sadique
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - S M Muniruzzaman
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Anika Tabassum
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Farhana Halim
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nasrin Akter
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Dilruba Ahmed
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Dinesh Mondal
- Genomics Center, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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