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Peirano G, Castellanos LR, Matsumura Y, Chaffee R, Castañeda-Mogollón D, Pillai DR, Pitout JDD. Clinical validation of loop-mediated isothermal amplification for the detection of Escherichia coli sequence type complex 131. J Clin Microbiol 2024; 62:e0168723. [PMID: 38385692 PMCID: PMC10935629 DOI: 10.1128/jcm.01687-23] [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: 12/13/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
The dissemination of Escherichia coli multidrug-resistant (MDR) STc131 is related to its persistence in the human gastrointestinal tract as efficient gut colonizers. Infection and prevention measures are the cornerstones for preventing STc131 spread. Oral decolonization therapies that target ST131 are being developed. There are no rapid methods available to identify STc131 in human specimens. A loop-mediated isothermal amplification (LAMP) assay (named LAMP-ST131) was developed for the detection of STc131 on well-characterized E. coli isolates and then compared to culture and PCR for urines and stool swabs. With E. coli isolates (n = 720), LAMP-ST131 had a sensitivity (sens) of 100% [95% confidence interval (C.I.) = 98.1-100%)] and a specificity (spec) of 98.9% (95% C.I. = 97.5-99.5%). On urines (n = 550), LAMP-ST131 had a sens of 97.6% (95% C.I. = 89.68-94.33%) and a spec of 92.3% (95% C.I. = 87.68-99.88%), while on stool swabs (n = 278), LAMP-ST131 had a sens of 100% (95% C.I. = 88.7-100%) and a spec of 83.9% (95% C.I. = 78.8-87.9%). LAMP-ST131 detected 10 (urines) and 100 (stool swabs) gene copies/μL. LAMP-ST131 accurately identified STc131 within E. coli isolates and human specimens. The implementation of LAMP-ST131 will aid genomic surveys, enable the rapid implementation of effective infection prevention measures, and identify patients suitable for ST131 decolonization therapies. Such approaches will curb the spread of STc131 and decrease incidence rates of global MDR E. coli infections. IMPORTANCE We developed an accurate non-culture-based loop-mediated isothermal amplification (LAMP) methodology for the detection of (sequence type) STc131 among Escherichia coli isolates and human specimens. The use of LAMP-ST131 for global genomic surveillance studies and to identify patients that are suitable for ST131 decolonization therapies will be important for decreasing multidrug-resistant E. coli infections across the globe.
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Affiliation(s)
- Gisele Peirano
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | | | | | - Ryan Chaffee
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Dylan R. Pillai
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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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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Chen L, Peirano G, Yen K, Wang B, Terlecky A, DeVinney R, Kreiswirth BN, Pitout JDD. CRISPR-Cas9-mediated IncF plasmid curing in extraintestinal pathogenic Escherichia coli. Microbiol Spectr 2024; 12:e0369223. [PMID: 38018989 PMCID: PMC10783119 DOI: 10.1128/spectrum.03692-23] [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: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Understanding the role of IncF plasmids in the success of drug-resistant bacteria has far-reaching implications for tackling antibiotic resistance. The study's use of a novel CRISPR-Cas9-mediated plasmid-curing system provides a precision tool for dissecting the specific impact of IncF plasmids on ExPEC clones, especially high-risk, multidrug-resistant strains like ST131, ST1193, and ST410. The study offers a crucial stepping stone for future research into understanding how these plasmids influence more complex aspects of bacterial behavior, such as cell invasion and in vivo fitness.
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Affiliation(s)
- Liang Chen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Gisele Peirano
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Kelly Yen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
| | - Bingjie Wang
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Austin Terlecky
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
| | - Rebekah DeVinney
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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Xiao R, Li Y, Liu X, Ding Y, Lai J, Li Y, Kang W, Zou P, Wang J, Du Y, Zhang J, Wang Y. Antibiotic susceptibility of Escherichia coli isolated from neonates admitted to neonatal intensive care units across China from 2015 to 2020. Front Cell Infect Microbiol 2023; 13:1183736. [PMID: 37325509 PMCID: PMC10267875 DOI: 10.3389/fcimb.2023.1183736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Background Escherichia coli is one of the most common pathogens causing neonatal infections. Recently, the incidence and drug resistance of E. coli have increased, posing a major threat to neonatal health. The aim of this study was to describe and analyze the antibiotic resistance and multilocus sequence typing (MLST) characteristics of E. coli derived from infants admitted to neonatal intensive care units (NICUs) across China. Methods In this study, 370 strains of E. coli from neonates were collected. E. coli isolated from these specimens were subjected to antimicrobial susceptibility testing (by broth microdilution method) and MLST. Results The overall resistance rate was 82.68%, with the highest rate of methicillin/sulfamethoxazole (55.68%) followed by cefotaxime (46.22%). Multiple resistance rate was 36.74%, 132 strains (35.68%) had extended-spectrum β-lactamase (ESBL) phenotype and 5 strains (1.35%) had insensitivity to the tested carbapenem antibiotics. The resistance of E. coli isolated from different pathogenicity and different sites of infections varied, strains derived from sputum were significantly more resistant to β-lactams and tetracyclines. Currently, the prevalence spectrum in NICUs was dominated by ST1193, ST95, ST73, ST69 and ST131 across China. And the multidrug resistance of ST410 was the most severe. ST410 had the highest resistance rate to cefotaxime (86.67%), and its most common multidrug resistance pattern was β-lactams + aminoglycosides + quinolones + tetracyclines + sulfonamides. Conclusions Substantial proportions of neonatal E. coli isolates were severely resistant to commonly administered antibiotics. MLST results can suggest the prevalent characteristics of antibiotic resistance in E. coli with different ST types.
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Affiliation(s)
- Ruiqi Xiao
- Capital Institute of Pediatrics, Beijing, China
| | - Ying Li
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Xiaowei Liu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yijun Ding
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jidong Lai
- Department of Neonatology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yangfang Li
- Department of Neonatology, Children’s Hospital of Kunming, Kunming, Yunnan, China
| | - Wenqing Kang
- Neonatal Intensive Care Unit, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou, Henan, China
| | - Peicen Zou
- Capital Institute of Pediatrics, Beijing, China
| | - Jie Wang
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yue Du
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Jinjing Zhang
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yajuan Wang
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
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